Starting phenix.real_space_refine on Mon Oct 13 03:09:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jn4_36432/10_2025/8jn4_36432.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jn4_36432/10_2025/8jn4_36432.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jn4_36432/10_2025/8jn4_36432.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jn4_36432/10_2025/8jn4_36432.map" model { file = "/net/cci-nas-00/data/ceres_data/8jn4_36432/10_2025/8jn4_36432.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jn4_36432/10_2025/8jn4_36432.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 202 5.16 5 C 19184 2.51 5 N 5062 2.21 5 O 5778 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 152 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 30226 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 3757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3757 Classifications: {'peptide': 493} Link IDs: {'PTRANS': 16, 'TRANS': 476} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "B" Number of atoms: 585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 585 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "C" Number of atoms: 3757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3757 Classifications: {'peptide': 493} Link IDs: {'PTRANS': 16, 'TRANS': 476} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "D" Number of atoms: 585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 585 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "E" Number of atoms: 3757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3757 Classifications: {'peptide': 493} Link IDs: {'PTRANS': 16, 'TRANS': 476} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "F" Number of atoms: 585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 585 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "H" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 950 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "L" Number of atoms: 870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 870 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 6, 'TRANS': 106} Chain: "G" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 2, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 2, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 3757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3757 Classifications: {'peptide': 493} Link IDs: {'PTRANS': 16, 'TRANS': 476} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "P" Number of atoms: 585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 585 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "Q" Number of atoms: 3757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3757 Classifications: {'peptide': 493} Link IDs: {'PTRANS': 16, 'TRANS': 476} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "R" Number of atoms: 585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 585 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "S" Number of atoms: 3757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3757 Classifications: {'peptide': 493} Link IDs: {'PTRANS': 16, 'TRANS': 476} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "T" Number of atoms: 585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 585 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "U" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 950 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "V" Number of atoms: 870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 870 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 6, 'TRANS': 106} Chain: "W" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 2, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "X" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Y" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 2, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "Z" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "0" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "1" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 6.34, per 1000 atoms: 0.21 Number of scatterers: 30226 At special positions: 0 Unit cell: (165.87, 237.69, 117.99, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 202 16.00 O 5778 8.00 N 5062 7.00 C 19184 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=30, symmetry=0 Simple disulfide: pdb=" SG CYS A 3 " - pdb=" SG CYS A 30 " distance=2.03 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 121 " distance=2.02 Simple disulfide: pdb=" SG CYS A 92 " - pdb=" SG CYS A 116 " distance=2.03 Simple disulfide: pdb=" SG CYS A 183 " - pdb=" SG CYS A 283 " distance=2.03 Simple disulfide: pdb=" SG CYS C 3 " - pdb=" SG CYS C 30 " distance=2.03 Simple disulfide: pdb=" SG CYS C 60 " - pdb=" SG CYS C 121 " distance=2.03 Simple disulfide: pdb=" SG CYS C 74 " - pdb=" SG CYS C 105 " distance=2.03 Simple disulfide: pdb=" SG CYS C 92 " - pdb=" SG CYS C 116 " distance=2.03 Simple disulfide: pdb=" SG CYS C 300 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 3 " - pdb=" SG CYS E 30 " distance=2.02 Simple disulfide: pdb=" SG CYS E 60 " - pdb=" SG CYS E 121 " distance=2.03 Simple disulfide: pdb=" SG CYS E 92 " - pdb=" SG CYS E 116 " distance=2.03 Simple disulfide: pdb=" SG CYS E 300 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 94 " distance=2.03 Simple disulfide: pdb=" SG CYS O 3 " - pdb=" SG CYS O 30 " distance=2.03 Simple disulfide: pdb=" SG CYS O 60 " - pdb=" SG CYS O 121 " distance=2.02 Simple disulfide: pdb=" SG CYS O 92 " - pdb=" SG CYS O 116 " distance=2.03 Simple disulfide: pdb=" SG CYS O 183 " - pdb=" SG CYS O 283 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 3 " - pdb=" SG CYS Q 30 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 60 " - pdb=" SG CYS Q 121 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 74 " - pdb=" SG CYS Q 105 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 92 " - pdb=" SG CYS Q 116 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 300 " - pdb=" SG CYS Q 331 " distance=2.03 Simple disulfide: pdb=" SG CYS S 3 " - pdb=" SG CYS S 30 " distance=2.02 Simple disulfide: pdb=" SG CYS S 60 " - pdb=" SG CYS S 121 " distance=2.03 Simple disulfide: pdb=" SG CYS S 92 " - pdb=" SG CYS S 116 " distance=2.03 Simple disulfide: pdb=" SG CYS S 300 " - pdb=" SG CYS S 331 " distance=2.03 Simple disulfide: pdb=" SG CYS U 22 " - pdb=" SG CYS U 96 " distance=2.03 Simple disulfide: pdb=" SG CYS V 23 " - pdb=" SG CYS V 94 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA G 3 " - " MAN G 4 " " BMA J 3 " - " MAN J 4 " " BMA W 3 " - " MAN W 4 " " BMA Y 3 " - " MAN Y 4 " BETA1-4 " NAG 0 1 " - " NAG 0 2 " " NAG 1 1 " - " NAG 1 2 " " NAG 1 2 " - " BMA 1 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " BETA1-6 " BMA G 3 " - " BMA G 5 " " BMA J 3 " - " BMA J 5 " " BMA W 3 " - " BMA W 5 " " BMA Y 3 " - " BMA Y 5 " NAG-ASN " NAG 0 1 " - " ASN S 67 " " NAG 1 1 " - " ASN S 153 " " NAG G 1 " - " ASN A 67 " " NAG I 1 " - " ASN A 153 " " NAG J 1 " - " ASN C 67 " " NAG K 1 " - " ASN C 153 " " NAG M 1 " - " ASN E 67 " " NAG N 1 " - " ASN E 153 " " NAG W 1 " - " ASN O 67 " " NAG X 1 " - " ASN O 153 " " NAG Y 1 " - " ASN Q 67 " " NAG Z 1 " - " ASN Q 153 " Time building additional restraints: 2.62 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 715.3 nanoseconds 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6984 Finding SS restraints... Secondary structure from input PDB file: 82 helices and 68 sheets defined 26.0% alpha, 26.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.02 Creating SS restraints... Processing helix chain 'A' and resid 100 through 104 Processing helix chain 'A' and resid 131 through 133 No H-bonds generated for 'chain 'A' and resid 131 through 133' Processing helix chain 'A' and resid 208 through 213 Processing helix chain 'A' and resid 231 through 235 removed outlier: 3.776A pdb=" N LEU A 234 " --> pdb=" O ARG A 231 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU A 235 " --> pdb=" O LYS A 232 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 231 through 235' Processing helix chain 'A' and resid 254 through 262 Processing helix chain 'A' and resid 394 through 414 Processing helix chain 'A' and resid 415 through 420 removed outlier: 3.820A pdb=" N PHE A 420 " --> pdb=" O ALA A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 447 Processing helix chain 'A' and resid 450 through 467 Processing helix chain 'A' and resid 470 through 489 removed outlier: 4.010A pdb=" N SER A 476 " --> pdb=" O SER A 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 39 removed outlier: 4.530A pdb=" N VAL B 32 " --> pdb=" O GLN B 28 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLU B 33 " --> pdb=" O VAL B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 54 removed outlier: 4.008A pdb=" N ILE B 44 " --> pdb=" O PRO B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 75 Proline residue: B 72 - end of helix Processing helix chain 'C' and resid 82 through 86 removed outlier: 3.799A pdb=" N GLN C 86 " --> pdb=" O PRO C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 104 Processing helix chain 'C' and resid 131 through 135 removed outlier: 3.990A pdb=" N LEU C 135 " --> pdb=" O TYR C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 214 Processing helix chain 'C' and resid 231 through 235 removed outlier: 3.683A pdb=" N LEU C 234 " --> pdb=" O ARG C 231 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 261 Processing helix chain 'C' and resid 394 through 411 Processing helix chain 'C' and resid 415 through 420 Processing helix chain 'C' and resid 425 through 447 removed outlier: 3.553A pdb=" N LEU C 430 " --> pdb=" O VAL C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 468 Processing helix chain 'C' and resid 470 through 491 removed outlier: 3.656A pdb=" N VAL C 490 " --> pdb=" O TYR C 486 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 39 Processing helix chain 'D' and resid 40 through 54 removed outlier: 3.790A pdb=" N ILE D 44 " --> pdb=" O PRO D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 75 removed outlier: 3.551A pdb=" N THR D 71 " --> pdb=" O LEU D 67 " (cutoff:3.500A) Proline residue: D 72 - end of helix Processing helix chain 'E' and resid 16 through 18 No H-bonds generated for 'chain 'E' and resid 16 through 18' Processing helix chain 'E' and resid 82 through 87 removed outlier: 3.531A pdb=" N GLN E 86 " --> pdb=" O PRO E 83 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 194 removed outlier: 3.890A pdb=" N MET E 194 " --> pdb=" O PHE E 191 " (cutoff:3.500A) Processing helix chain 'E' and resid 207 through 213 Processing helix chain 'E' and resid 231 through 234 removed outlier: 4.244A pdb=" N LEU E 234 " --> pdb=" O ARG E 231 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 231 through 234' Processing helix chain 'E' and resid 254 through 262 Processing helix chain 'E' and resid 394 through 413 Processing helix chain 'E' and resid 415 through 419 Processing helix chain 'E' and resid 426 through 446 Processing helix chain 'E' and resid 450 through 468 removed outlier: 4.145A pdb=" N ILE E 455 " --> pdb=" O TRP E 451 " (cutoff:3.500A) Processing helix chain 'E' and resid 471 through 489 removed outlier: 4.380A pdb=" N PHE E 475 " --> pdb=" O THR E 471 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ILE E 478 " --> pdb=" O SER E 474 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ILE E 482 " --> pdb=" O ILE E 478 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N ILE E 483 " --> pdb=" O ALA E 479 " (cutoff:3.500A) Processing helix chain 'F' and resid 26 through 39 Processing helix chain 'F' and resid 40 through 52 removed outlier: 3.893A pdb=" N ILE F 44 " --> pdb=" O PRO F 40 " (cutoff:3.500A) Processing helix chain 'F' and resid 58 through 75 removed outlier: 3.662A pdb=" N PHE F 64 " --> pdb=" O LYS F 60 " (cutoff:3.500A) Proline residue: F 72 - end of helix Processing helix chain 'O' and resid 100 through 104 Processing helix chain 'O' and resid 131 through 133 No H-bonds generated for 'chain 'O' and resid 131 through 133' Processing helix chain 'O' and resid 208 through 213 Processing helix chain 'O' and resid 231 through 235 removed outlier: 3.776A pdb=" N LEU O 234 " --> pdb=" O ARG O 231 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU O 235 " --> pdb=" O LYS O 232 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 231 through 235' Processing helix chain 'O' and resid 254 through 262 Processing helix chain 'O' and resid 394 through 414 Processing helix chain 'O' and resid 415 through 420 removed outlier: 3.820A pdb=" N PHE O 420 " --> pdb=" O ALA O 417 " (cutoff:3.500A) Processing helix chain 'O' and resid 426 through 447 Processing helix chain 'O' and resid 450 through 467 Processing helix chain 'O' and resid 470 through 489 removed outlier: 4.010A pdb=" N SER O 476 " --> pdb=" O SER O 472 " (cutoff:3.500A) Processing helix chain 'P' and resid 20 through 39 removed outlier: 4.530A pdb=" N VAL P 32 " --> pdb=" O GLN P 28 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLU P 33 " --> pdb=" O VAL P 29 " (cutoff:3.500A) Processing helix chain 'P' and resid 40 through 54 removed outlier: 4.008A pdb=" N ILE P 44 " --> pdb=" O PRO P 40 " (cutoff:3.500A) Processing helix chain 'P' and resid 56 through 75 Proline residue: P 72 - end of helix Processing helix chain 'Q' and resid 82 through 86 removed outlier: 3.799A pdb=" N GLN Q 86 " --> pdb=" O PRO Q 83 " (cutoff:3.500A) Processing helix chain 'Q' and resid 100 through 104 Processing helix chain 'Q' and resid 131 through 135 removed outlier: 3.990A pdb=" N LEU Q 135 " --> pdb=" O TYR Q 132 " (cutoff:3.500A) Processing helix chain 'Q' and resid 208 through 214 Processing helix chain 'Q' and resid 231 through 235 removed outlier: 3.683A pdb=" N LEU Q 234 " --> pdb=" O ARG Q 231 " (cutoff:3.500A) Processing helix chain 'Q' and resid 254 through 261 Processing helix chain 'Q' and resid 394 through 411 Processing helix chain 'Q' and resid 415 through 420 Processing helix chain 'Q' and resid 425 through 447 removed outlier: 3.553A pdb=" N LEU Q 430 " --> pdb=" O VAL Q 426 " (cutoff:3.500A) Processing helix chain 'Q' and resid 450 through 468 Processing helix chain 'Q' and resid 470 through 491 removed outlier: 3.656A pdb=" N VAL Q 490 " --> pdb=" O TYR Q 486 " (cutoff:3.500A) Processing helix chain 'R' and resid 26 through 39 Processing helix chain 'R' and resid 40 through 54 removed outlier: 3.790A pdb=" N ILE R 44 " --> pdb=" O PRO R 40 " (cutoff:3.500A) Processing helix chain 'R' and resid 56 through 75 removed outlier: 3.551A pdb=" N THR R 71 " --> pdb=" O LEU R 67 " (cutoff:3.500A) Proline residue: R 72 - end of helix Processing helix chain 'S' and resid 16 through 18 No H-bonds generated for 'chain 'S' and resid 16 through 18' Processing helix chain 'S' and resid 82 through 87 removed outlier: 3.531A pdb=" N GLN S 86 " --> pdb=" O PRO S 83 " (cutoff:3.500A) Processing helix chain 'S' and resid 190 through 194 removed outlier: 3.890A pdb=" N MET S 194 " --> pdb=" O PHE S 191 " (cutoff:3.500A) Processing helix chain 'S' and resid 207 through 213 Processing helix chain 'S' and resid 231 through 234 removed outlier: 4.244A pdb=" N LEU S 234 " --> pdb=" O ARG S 231 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 231 through 234' Processing helix chain 'S' and resid 254 through 262 Processing helix chain 'S' and resid 394 through 413 Processing helix chain 'S' and resid 415 through 419 Processing helix chain 'S' and resid 426 through 446 Processing helix chain 'S' and resid 450 through 468 removed outlier: 4.145A pdb=" N ILE S 455 " --> pdb=" O TRP S 451 " (cutoff:3.500A) Processing helix chain 'S' and resid 471 through 489 removed outlier: 4.380A pdb=" N PHE S 475 " --> pdb=" O THR S 471 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ILE S 478 " --> pdb=" O SER S 474 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ILE S 482 " --> pdb=" O ILE S 478 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N ILE S 483 " --> pdb=" O ALA S 479 " (cutoff:3.500A) Processing helix chain 'T' and resid 26 through 39 Processing helix chain 'T' and resid 40 through 52 removed outlier: 3.893A pdb=" N ILE T 44 " --> pdb=" O PRO T 40 " (cutoff:3.500A) Processing helix chain 'T' and resid 58 through 75 removed outlier: 3.662A pdb=" N PHE T 64 " --> pdb=" O LYS T 60 " (cutoff:3.500A) Proline residue: T 72 - end of helix Processing sheet with id=1, first strand: chain 'A' and resid 10 through 12 removed outlier: 6.823A pdb=" N ASP A 10 " --> pdb=" O THR A 32 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N THR A 138 " --> pdb=" O GLN A 46 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N THR A 48 " --> pdb=" O LYS A 136 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LYS A 136 " --> pdb=" O THR A 48 " (cutoff:3.500A) Processing sheet with id=2, first strand: chain 'A' and resid 10 through 12 removed outlier: 6.823A pdb=" N ASP A 10 " --> pdb=" O THR A 32 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR A 48 " --> pdb=" O ILE A 276 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ALA A 50 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N THR A 274 " --> pdb=" O ALA A 50 " (cutoff:3.500A) Processing sheet with id=3, first strand: chain 'A' and resid 20 through 26 removed outlier: 4.044A pdb=" N GLY A 177 " --> pdb=" O LEU A 173 " (cutoff:3.500A) Processing sheet with id=4, first strand: chain 'A' and resid 54 through 55 Processing sheet with id=5, first strand: chain 'A' and resid 58 through 59 Processing sheet with id=6, first strand: chain 'A' and resid 64 through 73 removed outlier: 5.409A pdb=" N ILE A 65 " --> pdb=" O GLN A 120 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N GLN A 120 " --> pdb=" O ILE A 65 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ASN A 67 " --> pdb=" O LYS A 118 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL A 114 " --> pdb=" O ASP A 71 " (cutoff:3.500A) Processing sheet with id=7, first strand: chain 'A' and resid 194 through 195 Processing sheet with id=8, first strand: chain 'A' and resid 198 through 199 removed outlier: 3.829A pdb=" N ALA A 203 " --> pdb=" O ILE A 268 " (cutoff:3.500A) Processing sheet with id=9, first strand: chain 'A' and resid 237 through 240 Processing sheet with id=10, first strand: chain 'A' and resid 305 through 313 removed outlier: 7.151A pdb=" N LYS A 307 " --> pdb=" O GLU A 323 " (cutoff:3.500A) removed outlier: 8.350A pdb=" N GLU A 323 " --> pdb=" O LYS A 307 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N GLU A 309 " --> pdb=" O LYS A 321 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N LYS A 321 " --> pdb=" O GLU A 309 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER A 311 " --> pdb=" O LEU A 319 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N THR A 317 " --> pdb=" O THR A 313 " (cutoff:3.500A) Processing sheet with id=11, first strand: chain 'A' and resid 336 through 339 removed outlier: 3.673A pdb=" N SER A 374 " --> pdb=" O TRP A 389 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE A 387 " --> pdb=" O ILE A 376 " (cutoff:3.500A) Processing sheet with id=12, first strand: chain 'C' and resid 10 through 12 removed outlier: 3.564A pdb=" N THR C 32 " --> pdb=" O ASP C 10 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N THR C 138 " --> pdb=" O GLN C 46 " (cutoff:3.500A) Processing sheet with id=13, first strand: chain 'C' and resid 20 through 26 removed outlier: 3.598A pdb=" N GLY C 177 " --> pdb=" O LEU C 173 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA C 171 " --> pdb=" O LEU C 179 " (cutoff:3.500A) Processing sheet with id=14, first strand: chain 'C' and resid 54 through 59 removed outlier: 5.584A pdb=" N THR C 55 " --> pdb=" O VAL C 129 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N VAL C 129 " --> pdb=" O THR C 55 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ARG C 57 " --> pdb=" O GLY C 127 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ALA C 203 " --> pdb=" O ILE C 268 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE C 268 " --> pdb=" O ALA C 203 " (cutoff:3.500A) Processing sheet with id=15, first strand: chain 'C' and resid 62 through 72 removed outlier: 4.420A pdb=" N ILE C 68 " --> pdb=" O CYS C 116 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N CYS C 116 " --> pdb=" O ILE C 68 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N THR C 70 " --> pdb=" O VAL C 114 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N VAL C 114 " --> pdb=" O THR C 70 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N SER C 72 " --> pdb=" O SER C 112 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N SER C 112 " --> pdb=" O SER C 72 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLY C 109 " --> pdb=" O ARG C 99 " (cutoff:3.500A) Processing sheet with id=16, first strand: chain 'C' and resid 237 through 238 Processing sheet with id=17, first strand: chain 'C' and resid 304 through 312 removed outlier: 7.415A pdb=" N LYS C 321 " --> pdb=" O LYS C 307 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N GLU C 309 " --> pdb=" O LEU C 319 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N LEU C 319 " --> pdb=" O GLU C 309 " (cutoff:3.500A) Processing sheet with id=18, first strand: chain 'C' and resid 373 through 377 removed outlier: 3.666A pdb=" N SER C 374 " --> pdb=" O TRP C 389 " (cutoff:3.500A) Processing sheet with id=19, first strand: chain 'E' and resid 10 through 12 removed outlier: 7.201A pdb=" N THR E 138 " --> pdb=" O GLN E 46 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N THR E 48 " --> pdb=" O LYS E 136 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N LYS E 136 " --> pdb=" O THR E 48 " (cutoff:3.500A) Processing sheet with id=20, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.804A pdb=" N ALA E 50 " --> pdb=" O THR E 274 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N THR E 274 " --> pdb=" O ALA E 50 " (cutoff:3.500A) Processing sheet with id=21, first strand: chain 'E' and resid 20 through 25 removed outlier: 4.808A pdb=" N LYS E 282 " --> pdb=" O SER E 184 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N SER E 184 " --> pdb=" O LYS E 282 " (cutoff:3.500A) Processing sheet with id=22, first strand: chain 'E' and resid 54 through 72 removed outlier: 5.619A pdb=" N THR E 55 " --> pdb=" O VAL E 129 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N VAL E 129 " --> pdb=" O THR E 55 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE E 61 " --> pdb=" O GLU E 123 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N GLU E 123 " --> pdb=" O ILE E 61 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N GLY E 63 " --> pdb=" O CYS E 121 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N CYS E 121 " --> pdb=" O GLY E 63 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N ILE E 65 " --> pdb=" O PHE E 119 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N PHE E 119 " --> pdb=" O ILE E 65 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N ASN E 67 " --> pdb=" O ALA E 117 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N ALA E 117 " --> pdb=" O ASN E 67 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N THR E 69 " --> pdb=" O THR E 115 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N THR E 115 " --> pdb=" O THR E 69 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ASP E 71 " --> pdb=" O LEU E 113 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N LEU E 113 " --> pdb=" O ASP E 71 " (cutoff:3.500A) Processing sheet with id=23, first strand: chain 'E' and resid 54 through 72 removed outlier: 5.619A pdb=" N THR E 55 " --> pdb=" O VAL E 129 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N VAL E 129 " --> pdb=" O THR E 55 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE E 61 " --> pdb=" O GLU E 123 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N GLU E 123 " --> pdb=" O ILE E 61 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N GLY E 63 " --> pdb=" O CYS E 121 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N CYS E 121 " --> pdb=" O GLY E 63 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N ILE E 65 " --> pdb=" O PHE E 119 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N PHE E 119 " --> pdb=" O ILE E 65 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N ASN E 67 " --> pdb=" O ALA E 117 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N ALA E 117 " --> pdb=" O ASN E 67 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N THR E 69 " --> pdb=" O THR E 115 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N THR E 115 " --> pdb=" O THR E 69 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ASP E 71 " --> pdb=" O LEU E 113 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N LEU E 113 " --> pdb=" O ASP E 71 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU E 126 " --> pdb=" O THR E 198 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N TRP E 204 " --> pdb=" O LEU E 197 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ALA E 203 " --> pdb=" O ILE E 268 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE E 268 " --> pdb=" O ALA E 203 " (cutoff:3.500A) Processing sheet with id=24, first strand: chain 'E' and resid 218 through 219 Processing sheet with id=25, first strand: chain 'E' and resid 236 through 239 removed outlier: 3.669A pdb=" N VAL E 249 " --> pdb=" O THR E 237 " (cutoff:3.500A) Processing sheet with id=26, first strand: chain 'E' and resid 304 through 308 removed outlier: 7.963A pdb=" N LYS E 321 " --> pdb=" O LYS E 307 " (cutoff:3.500A) Processing sheet with id=27, first strand: chain 'E' and resid 331 through 332 Processing sheet with id=28, first strand: chain 'E' and resid 336 through 338 Processing sheet with id=29, first strand: chain 'E' and resid 348 through 349 Processing sheet with id=30, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=31, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.919A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=32, first strand: chain 'L' and resid 4 through 6 removed outlier: 3.611A pdb=" N PHE L 77 " --> pdb=" O CYS L 23 " (cutoff:3.500A) Processing sheet with id=33, first strand: chain 'L' and resid 11 through 13 removed outlier: 3.915A pdb=" N THR L 108 " --> pdb=" O TYR L 92 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLY L 90 " --> pdb=" O LEU L 110 " (cutoff:3.500A) Processing sheet with id=34, first strand: chain 'L' and resid 50 through 54 removed outlier: 6.882A pdb=" N TRP L 41 " --> pdb=" O LEU L 53 " (cutoff:3.500A) Processing sheet with id=35, first strand: chain 'O' and resid 10 through 12 removed outlier: 6.823A pdb=" N ASP O 10 " --> pdb=" O THR O 32 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N THR O 138 " --> pdb=" O GLN O 46 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N THR O 48 " --> pdb=" O LYS O 136 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LYS O 136 " --> pdb=" O THR O 48 " (cutoff:3.500A) Processing sheet with id=36, first strand: chain 'O' and resid 10 through 12 removed outlier: 6.823A pdb=" N ASP O 10 " --> pdb=" O THR O 32 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR O 48 " --> pdb=" O ILE O 276 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ALA O 50 " --> pdb=" O THR O 274 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N THR O 274 " --> pdb=" O ALA O 50 " (cutoff:3.500A) Processing sheet with id=37, first strand: chain 'O' and resid 20 through 26 removed outlier: 4.044A pdb=" N GLY O 177 " --> pdb=" O LEU O 173 " (cutoff:3.500A) Processing sheet with id=38, first strand: chain 'O' and resid 54 through 55 Processing sheet with id=39, first strand: chain 'O' and resid 58 through 59 Processing sheet with id=40, first strand: chain 'O' and resid 64 through 73 removed outlier: 5.409A pdb=" N ILE O 65 " --> pdb=" O GLN O 120 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N GLN O 120 " --> pdb=" O ILE O 65 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ASN O 67 " --> pdb=" O LYS O 118 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL O 114 " --> pdb=" O ASP O 71 " (cutoff:3.500A) Processing sheet with id=41, first strand: chain 'O' and resid 194 through 195 Processing sheet with id=42, first strand: chain 'O' and resid 198 through 199 removed outlier: 3.829A pdb=" N ALA O 203 " --> pdb=" O ILE O 268 " (cutoff:3.500A) Processing sheet with id=43, first strand: chain 'O' and resid 237 through 240 Processing sheet with id=44, first strand: chain 'O' and resid 305 through 313 removed outlier: 7.151A pdb=" N LYS O 307 " --> pdb=" O GLU O 323 " (cutoff:3.500A) removed outlier: 8.350A pdb=" N GLU O 323 " --> pdb=" O LYS O 307 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N GLU O 309 " --> pdb=" O LYS O 321 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N LYS O 321 " --> pdb=" O GLU O 309 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER O 311 " --> pdb=" O LEU O 319 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N THR O 317 " --> pdb=" O THR O 313 " (cutoff:3.500A) Processing sheet with id=45, first strand: chain 'O' and resid 336 through 339 removed outlier: 3.673A pdb=" N SER O 374 " --> pdb=" O TRP O 389 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE O 387 " --> pdb=" O ILE O 376 " (cutoff:3.500A) Processing sheet with id=46, first strand: chain 'Q' and resid 10 through 12 removed outlier: 3.564A pdb=" N THR Q 32 " --> pdb=" O ASP Q 10 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N THR Q 138 " --> pdb=" O GLN Q 46 " (cutoff:3.500A) Processing sheet with id=47, first strand: chain 'Q' and resid 20 through 26 removed outlier: 3.598A pdb=" N GLY Q 177 " --> pdb=" O LEU Q 173 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA Q 171 " --> pdb=" O LEU Q 179 " (cutoff:3.500A) Processing sheet with id=48, first strand: chain 'Q' and resid 54 through 59 removed outlier: 5.584A pdb=" N THR Q 55 " --> pdb=" O VAL Q 129 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N VAL Q 129 " --> pdb=" O THR Q 55 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ARG Q 57 " --> pdb=" O GLY Q 127 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ALA Q 203 " --> pdb=" O ILE Q 268 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE Q 268 " --> pdb=" O ALA Q 203 " (cutoff:3.500A) Processing sheet with id=49, first strand: chain 'Q' and resid 62 through 72 removed outlier: 4.420A pdb=" N ILE Q 68 " --> pdb=" O CYS Q 116 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N CYS Q 116 " --> pdb=" O ILE Q 68 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N THR Q 70 " --> pdb=" O VAL Q 114 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N VAL Q 114 " --> pdb=" O THR Q 70 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N SER Q 72 " --> pdb=" O SER Q 112 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N SER Q 112 " --> pdb=" O SER Q 72 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLY Q 109 " --> pdb=" O ARG Q 99 " (cutoff:3.500A) Processing sheet with id=50, first strand: chain 'Q' and resid 237 through 238 Processing sheet with id=51, first strand: chain 'Q' and resid 304 through 312 removed outlier: 7.415A pdb=" N LYS Q 321 " --> pdb=" O LYS Q 307 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N GLU Q 309 " --> pdb=" O LEU Q 319 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N LEU Q 319 " --> pdb=" O GLU Q 309 " (cutoff:3.500A) Processing sheet with id=52, first strand: chain 'Q' and resid 373 through 377 removed outlier: 3.666A pdb=" N SER Q 374 " --> pdb=" O TRP Q 389 " (cutoff:3.500A) Processing sheet with id=53, first strand: chain 'S' and resid 10 through 12 removed outlier: 7.201A pdb=" N THR S 138 " --> pdb=" O GLN S 46 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N THR S 48 " --> pdb=" O LYS S 136 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N LYS S 136 " --> pdb=" O THR S 48 " (cutoff:3.500A) Processing sheet with id=54, first strand: chain 'S' and resid 10 through 12 removed outlier: 3.804A pdb=" N ALA S 50 " --> pdb=" O THR S 274 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N THR S 274 " --> pdb=" O ALA S 50 " (cutoff:3.500A) Processing sheet with id=55, first strand: chain 'S' and resid 20 through 25 removed outlier: 4.808A pdb=" N LYS S 282 " --> pdb=" O SER S 184 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N SER S 184 " --> pdb=" O LYS S 282 " (cutoff:3.500A) Processing sheet with id=56, first strand: chain 'S' and resid 54 through 72 removed outlier: 5.619A pdb=" N THR S 55 " --> pdb=" O VAL S 129 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N VAL S 129 " --> pdb=" O THR S 55 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE S 61 " --> pdb=" O GLU S 123 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N GLU S 123 " --> pdb=" O ILE S 61 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N GLY S 63 " --> pdb=" O CYS S 121 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N CYS S 121 " --> pdb=" O GLY S 63 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N ILE S 65 " --> pdb=" O PHE S 119 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N PHE S 119 " --> pdb=" O ILE S 65 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N ASN S 67 " --> pdb=" O ALA S 117 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N ALA S 117 " --> pdb=" O ASN S 67 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N THR S 69 " --> pdb=" O THR S 115 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N THR S 115 " --> pdb=" O THR S 69 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ASP S 71 " --> pdb=" O LEU S 113 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N LEU S 113 " --> pdb=" O ASP S 71 " (cutoff:3.500A) Processing sheet with id=57, first strand: chain 'S' and resid 54 through 72 removed outlier: 5.619A pdb=" N THR S 55 " --> pdb=" O VAL S 129 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N VAL S 129 " --> pdb=" O THR S 55 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE S 61 " --> pdb=" O GLU S 123 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N GLU S 123 " --> pdb=" O ILE S 61 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N GLY S 63 " --> pdb=" O CYS S 121 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N CYS S 121 " --> pdb=" O GLY S 63 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N ILE S 65 " --> pdb=" O PHE S 119 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N PHE S 119 " --> pdb=" O ILE S 65 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N ASN S 67 " --> pdb=" O ALA S 117 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N ALA S 117 " --> pdb=" O ASN S 67 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N THR S 69 " --> pdb=" O THR S 115 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N THR S 115 " --> pdb=" O THR S 69 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ASP S 71 " --> pdb=" O LEU S 113 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N LEU S 113 " --> pdb=" O ASP S 71 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU S 126 " --> pdb=" O THR S 198 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N TRP S 204 " --> pdb=" O LEU S 197 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ALA S 203 " --> pdb=" O ILE S 268 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE S 268 " --> pdb=" O ALA S 203 " (cutoff:3.500A) Processing sheet with id=58, first strand: chain 'S' and resid 218 through 219 Processing sheet with id=59, first strand: chain 'S' and resid 236 through 239 removed outlier: 3.669A pdb=" N VAL S 249 " --> pdb=" O THR S 237 " (cutoff:3.500A) Processing sheet with id=60, first strand: chain 'S' and resid 304 through 308 removed outlier: 7.963A pdb=" N LYS S 321 " --> pdb=" O LYS S 307 " (cutoff:3.500A) Processing sheet with id=61, first strand: chain 'S' and resid 331 through 332 Processing sheet with id=62, first strand: chain 'S' and resid 336 through 338 Processing sheet with id=63, first strand: chain 'S' and resid 348 through 349 Processing sheet with id=64, first strand: chain 'U' and resid 3 through 7 Processing sheet with id=65, first strand: chain 'U' and resid 11 through 12 removed outlier: 6.919A pdb=" N MET U 34 " --> pdb=" O VAL U 50 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N VAL U 50 " --> pdb=" O MET U 34 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N TRP U 36 " --> pdb=" O VAL U 48 " (cutoff:3.500A) Processing sheet with id=66, first strand: chain 'V' and resid 4 through 6 removed outlier: 3.611A pdb=" N PHE V 77 " --> pdb=" O CYS V 23 " (cutoff:3.500A) Processing sheet with id=67, first strand: chain 'V' and resid 11 through 13 removed outlier: 3.915A pdb=" N THR V 108 " --> pdb=" O TYR V 92 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLY V 90 " --> pdb=" O LEU V 110 " (cutoff:3.500A) Processing sheet with id=68, first strand: chain 'V' and resid 50 through 54 removed outlier: 6.882A pdb=" N TRP V 41 " --> pdb=" O LEU V 53 " (cutoff:3.500A) 1204 hydrogen bonds defined for protein. 3216 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: 5.66 Time building geometry restraints manager: 3.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9516 1.34 - 1.46: 5050 1.46 - 1.58: 15952 1.58 - 1.69: 0 1.69 - 1.81: 318 Bond restraints: 30836 Sorted by residual: bond pdb=" C1 BMA G 5 " pdb=" C2 BMA G 5 " ideal model delta sigma weight residual 1.519 1.558 -0.039 2.00e-02 2.50e+03 3.72e+00 bond pdb=" C1 BMA W 5 " pdb=" C2 BMA W 5 " ideal model delta sigma weight residual 1.519 1.558 -0.039 2.00e-02 2.50e+03 3.72e+00 bond pdb=" C1 BMA J 5 " pdb=" C2 BMA J 5 " ideal model delta sigma weight residual 1.519 1.556 -0.037 2.00e-02 2.50e+03 3.46e+00 bond pdb=" C1 BMA Y 5 " pdb=" C2 BMA Y 5 " ideal model delta sigma weight residual 1.519 1.556 -0.037 2.00e-02 2.50e+03 3.46e+00 bond pdb=" C1 BMA K 3 " pdb=" C2 BMA K 3 " ideal model delta sigma weight residual 1.519 1.550 -0.031 2.00e-02 2.50e+03 2.40e+00 ... (remaining 30831 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.67: 40194 1.67 - 3.34: 1342 3.34 - 5.02: 204 5.02 - 6.69: 52 6.69 - 8.36: 14 Bond angle restraints: 41806 Sorted by residual: angle pdb=" C ALA E 479 " pdb=" N ILE E 480 " pdb=" CA ILE E 480 " ideal model delta sigma weight residual 123.16 117.65 5.51 1.06e+00 8.90e-01 2.70e+01 angle pdb=" C ALA S 479 " pdb=" N ILE S 480 " pdb=" CA ILE S 480 " ideal model delta sigma weight residual 123.16 117.65 5.51 1.06e+00 8.90e-01 2.70e+01 angle pdb=" N ILE B 53 " pdb=" CA ILE B 53 " pdb=" C ILE B 53 " ideal model delta sigma weight residual 112.96 109.47 3.49 1.00e+00 1.00e+00 1.22e+01 angle pdb=" N ILE P 53 " pdb=" CA ILE P 53 " pdb=" C ILE P 53 " ideal model delta sigma weight residual 112.96 109.47 3.49 1.00e+00 1.00e+00 1.22e+01 angle pdb=" N VAL C 491 " pdb=" CA VAL C 491 " pdb=" C VAL C 491 " ideal model delta sigma weight residual 110.62 114.13 -3.51 1.02e+00 9.61e-01 1.19e+01 ... (remaining 41801 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.24: 17658 22.24 - 44.48: 882 44.48 - 66.72: 112 66.72 - 88.96: 108 88.96 - 111.20: 56 Dihedral angle restraints: 18816 sinusoidal: 7878 harmonic: 10938 Sorted by residual: dihedral pdb=" CB CYS S 300 " pdb=" SG CYS S 300 " pdb=" SG CYS S 331 " pdb=" CB CYS S 331 " ideal model delta sinusoidal sigma weight residual -86.00 -158.81 72.81 1 1.00e+01 1.00e-02 6.76e+01 dihedral pdb=" CB CYS E 300 " pdb=" SG CYS E 300 " pdb=" SG CYS E 331 " pdb=" CB CYS E 331 " ideal model delta sinusoidal sigma weight residual -86.00 -158.81 72.81 1 1.00e+01 1.00e-02 6.76e+01 dihedral pdb=" CB CYS Q 74 " pdb=" SG CYS Q 74 " pdb=" SG CYS Q 105 " pdb=" CB CYS Q 105 " ideal model delta sinusoidal sigma weight residual 93.00 146.27 -53.27 1 1.00e+01 1.00e-02 3.86e+01 ... (remaining 18813 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 4014 0.055 - 0.110: 760 0.110 - 0.165: 142 0.165 - 0.221: 6 0.221 - 0.276: 16 Chirality restraints: 4938 Sorted by residual: chirality pdb=" C5 BMA I 3 " pdb=" C4 BMA I 3 " pdb=" C6 BMA I 3 " pdb=" O5 BMA I 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" C5 BMA X 3 " pdb=" C4 BMA X 3 " pdb=" C6 BMA X 3 " pdb=" O5 BMA X 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" C5 BMA N 3 " pdb=" C4 BMA N 3 " pdb=" C6 BMA N 3 " pdb=" O5 BMA N 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.28 2.00e-01 2.50e+01 1.89e+00 ... (remaining 4935 not shown) Planarity restraints: 5204 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR E 163 " -0.026 5.00e-02 4.00e+02 3.97e-02 2.52e+00 pdb=" N PRO E 164 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO E 164 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO E 164 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR S 163 " 0.026 5.00e-02 4.00e+02 3.97e-02 2.52e+00 pdb=" N PRO S 164 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO S 164 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO S 164 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 163 " 0.026 5.00e-02 4.00e+02 3.92e-02 2.46e+00 pdb=" N PRO A 164 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO A 164 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 164 " 0.022 5.00e-02 4.00e+02 ... (remaining 5201 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 556 2.67 - 3.23: 28619 3.23 - 3.79: 44817 3.79 - 4.34: 60117 4.34 - 4.90: 101578 Nonbonded interactions: 235687 Sorted by model distance: nonbonded pdb=" OG SER U 52 " pdb=" OD1 ASP U 54 " model vdw 2.113 3.040 nonbonded pdb=" OG SER H 52 " pdb=" OD1 ASP H 54 " model vdw 2.113 3.040 nonbonded pdb=" O ALA Q 50 " pdb=" OG1 THR Q 274 " model vdw 2.174 3.040 nonbonded pdb=" O ALA C 50 " pdb=" OG1 THR C 274 " model vdw 2.174 3.040 nonbonded pdb=" OD1 ASN H 105 " pdb=" OH TYR L 40 " model vdw 2.174 3.040 ... (remaining 235682 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: 0.02 Found NCS groups: ncs_group { reference = chain '0' selection = chain 'M' } ncs_group { reference = chain '1' selection = chain 'I' selection = chain 'K' selection = chain 'N' selection = chain 'X' selection = chain 'Z' } ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'O' selection = chain 'Q' selection = chain 'S' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'P' selection = chain 'R' selection = chain 'T' } ncs_group { reference = chain 'G' selection = chain 'J' selection = chain 'W' selection = chain 'Y' } ncs_group { reference = chain 'H' selection = chain 'U' } ncs_group { reference = chain 'L' selection = chain 'V' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 26.510 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 30908 Z= 0.197 Angle : 0.746 8.359 41992 Z= 0.417 Chirality : 0.047 0.276 4938 Planarity : 0.004 0.040 5192 Dihedral : 15.960 111.197 11742 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.28 (0.13), residues: 3846 helix: 1.15 (0.18), residues: 866 sheet: -1.18 (0.17), residues: 980 loop : -1.60 (0.12), residues: 2000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 9 TYR 0.014 0.001 TYR Q 486 PHE 0.021 0.002 PHE P 42 TRP 0.019 0.001 TRP P 26 HIS 0.006 0.001 HIS O 345 Details of bonding type rmsd covalent geometry : bond 0.00407 (30836) covalent geometry : angle 0.73552 (41806) SS BOND : bond 0.00376 ( 30) SS BOND : angle 1.39343 ( 60) hydrogen bonds : bond 0.21172 ( 1180) hydrogen bonds : angle 8.38563 ( 3216) link_ALPHA1-3 : bond 0.00441 ( 4) link_ALPHA1-3 : angle 2.19127 ( 12) link_BETA1-4 : bond 0.00427 ( 22) link_BETA1-4 : angle 2.55805 ( 66) link_BETA1-6 : bond 0.00657 ( 4) link_BETA1-6 : angle 1.20716 ( 12) link_NAG-ASN : bond 0.00462 ( 12) link_NAG-ASN : angle 1.98297 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 856 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 856 time to evaluate : 1.228 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: A 36 LYS cc_start: 0.8095 (tptp) cc_final: 0.7707 (tptp) REVERT: A 37 ASN cc_start: 0.7772 (m110) cc_final: 0.7444 (m110) REVERT: A 176 TYR cc_start: 0.8629 (m-80) cc_final: 0.8139 (m-80) REVERT: A 453 MET cc_start: 0.7673 (mmm) cc_final: 0.7258 (mmm) REVERT: A 457 ILE cc_start: 0.8567 (mt) cc_final: 0.8357 (mp) REVERT: B 57 LEU cc_start: 0.7905 (tp) cc_final: 0.7556 (tt) REVERT: B 70 VAL cc_start: 0.9030 (t) cc_final: 0.8582 (p) REVERT: B 73 SER cc_start: 0.8148 (m) cc_final: 0.7819 (p) REVERT: C 182 GLU cc_start: 0.6853 (tt0) cc_final: 0.6344 (tt0) REVERT: C 438 PHE cc_start: 0.7956 (m-10) cc_final: 0.7680 (m-10) REVERT: C 486 TYR cc_start: 0.7730 (t80) cc_final: 0.7256 (t80) REVERT: D 74 MET cc_start: 0.8247 (tpp) cc_final: 0.7587 (mmm) REVERT: E 460 LEU cc_start: 0.9366 (tt) cc_final: 0.9158 (tt) REVERT: E 485 LEU cc_start: 0.8627 (mp) cc_final: 0.8232 (mp) REVERT: H 34 MET cc_start: 0.8244 (mmm) cc_final: 0.8019 (mmm) REVERT: H 83 MET cc_start: 0.7236 (mtp) cc_final: 0.7015 (mtp) REVERT: H 111 TYR cc_start: 0.8043 (m-80) cc_final: 0.7798 (m-10) REVERT: L 55 TYR cc_start: 0.8253 (p90) cc_final: 0.7990 (p90) REVERT: O 36 LYS cc_start: 0.8092 (tptp) cc_final: 0.7710 (tptp) REVERT: O 37 ASN cc_start: 0.7772 (m110) cc_final: 0.7446 (m110) REVERT: O 176 TYR cc_start: 0.8628 (m-80) cc_final: 0.8140 (m-80) REVERT: O 453 MET cc_start: 0.7680 (mmm) cc_final: 0.7228 (mmm) REVERT: O 457 ILE cc_start: 0.8549 (mt) cc_final: 0.8344 (mp) REVERT: P 57 LEU cc_start: 0.7905 (tp) cc_final: 0.7558 (tt) REVERT: P 70 VAL cc_start: 0.9016 (t) cc_final: 0.8575 (p) REVERT: P 73 SER cc_start: 0.8148 (m) cc_final: 0.7835 (p) REVERT: Q 182 GLU cc_start: 0.6837 (tt0) cc_final: 0.6336 (tt0) REVERT: Q 438 PHE cc_start: 0.7954 (m-10) cc_final: 0.7677 (m-10) REVERT: Q 486 TYR cc_start: 0.7731 (t80) cc_final: 0.7263 (t80) REVERT: R 74 MET cc_start: 0.8258 (tpp) cc_final: 0.7576 (mmm) REVERT: S 460 LEU cc_start: 0.9365 (tt) cc_final: 0.9159 (tt) REVERT: S 485 LEU cc_start: 0.8624 (mp) cc_final: 0.8241 (mp) REVERT: U 34 MET cc_start: 0.8249 (mmm) cc_final: 0.8024 (mmm) REVERT: U 83 MET cc_start: 0.7231 (mtp) cc_final: 0.7005 (mtp) REVERT: U 111 TYR cc_start: 0.8039 (m-80) cc_final: 0.7797 (m-10) REVERT: V 55 TYR cc_start: 0.8256 (p90) cc_final: 0.7995 (p90) outliers start: 0 outliers final: 0 residues processed: 856 average time/residue: 0.2207 time to fit residues: 292.8126 Evaluate side-chains 539 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 539 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 197 optimal weight: 8.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 20.0000 chunk 298 optimal weight: 0.2980 overall best weight: 3.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 ASN A 230 ASN ** B 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 201 ASN E 280 HIS E 314 GLN ** H 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 1 HIS O 103 ASN O 230 ASN ** P 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 201 ASN S 280 HIS S 314 GLN V 1 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.094649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.082996 restraints weight = 70952.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.085164 restraints weight = 35772.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.086562 restraints weight = 22175.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.087455 restraints weight = 15844.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.088039 restraints weight = 12574.970| |-----------------------------------------------------------------------------| r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 30908 Z= 0.159 Angle : 0.691 8.989 41992 Z= 0.352 Chirality : 0.046 0.182 4938 Planarity : 0.004 0.040 5192 Dihedral : 12.527 80.305 4914 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.39 % Allowed : 11.30 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.15 (0.13), residues: 3846 helix: 1.30 (0.18), residues: 874 sheet: -1.15 (0.16), residues: 1050 loop : -1.50 (0.13), residues: 1922 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 284 TYR 0.014 0.001 TYR O 442 PHE 0.023 0.002 PHE E 475 TRP 0.022 0.002 TRP C 20 HIS 0.007 0.001 HIS A 144 Details of bonding type rmsd covalent geometry : bond 0.00369 (30836) covalent geometry : angle 0.67909 (41806) SS BOND : bond 0.00330 ( 30) SS BOND : angle 1.13899 ( 60) hydrogen bonds : bond 0.04707 ( 1180) hydrogen bonds : angle 6.14595 ( 3216) link_ALPHA1-3 : bond 0.01334 ( 4) link_ALPHA1-3 : angle 1.14650 ( 12) link_BETA1-4 : bond 0.00471 ( 22) link_BETA1-4 : angle 2.61981 ( 66) link_BETA1-6 : bond 0.01028 ( 4) link_BETA1-6 : angle 2.57655 ( 12) link_NAG-ASN : bond 0.00398 ( 12) link_NAG-ASN : angle 1.94259 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 650 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 573 time to evaluate : 1.228 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 GLU cc_start: 0.7515 (tm-30) cc_final: 0.7045 (tm-30) REVERT: A 36 LYS cc_start: 0.8360 (tptp) cc_final: 0.7804 (tptp) REVERT: A 37 ASN cc_start: 0.7847 (m110) cc_final: 0.7291 (m110) REVERT: A 176 TYR cc_start: 0.8766 (m-80) cc_final: 0.8286 (m-80) REVERT: A 199 MET cc_start: 0.8480 (ptp) cc_final: 0.8228 (ptm) REVERT: B 70 VAL cc_start: 0.9106 (t) cc_final: 0.8554 (p) REVERT: C 438 PHE cc_start: 0.8199 (m-10) cc_final: 0.7776 (m-80) REVERT: C 473 MET cc_start: 0.7386 (mmp) cc_final: 0.6979 (mtt) REVERT: C 486 TYR cc_start: 0.7768 (t80) cc_final: 0.7190 (t80) REVERT: D 10 MET cc_start: 0.7680 (OUTLIER) cc_final: 0.7362 (mpp) REVERT: D 60 LYS cc_start: 0.9134 (mttt) cc_final: 0.8928 (mttp) REVERT: D 74 MET cc_start: 0.8457 (tpp) cc_final: 0.7592 (mmm) REVERT: E 182 GLU cc_start: 0.6524 (mp0) cc_final: 0.6140 (mp0) REVERT: F 15 ARG cc_start: 0.8202 (ttt90) cc_final: 0.7807 (ttm-80) REVERT: H 34 MET cc_start: 0.8299 (mmm) cc_final: 0.8030 (mmm) REVERT: H 109 PHE cc_start: 0.8181 (m-10) cc_final: 0.7725 (m-10) REVERT: L 24 LYS cc_start: 0.8920 (tptp) cc_final: 0.8433 (mtpp) REVERT: L 55 TYR cc_start: 0.8397 (p90) cc_final: 0.8186 (p90) REVERT: L 85 GLN cc_start: 0.7934 (mp10) cc_final: 0.7462 (mp10) REVERT: O 13 GLU cc_start: 0.7517 (tm-30) cc_final: 0.7039 (tm-30) REVERT: O 36 LYS cc_start: 0.8353 (tptp) cc_final: 0.7807 (tptp) REVERT: O 37 ASN cc_start: 0.7840 (m110) cc_final: 0.7288 (m110) REVERT: O 176 TYR cc_start: 0.8760 (m-80) cc_final: 0.8280 (m-80) REVERT: O 199 MET cc_start: 0.8472 (ptp) cc_final: 0.8205 (ptm) REVERT: P 70 VAL cc_start: 0.9097 (t) cc_final: 0.8546 (p) REVERT: Q 438 PHE cc_start: 0.8204 (m-10) cc_final: 0.7781 (m-80) REVERT: Q 473 MET cc_start: 0.7381 (mmp) cc_final: 0.6984 (mtt) REVERT: Q 486 TYR cc_start: 0.7775 (t80) cc_final: 0.7192 (t80) REVERT: R 10 MET cc_start: 0.7671 (OUTLIER) cc_final: 0.7361 (mpp) REVERT: R 60 LYS cc_start: 0.9126 (mttt) cc_final: 0.8916 (mttp) REVERT: R 74 MET cc_start: 0.8441 (tpp) cc_final: 0.7589 (mmm) REVERT: U 34 MET cc_start: 0.8312 (mmm) cc_final: 0.8037 (mmm) REVERT: U 109 PHE cc_start: 0.8201 (m-10) cc_final: 0.7744 (m-10) REVERT: U 111 TYR cc_start: 0.7765 (m-80) cc_final: 0.7560 (m-10) REVERT: V 24 LYS cc_start: 0.8908 (tptp) cc_final: 0.8447 (mtpp) REVERT: V 55 TYR cc_start: 0.8399 (p90) cc_final: 0.8193 (p90) REVERT: V 85 GLN cc_start: 0.7939 (mp10) cc_final: 0.7460 (mp10) outliers start: 77 outliers final: 44 residues processed: 613 average time/residue: 0.2007 time to fit residues: 198.3047 Evaluate side-chains 535 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 489 time to evaluate : 1.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 392 LYS Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain D residue 10 MET Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain E residue 197 LEU Chi-restraints excluded: chain E residue 237 THR Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain H residue 56 ASN Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain L residue 14 THR Chi-restraints excluded: chain L residue 62 SER Chi-restraints excluded: chain L residue 95 MET Chi-restraints excluded: chain O residue 233 GLU Chi-restraints excluded: chain O residue 314 GLN Chi-restraints excluded: chain O residue 392 LYS Chi-restraints excluded: chain O residue 476 SER Chi-restraints excluded: chain P residue 17 GLN Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain Q residue 10 ASP Chi-restraints excluded: chain Q residue 363 VAL Chi-restraints excluded: chain Q residue 461 LEU Chi-restraints excluded: chain R residue 10 MET Chi-restraints excluded: chain R residue 66 LEU Chi-restraints excluded: chain R residue 70 VAL Chi-restraints excluded: chain S residue 15 LEU Chi-restraints excluded: chain S residue 197 LEU Chi-restraints excluded: chain S residue 237 THR Chi-restraints excluded: chain T residue 47 LEU Chi-restraints excluded: chain T residue 49 LEU Chi-restraints excluded: chain T residue 58 THR Chi-restraints excluded: chain U residue 56 ASN Chi-restraints excluded: chain U residue 102 VAL Chi-restraints excluded: chain V residue 14 THR Chi-restraints excluded: chain V residue 62 SER Chi-restraints excluded: chain V residue 95 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 307 optimal weight: 5.9990 chunk 183 optimal weight: 20.0000 chunk 150 optimal weight: 9.9990 chunk 333 optimal weight: 7.9990 chunk 47 optimal weight: 6.9990 chunk 263 optimal weight: 0.0870 chunk 121 optimal weight: 20.0000 chunk 365 optimal weight: 8.9990 chunk 123 optimal weight: 7.9990 chunk 298 optimal weight: 10.0000 chunk 4 optimal weight: 9.9990 overall best weight: 5.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 ASN ** B 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 201 ASN ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 1 HIS O 230 ASN ** P 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 201 ASN ** R 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 1 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.090918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.079096 restraints weight = 72020.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.081110 restraints weight = 38465.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.082432 restraints weight = 24788.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.083293 restraints weight = 18212.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.083807 restraints weight = 14717.617| |-----------------------------------------------------------------------------| r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.113 30908 Z= 0.205 Angle : 0.681 8.622 41992 Z= 0.344 Chirality : 0.046 0.175 4938 Planarity : 0.004 0.040 5192 Dihedral : 10.244 66.676 4914 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 3.66 % Allowed : 14.37 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.10 (0.13), residues: 3846 helix: 1.46 (0.18), residues: 866 sheet: -1.07 (0.16), residues: 1016 loop : -1.57 (0.13), residues: 1964 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 27 TYR 0.018 0.002 TYR C 176 PHE 0.018 0.002 PHE S 475 TRP 0.017 0.002 TRP V 31 HIS 0.005 0.001 HIS O 207 Details of bonding type rmsd covalent geometry : bond 0.00472 (30836) covalent geometry : angle 0.66909 (41806) SS BOND : bond 0.00396 ( 30) SS BOND : angle 1.14297 ( 60) hydrogen bonds : bond 0.04526 ( 1180) hydrogen bonds : angle 5.64969 ( 3216) link_ALPHA1-3 : bond 0.01375 ( 4) link_ALPHA1-3 : angle 1.26266 ( 12) link_BETA1-4 : bond 0.00480 ( 22) link_BETA1-4 : angle 2.60651 ( 66) link_BETA1-6 : bond 0.00835 ( 4) link_BETA1-6 : angle 2.41174 ( 12) link_NAG-ASN : bond 0.00576 ( 12) link_NAG-ASN : angle 1.97401 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 620 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 502 time to evaluate : 1.241 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 GLU cc_start: 0.7480 (tm-30) cc_final: 0.6821 (tm-30) REVERT: A 36 LYS cc_start: 0.8329 (tptp) cc_final: 0.8024 (tptp) REVERT: A 176 TYR cc_start: 0.8701 (m-80) cc_final: 0.8296 (m-80) REVERT: A 199 MET cc_start: 0.8537 (ptp) cc_final: 0.8039 (ptm) REVERT: B 70 VAL cc_start: 0.9083 (t) cc_final: 0.8772 (p) REVERT: C 438 PHE cc_start: 0.8171 (m-10) cc_final: 0.7875 (m-10) REVERT: C 473 MET cc_start: 0.7299 (mmp) cc_final: 0.6913 (mtt) REVERT: D 10 MET cc_start: 0.7877 (OUTLIER) cc_final: 0.7496 (mpp) REVERT: D 59 GLN cc_start: 0.8055 (mm-40) cc_final: 0.7562 (mt0) REVERT: D 74 MET cc_start: 0.8539 (tpp) cc_final: 0.8066 (mmm) REVERT: E 182 GLU cc_start: 0.6541 (mp0) cc_final: 0.6067 (mp0) REVERT: F 10 MET cc_start: 0.8700 (ppp) cc_final: 0.8447 (ppp) REVERT: L 4 MET cc_start: 0.8366 (OUTLIER) cc_final: 0.8160 (mtp) REVERT: L 24 LYS cc_start: 0.8723 (tptp) cc_final: 0.8303 (mtpp) REVERT: O 13 GLU cc_start: 0.7478 (tm-30) cc_final: 0.6810 (tm-30) REVERT: O 36 LYS cc_start: 0.8317 (tptp) cc_final: 0.8020 (tptp) REVERT: O 176 TYR cc_start: 0.8695 (m-80) cc_final: 0.8290 (m-80) REVERT: O 199 MET cc_start: 0.8547 (ptp) cc_final: 0.7984 (ptm) REVERT: P 70 VAL cc_start: 0.9076 (t) cc_final: 0.8775 (p) REVERT: Q 438 PHE cc_start: 0.8173 (m-10) cc_final: 0.7877 (m-10) REVERT: Q 473 MET cc_start: 0.7295 (mmp) cc_final: 0.6920 (mtt) REVERT: R 10 MET cc_start: 0.7888 (OUTLIER) cc_final: 0.7498 (mpp) REVERT: R 59 GLN cc_start: 0.8056 (mm-40) cc_final: 0.7560 (mt0) REVERT: R 74 MET cc_start: 0.8547 (tpp) cc_final: 0.8063 (mmm) REVERT: T 10 MET cc_start: 0.8696 (ppp) cc_final: 0.8450 (ppp) REVERT: V 4 MET cc_start: 0.8366 (OUTLIER) cc_final: 0.8150 (mtp) REVERT: V 24 LYS cc_start: 0.8709 (tptp) cc_final: 0.8259 (mtpp) outliers start: 118 outliers final: 79 residues processed: 568 average time/residue: 0.1924 time to fit residues: 179.2251 Evaluate side-chains 549 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 466 time to evaluate : 1.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 60 CYS Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 392 LYS Chi-restraints excluded: chain A residue 473 MET Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 271 SER Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 371 PHE Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain C residue 455 ILE Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain D residue 10 MET Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 197 LEU Chi-restraints excluded: chain E residue 205 MET Chi-restraints excluded: chain E residue 237 THR Chi-restraints excluded: chain E residue 373 GLU Chi-restraints excluded: chain E residue 422 SER Chi-restraints excluded: chain E residue 426 VAL Chi-restraints excluded: chain E residue 457 ILE Chi-restraints excluded: chain F residue 18 THR Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 56 ASN Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 62 SER Chi-restraints excluded: chain L residue 95 MET Chi-restraints excluded: chain O residue 41 LEU Chi-restraints excluded: chain O residue 60 CYS Chi-restraints excluded: chain O residue 233 GLU Chi-restraints excluded: chain O residue 314 GLN Chi-restraints excluded: chain O residue 392 LYS Chi-restraints excluded: chain O residue 476 SER Chi-restraints excluded: chain P residue 17 GLN Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain P residue 58 THR Chi-restraints excluded: chain Q residue 10 ASP Chi-restraints excluded: chain Q residue 271 SER Chi-restraints excluded: chain Q residue 363 VAL Chi-restraints excluded: chain Q residue 371 PHE Chi-restraints excluded: chain Q residue 423 VAL Chi-restraints excluded: chain Q residue 430 LEU Chi-restraints excluded: chain Q residue 455 ILE Chi-restraints excluded: chain Q residue 461 LEU Chi-restraints excluded: chain R residue 10 MET Chi-restraints excluded: chain R residue 66 LEU Chi-restraints excluded: chain R residue 70 VAL Chi-restraints excluded: chain S residue 107 LEU Chi-restraints excluded: chain S residue 197 LEU Chi-restraints excluded: chain S residue 205 MET Chi-restraints excluded: chain S residue 237 THR Chi-restraints excluded: chain S residue 373 GLU Chi-restraints excluded: chain S residue 422 SER Chi-restraints excluded: chain S residue 426 VAL Chi-restraints excluded: chain S residue 457 ILE Chi-restraints excluded: chain T residue 18 THR Chi-restraints excluded: chain T residue 47 LEU Chi-restraints excluded: chain T residue 49 LEU Chi-restraints excluded: chain T residue 58 THR Chi-restraints excluded: chain T residue 61 VAL Chi-restraints excluded: chain U residue 7 SER Chi-restraints excluded: chain U residue 43 LYS Chi-restraints excluded: chain U residue 56 ASN Chi-restraints excluded: chain U residue 69 THR Chi-restraints excluded: chain U residue 102 VAL Chi-restraints excluded: chain V residue 4 MET Chi-restraints excluded: chain V residue 62 SER Chi-restraints excluded: chain V residue 95 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 147 optimal weight: 20.0000 chunk 68 optimal weight: 10.0000 chunk 173 optimal weight: 2.9990 chunk 305 optimal weight: 8.9990 chunk 132 optimal weight: 9.9990 chunk 161 optimal weight: 8.9990 chunk 150 optimal weight: 9.9990 chunk 42 optimal weight: 20.0000 chunk 252 optimal weight: 9.9990 chunk 171 optimal weight: 7.9990 chunk 264 optimal weight: 8.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 27 HIS C 201 ASN ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 314 GLN ** P 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 27 HIS Q 201 ASN ** R 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 314 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.089333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.077116 restraints weight = 72661.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.079220 restraints weight = 37442.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.080590 restraints weight = 23677.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.081482 restraints weight = 17214.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.082067 restraints weight = 13831.093| |-----------------------------------------------------------------------------| r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.3085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.126 30908 Z= 0.242 Angle : 0.705 11.295 41992 Z= 0.357 Chirality : 0.047 0.197 4938 Planarity : 0.004 0.042 5192 Dihedral : 8.586 59.055 4914 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 4.81 % Allowed : 16.01 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.13 (0.13), residues: 3846 helix: 1.45 (0.18), residues: 866 sheet: -1.11 (0.16), residues: 996 loop : -1.57 (0.13), residues: 1984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 9 TYR 0.016 0.002 TYR L 38 PHE 0.022 0.002 PHE P 48 TRP 0.013 0.002 TRP H 107 HIS 0.006 0.001 HIS O 207 Details of bonding type rmsd covalent geometry : bond 0.00570 (30836) covalent geometry : angle 0.69329 (41806) SS BOND : bond 0.00408 ( 30) SS BOND : angle 1.18983 ( 60) hydrogen bonds : bond 0.04572 ( 1180) hydrogen bonds : angle 5.51228 ( 3216) link_ALPHA1-3 : bond 0.01157 ( 4) link_ALPHA1-3 : angle 1.39965 ( 12) link_BETA1-4 : bond 0.00420 ( 22) link_BETA1-4 : angle 2.48102 ( 66) link_BETA1-6 : bond 0.00848 ( 4) link_BETA1-6 : angle 2.47179 ( 12) link_NAG-ASN : bond 0.00728 ( 12) link_NAG-ASN : angle 2.12133 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 646 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 491 time to evaluate : 1.198 Fit side-chains REVERT: A 13 GLU cc_start: 0.7642 (tm-30) cc_final: 0.6855 (tm-30) REVERT: A 36 LYS cc_start: 0.8476 (tptp) cc_final: 0.8224 (tmtt) REVERT: B 30 GLU cc_start: 0.7203 (pt0) cc_final: 0.6928 (pt0) REVERT: B 70 VAL cc_start: 0.9107 (t) cc_final: 0.8763 (p) REVERT: C 438 PHE cc_start: 0.8122 (m-10) cc_final: 0.7910 (m-10) REVERT: C 473 MET cc_start: 0.7462 (mmp) cc_final: 0.7009 (mtt) REVERT: C 482 ILE cc_start: 0.9025 (mm) cc_final: 0.8730 (mt) REVERT: D 10 MET cc_start: 0.8034 (tpp) cc_final: 0.7536 (mpp) REVERT: D 64 PHE cc_start: 0.9040 (t80) cc_final: 0.8818 (t80) REVERT: D 74 MET cc_start: 0.8705 (tpp) cc_final: 0.8283 (mmm) REVERT: E 182 GLU cc_start: 0.6698 (mp0) cc_final: 0.6134 (mp0) REVERT: F 10 MET cc_start: 0.8640 (ppp) cc_final: 0.8375 (ppp) REVERT: H 6 GLU cc_start: 0.7370 (mm-30) cc_final: 0.6510 (mp0) REVERT: H 62 ASP cc_start: 0.8168 (OUTLIER) cc_final: 0.7921 (t0) REVERT: H 89 GLU cc_start: 0.7308 (tm-30) cc_final: 0.7091 (tm-30) REVERT: L 24 LYS cc_start: 0.8729 (tptp) cc_final: 0.8287 (mtpp) REVERT: O 13 GLU cc_start: 0.7623 (tm-30) cc_final: 0.7090 (tm-30) REVERT: O 36 LYS cc_start: 0.8470 (tptp) cc_final: 0.8222 (tmtt) REVERT: O 199 MET cc_start: 0.8577 (ptp) cc_final: 0.8022 (ptm) REVERT: P 30 GLU cc_start: 0.7283 (pt0) cc_final: 0.6976 (pt0) REVERT: P 70 VAL cc_start: 0.9118 (t) cc_final: 0.8768 (p) REVERT: Q 438 PHE cc_start: 0.8117 (m-10) cc_final: 0.7916 (m-10) REVERT: Q 473 MET cc_start: 0.7456 (mmp) cc_final: 0.7030 (mtt) REVERT: Q 482 ILE cc_start: 0.9023 (mm) cc_final: 0.8725 (mt) REVERT: R 10 MET cc_start: 0.8039 (tpp) cc_final: 0.7536 (mpp) REVERT: R 64 PHE cc_start: 0.9047 (t80) cc_final: 0.8827 (t80) REVERT: R 74 MET cc_start: 0.8713 (tpp) cc_final: 0.8284 (mmm) REVERT: T 10 MET cc_start: 0.8630 (ppp) cc_final: 0.8370 (ppp) REVERT: U 3 GLU cc_start: 0.7141 (mm-30) cc_final: 0.6883 (mm-30) REVERT: U 6 GLU cc_start: 0.7362 (mm-30) cc_final: 0.6464 (mp0) REVERT: U 62 ASP cc_start: 0.8175 (OUTLIER) cc_final: 0.7918 (t0) REVERT: U 107 TRP cc_start: 0.8593 (OUTLIER) cc_final: 0.7552 (p90) REVERT: V 24 LYS cc_start: 0.8721 (tptp) cc_final: 0.8301 (mtpp) outliers start: 155 outliers final: 104 residues processed: 598 average time/residue: 0.1888 time to fit residues: 186.7035 Evaluate side-chains 568 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 461 time to evaluate : 1.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 CYS Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 473 MET Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 65 ILE Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 183 CYS Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain C residue 271 SER Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 371 PHE Chi-restraints excluded: chain C residue 388 ASN Chi-restraints excluded: chain C residue 400 PHE Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain C residue 455 ILE Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 141 ILE Chi-restraints excluded: chain E residue 197 LEU Chi-restraints excluded: chain E residue 205 MET Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 237 THR Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 373 GLU Chi-restraints excluded: chain E residue 422 SER Chi-restraints excluded: chain E residue 426 VAL Chi-restraints excluded: chain F residue 18 THR Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 56 ASN Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain L residue 53 LEU Chi-restraints excluded: chain L residue 62 SER Chi-restraints excluded: chain L residue 95 MET Chi-restraints excluded: chain O residue 60 CYS Chi-restraints excluded: chain O residue 95 THR Chi-restraints excluded: chain O residue 163 THR Chi-restraints excluded: chain O residue 233 GLU Chi-restraints excluded: chain O residue 314 GLN Chi-restraints excluded: chain O residue 337 THR Chi-restraints excluded: chain O residue 476 SER Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain P residue 58 THR Chi-restraints excluded: chain P residue 65 ILE Chi-restraints excluded: chain P residue 67 LEU Chi-restraints excluded: chain Q residue 10 ASP Chi-restraints excluded: chain Q residue 183 CYS Chi-restraints excluded: chain Q residue 266 THR Chi-restraints excluded: chain Q residue 271 SER Chi-restraints excluded: chain Q residue 363 VAL Chi-restraints excluded: chain Q residue 371 PHE Chi-restraints excluded: chain Q residue 388 ASN Chi-restraints excluded: chain Q residue 400 PHE Chi-restraints excluded: chain Q residue 423 VAL Chi-restraints excluded: chain Q residue 430 LEU Chi-restraints excluded: chain Q residue 455 ILE Chi-restraints excluded: chain Q residue 461 LEU Chi-restraints excluded: chain R residue 12 LEU Chi-restraints excluded: chain R residue 43 THR Chi-restraints excluded: chain R residue 66 LEU Chi-restraints excluded: chain R residue 70 VAL Chi-restraints excluded: chain S residue 49 GLU Chi-restraints excluded: chain S residue 91 VAL Chi-restraints excluded: chain S residue 107 LEU Chi-restraints excluded: chain S residue 141 ILE Chi-restraints excluded: chain S residue 197 LEU Chi-restraints excluded: chain S residue 205 MET Chi-restraints excluded: chain S residue 223 THR Chi-restraints excluded: chain S residue 236 VAL Chi-restraints excluded: chain S residue 237 THR Chi-restraints excluded: chain S residue 373 GLU Chi-restraints excluded: chain S residue 422 SER Chi-restraints excluded: chain S residue 426 VAL Chi-restraints excluded: chain T residue 18 THR Chi-restraints excluded: chain T residue 47 LEU Chi-restraints excluded: chain T residue 49 LEU Chi-restraints excluded: chain T residue 55 THR Chi-restraints excluded: chain T residue 58 THR Chi-restraints excluded: chain T residue 61 VAL Chi-restraints excluded: chain U residue 7 SER Chi-restraints excluded: chain U residue 56 ASN Chi-restraints excluded: chain U residue 62 ASP Chi-restraints excluded: chain U residue 87 THR Chi-restraints excluded: chain U residue 102 VAL Chi-restraints excluded: chain U residue 107 TRP Chi-restraints excluded: chain V residue 53 LEU Chi-restraints excluded: chain V residue 62 SER Chi-restraints excluded: chain V residue 95 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 38 optimal weight: 4.9990 chunk 134 optimal weight: 1.9990 chunk 371 optimal weight: 20.0000 chunk 91 optimal weight: 2.9990 chunk 358 optimal weight: 10.0000 chunk 59 optimal weight: 20.0000 chunk 24 optimal weight: 3.9990 chunk 92 optimal weight: 7.9990 chunk 254 optimal weight: 10.0000 chunk 180 optimal weight: 20.0000 chunk 218 optimal weight: 10.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 ASN ** B 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 201 ASN ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 144 HIS L 1 HIS O 8 ASN ** O 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 201 ASN ** R 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 144 HIS V 1 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.090553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.078291 restraints weight = 72273.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.080442 restraints weight = 37108.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.081845 restraints weight = 23402.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.082757 restraints weight = 16939.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.083354 restraints weight = 13554.568| |-----------------------------------------------------------------------------| r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.3211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.098 30908 Z= 0.161 Angle : 0.639 9.770 41992 Z= 0.321 Chirality : 0.045 0.200 4938 Planarity : 0.004 0.041 5192 Dihedral : 7.950 59.948 4914 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 4.53 % Allowed : 17.85 % Favored : 77.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.02 (0.13), residues: 3846 helix: 1.60 (0.18), residues: 866 sheet: -1.06 (0.16), residues: 996 loop : -1.53 (0.13), residues: 1984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 15 TYR 0.012 0.001 TYR U 111 PHE 0.020 0.001 PHE E 475 TRP 0.010 0.001 TRP E 451 HIS 0.004 0.001 HIS F 7 Details of bonding type rmsd covalent geometry : bond 0.00378 (30836) covalent geometry : angle 0.62806 (41806) SS BOND : bond 0.00323 ( 30) SS BOND : angle 1.01654 ( 60) hydrogen bonds : bond 0.04114 ( 1180) hydrogen bonds : angle 5.31532 ( 3216) link_ALPHA1-3 : bond 0.01105 ( 4) link_ALPHA1-3 : angle 1.29223 ( 12) link_BETA1-4 : bond 0.00431 ( 22) link_BETA1-4 : angle 2.34283 ( 66) link_BETA1-6 : bond 0.00743 ( 4) link_BETA1-6 : angle 2.19332 ( 12) link_NAG-ASN : bond 0.00490 ( 12) link_NAG-ASN : angle 1.88933 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 626 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 480 time to evaluate : 1.195 Fit side-chains REVERT: A 13 GLU cc_start: 0.7672 (tm-30) cc_final: 0.7060 (tm-30) REVERT: A 430 LEU cc_start: 0.8846 (mt) cc_final: 0.8572 (mt) REVERT: B 30 GLU cc_start: 0.7180 (pt0) cc_final: 0.6804 (pt0) REVERT: B 70 VAL cc_start: 0.9121 (t) cc_final: 0.8764 (p) REVERT: C 438 PHE cc_start: 0.7975 (m-10) cc_final: 0.7767 (m-10) REVERT: C 473 MET cc_start: 0.7547 (mmp) cc_final: 0.7126 (mtt) REVERT: C 482 ILE cc_start: 0.8993 (mm) cc_final: 0.8694 (mt) REVERT: D 10 MET cc_start: 0.8075 (tpp) cc_final: 0.7522 (mpp) REVERT: D 27 ARG cc_start: 0.8368 (ttp-110) cc_final: 0.8142 (ttp-110) REVERT: D 74 MET cc_start: 0.8708 (tpp) cc_final: 0.8266 (mmm) REVERT: E 182 GLU cc_start: 0.6685 (mp0) cc_final: 0.6133 (mp0) REVERT: E 234 LEU cc_start: 0.8199 (OUTLIER) cc_final: 0.7576 (pp) REVERT: E 480 ILE cc_start: 0.8134 (mm) cc_final: 0.7929 (mm) REVERT: F 10 MET cc_start: 0.8620 (ppp) cc_final: 0.8390 (ppp) REVERT: H 62 ASP cc_start: 0.8174 (OUTLIER) cc_final: 0.7823 (t0) REVERT: H 107 TRP cc_start: 0.8324 (OUTLIER) cc_final: 0.7240 (p90) REVERT: O 13 GLU cc_start: 0.7657 (tm-30) cc_final: 0.7007 (tm-30) REVERT: O 199 MET cc_start: 0.8456 (ptp) cc_final: 0.7992 (ptm) REVERT: O 430 LEU cc_start: 0.8852 (mt) cc_final: 0.8576 (mt) REVERT: P 30 GLU cc_start: 0.7198 (pt0) cc_final: 0.6849 (pt0) REVERT: P 70 VAL cc_start: 0.9133 (t) cc_final: 0.8773 (p) REVERT: Q 473 MET cc_start: 0.7300 (mmp) cc_final: 0.6978 (mtt) REVERT: Q 482 ILE cc_start: 0.9100 (mm) cc_final: 0.8806 (mt) REVERT: R 10 MET cc_start: 0.8094 (tpp) cc_final: 0.7532 (mpp) REVERT: R 27 ARG cc_start: 0.8367 (ttp-110) cc_final: 0.8128 (ttp-110) REVERT: R 74 MET cc_start: 0.8716 (tpp) cc_final: 0.8268 (mmm) REVERT: S 234 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7570 (pp) REVERT: S 480 ILE cc_start: 0.8128 (mm) cc_final: 0.7774 (mm) REVERT: T 10 MET cc_start: 0.8609 (ppp) cc_final: 0.8382 (ppp) REVERT: U 62 ASP cc_start: 0.8181 (OUTLIER) cc_final: 0.7828 (t0) REVERT: U 107 TRP cc_start: 0.8520 (OUTLIER) cc_final: 0.7378 (p90) outliers start: 146 outliers final: 109 residues processed: 587 average time/residue: 0.1881 time to fit residues: 182.6501 Evaluate side-chains 573 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 458 time to evaluate : 1.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 60 CYS Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 473 MET Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 183 CYS Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain C residue 271 SER Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 371 PHE Chi-restraints excluded: chain C residue 400 PHE Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain C residue 455 ILE Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 141 ILE Chi-restraints excluded: chain E residue 197 LEU Chi-restraints excluded: chain E residue 205 MET Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 237 THR Chi-restraints excluded: chain E residue 310 VAL Chi-restraints excluded: chain E residue 373 GLU Chi-restraints excluded: chain E residue 422 SER Chi-restraints excluded: chain E residue 426 VAL Chi-restraints excluded: chain E residue 471 THR Chi-restraints excluded: chain F residue 18 THR Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain H residue 56 ASN Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 107 TRP Chi-restraints excluded: chain L residue 14 THR Chi-restraints excluded: chain L residue 62 SER Chi-restraints excluded: chain L residue 95 MET Chi-restraints excluded: chain O residue 41 LEU Chi-restraints excluded: chain O residue 60 CYS Chi-restraints excluded: chain O residue 163 THR Chi-restraints excluded: chain O residue 233 GLU Chi-restraints excluded: chain O residue 314 GLN Chi-restraints excluded: chain O residue 337 THR Chi-restraints excluded: chain O residue 476 SER Chi-restraints excluded: chain P residue 17 GLN Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain P residue 58 THR Chi-restraints excluded: chain Q residue 10 ASP Chi-restraints excluded: chain Q residue 41 LEU Chi-restraints excluded: chain Q residue 61 ILE Chi-restraints excluded: chain Q residue 183 CYS Chi-restraints excluded: chain Q residue 266 THR Chi-restraints excluded: chain Q residue 271 SER Chi-restraints excluded: chain Q residue 363 VAL Chi-restraints excluded: chain Q residue 371 PHE Chi-restraints excluded: chain Q residue 400 PHE Chi-restraints excluded: chain Q residue 423 VAL Chi-restraints excluded: chain Q residue 430 LEU Chi-restraints excluded: chain Q residue 455 ILE Chi-restraints excluded: chain Q residue 461 LEU Chi-restraints excluded: chain R residue 66 LEU Chi-restraints excluded: chain R residue 70 VAL Chi-restraints excluded: chain S residue 15 LEU Chi-restraints excluded: chain S residue 49 GLU Chi-restraints excluded: chain S residue 107 LEU Chi-restraints excluded: chain S residue 141 ILE Chi-restraints excluded: chain S residue 197 LEU Chi-restraints excluded: chain S residue 205 MET Chi-restraints excluded: chain S residue 223 THR Chi-restraints excluded: chain S residue 234 LEU Chi-restraints excluded: chain S residue 236 VAL Chi-restraints excluded: chain S residue 237 THR Chi-restraints excluded: chain S residue 310 VAL Chi-restraints excluded: chain S residue 422 SER Chi-restraints excluded: chain S residue 426 VAL Chi-restraints excluded: chain S residue 471 THR Chi-restraints excluded: chain T residue 18 THR Chi-restraints excluded: chain T residue 37 LEU Chi-restraints excluded: chain T residue 47 LEU Chi-restraints excluded: chain T residue 49 LEU Chi-restraints excluded: chain T residue 58 THR Chi-restraints excluded: chain T residue 66 LEU Chi-restraints excluded: chain U residue 7 SER Chi-restraints excluded: chain U residue 12 VAL Chi-restraints excluded: chain U residue 43 LYS Chi-restraints excluded: chain U residue 50 VAL Chi-restraints excluded: chain U residue 56 ASN Chi-restraints excluded: chain U residue 62 ASP Chi-restraints excluded: chain U residue 87 THR Chi-restraints excluded: chain U residue 102 VAL Chi-restraints excluded: chain U residue 107 TRP Chi-restraints excluded: chain V residue 14 THR Chi-restraints excluded: chain V residue 62 SER Chi-restraints excluded: chain V residue 95 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 162 optimal weight: 20.0000 chunk 201 optimal weight: 0.4980 chunk 268 optimal weight: 9.9990 chunk 311 optimal weight: 0.9990 chunk 262 optimal weight: 20.0000 chunk 97 optimal weight: 10.0000 chunk 351 optimal weight: 10.0000 chunk 5 optimal weight: 2.9990 chunk 90 optimal weight: 30.0000 chunk 231 optimal weight: 20.0000 chunk 211 optimal weight: 6.9990 overall best weight: 4.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 201 ASN ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 201 ASN ** R 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.090598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.078329 restraints weight = 72462.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.080477 restraints weight = 37116.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.081878 restraints weight = 23380.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.082790 restraints weight = 16913.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.083370 restraints weight = 13532.181| |-----------------------------------------------------------------------------| r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.3362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.098 30908 Z= 0.161 Angle : 0.629 8.427 41992 Z= 0.318 Chirality : 0.045 0.262 4938 Planarity : 0.004 0.125 5192 Dihedral : 7.616 57.882 4914 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 5.09 % Allowed : 18.53 % Favored : 76.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.96 (0.13), residues: 3846 helix: 1.65 (0.18), residues: 866 sheet: -1.00 (0.16), residues: 996 loop : -1.49 (0.13), residues: 1984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG O 2 TYR 0.011 0.001 TYR U 111 PHE 0.023 0.002 PHE P 48 TRP 0.010 0.001 TRP H 107 HIS 0.004 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00379 (30836) covalent geometry : angle 0.61852 (41806) SS BOND : bond 0.00322 ( 30) SS BOND : angle 1.12897 ( 60) hydrogen bonds : bond 0.04012 ( 1180) hydrogen bonds : angle 5.20522 ( 3216) link_ALPHA1-3 : bond 0.01098 ( 4) link_ALPHA1-3 : angle 1.38285 ( 12) link_BETA1-4 : bond 0.00396 ( 22) link_BETA1-4 : angle 2.29201 ( 66) link_BETA1-6 : bond 0.00724 ( 4) link_BETA1-6 : angle 2.01673 ( 12) link_NAG-ASN : bond 0.00519 ( 12) link_NAG-ASN : angle 1.85432 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 644 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 164 poor density : 480 time to evaluate : 1.234 Fit side-chains revert: symmetry clash REVERT: A 13 GLU cc_start: 0.7536 (tm-30) cc_final: 0.6861 (tm-30) REVERT: A 430 LEU cc_start: 0.8854 (mt) cc_final: 0.8574 (mt) REVERT: B 30 GLU cc_start: 0.7181 (pt0) cc_final: 0.6835 (pt0) REVERT: B 47 LEU cc_start: 0.9054 (mt) cc_final: 0.8815 (mt) REVERT: B 70 VAL cc_start: 0.9130 (t) cc_final: 0.8764 (p) REVERT: C 415 ASP cc_start: 0.7953 (t0) cc_final: 0.7671 (m-30) REVERT: C 438 PHE cc_start: 0.7897 (m-10) cc_final: 0.7660 (m-10) REVERT: C 473 MET cc_start: 0.7523 (mmp) cc_final: 0.7082 (mtt) REVERT: C 482 ILE cc_start: 0.9086 (mm) cc_final: 0.8801 (mt) REVERT: D 10 MET cc_start: 0.8143 (tpp) cc_final: 0.7606 (mpp) REVERT: D 27 ARG cc_start: 0.8293 (ttp-110) cc_final: 0.8050 (ttp-110) REVERT: D 49 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8516 (mt) REVERT: D 59 GLN cc_start: 0.8800 (mm-40) cc_final: 0.8191 (mt0) REVERT: D 74 MET cc_start: 0.8734 (tpp) cc_final: 0.8319 (mmm) REVERT: E 182 GLU cc_start: 0.6696 (mp0) cc_final: 0.6453 (tt0) REVERT: E 234 LEU cc_start: 0.8202 (OUTLIER) cc_final: 0.7606 (pp) REVERT: F 10 MET cc_start: 0.8619 (ppp) cc_final: 0.8383 (ppp) REVERT: H 62 ASP cc_start: 0.8144 (OUTLIER) cc_final: 0.7842 (t0) REVERT: H 107 TRP cc_start: 0.8336 (OUTLIER) cc_final: 0.7268 (p90) REVERT: L 24 LYS cc_start: 0.8865 (tptp) cc_final: 0.8329 (mtpp) REVERT: L 80 LYS cc_start: 0.8603 (mptt) cc_final: 0.8334 (mmtm) REVERT: O 13 GLU cc_start: 0.7479 (tm-30) cc_final: 0.6839 (tm-30) REVERT: O 430 LEU cc_start: 0.8864 (mt) cc_final: 0.8579 (mt) REVERT: P 30 GLU cc_start: 0.7200 (pt0) cc_final: 0.6847 (pt0) REVERT: P 70 VAL cc_start: 0.9144 (t) cc_final: 0.8786 (p) REVERT: Q 415 ASP cc_start: 0.7952 (t0) cc_final: 0.7675 (m-30) REVERT: Q 473 MET cc_start: 0.7177 (mmp) cc_final: 0.6824 (mtt) REVERT: R 10 MET cc_start: 0.8156 (tpp) cc_final: 0.7616 (mpp) REVERT: R 27 ARG cc_start: 0.8288 (ttp-110) cc_final: 0.8037 (ttp-110) REVERT: R 49 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8489 (mt) REVERT: R 59 GLN cc_start: 0.8849 (mm-40) cc_final: 0.8187 (mt0) REVERT: R 63 ILE cc_start: 0.8712 (mm) cc_final: 0.8477 (mt) REVERT: R 74 MET cc_start: 0.8751 (tpp) cc_final: 0.8326 (mmm) REVERT: S 234 LEU cc_start: 0.8220 (OUTLIER) cc_final: 0.7624 (pp) REVERT: T 10 MET cc_start: 0.8605 (ppp) cc_final: 0.8374 (ppp) REVERT: U 3 GLU cc_start: 0.6847 (mm-30) cc_final: 0.6608 (mm-30) REVERT: U 62 ASP cc_start: 0.8154 (OUTLIER) cc_final: 0.7864 (t0) REVERT: U 107 TRP cc_start: 0.8289 (OUTLIER) cc_final: 0.7153 (p90) REVERT: V 24 LYS cc_start: 0.8976 (tptp) cc_final: 0.8289 (mtpp) REVERT: V 80 LYS cc_start: 0.8684 (mptt) cc_final: 0.8365 (mmtm) outliers start: 164 outliers final: 123 residues processed: 601 average time/residue: 0.1942 time to fit residues: 191.2798 Evaluate side-chains 590 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 459 time to evaluate : 1.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 60 CYS Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 183 CYS Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain C residue 271 SER Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 371 PHE Chi-restraints excluded: chain C residue 388 ASN Chi-restraints excluded: chain C residue 400 PHE Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 426 VAL Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 455 ILE Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 464 ILE Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 141 ILE Chi-restraints excluded: chain E residue 197 LEU Chi-restraints excluded: chain E residue 205 MET Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 237 THR Chi-restraints excluded: chain E residue 373 GLU Chi-restraints excluded: chain E residue 416 THR Chi-restraints excluded: chain E residue 422 SER Chi-restraints excluded: chain E residue 426 VAL Chi-restraints excluded: chain E residue 460 LEU Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain E residue 471 THR Chi-restraints excluded: chain F residue 18 THR Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 56 ASN Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 107 TRP Chi-restraints excluded: chain L residue 14 THR Chi-restraints excluded: chain L residue 53 LEU Chi-restraints excluded: chain L residue 62 SER Chi-restraints excluded: chain O residue 41 LEU Chi-restraints excluded: chain O residue 60 CYS Chi-restraints excluded: chain O residue 70 THR Chi-restraints excluded: chain O residue 163 THR Chi-restraints excluded: chain O residue 233 GLU Chi-restraints excluded: chain O residue 314 GLN Chi-restraints excluded: chain O residue 337 THR Chi-restraints excluded: chain O residue 376 ILE Chi-restraints excluded: chain O residue 476 SER Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain P residue 58 THR Chi-restraints excluded: chain Q residue 10 ASP Chi-restraints excluded: chain Q residue 41 LEU Chi-restraints excluded: chain Q residue 61 ILE Chi-restraints excluded: chain Q residue 183 CYS Chi-restraints excluded: chain Q residue 266 THR Chi-restraints excluded: chain Q residue 271 SER Chi-restraints excluded: chain Q residue 363 VAL Chi-restraints excluded: chain Q residue 371 PHE Chi-restraints excluded: chain Q residue 388 ASN Chi-restraints excluded: chain Q residue 400 PHE Chi-restraints excluded: chain Q residue 423 VAL Chi-restraints excluded: chain Q residue 426 VAL Chi-restraints excluded: chain Q residue 430 LEU Chi-restraints excluded: chain Q residue 452 VAL Chi-restraints excluded: chain Q residue 455 ILE Chi-restraints excluded: chain Q residue 461 LEU Chi-restraints excluded: chain Q residue 464 ILE Chi-restraints excluded: chain R residue 12 LEU Chi-restraints excluded: chain R residue 49 LEU Chi-restraints excluded: chain R residue 66 LEU Chi-restraints excluded: chain R residue 70 VAL Chi-restraints excluded: chain S residue 15 LEU Chi-restraints excluded: chain S residue 48 THR Chi-restraints excluded: chain S residue 49 GLU Chi-restraints excluded: chain S residue 91 VAL Chi-restraints excluded: chain S residue 107 LEU Chi-restraints excluded: chain S residue 141 ILE Chi-restraints excluded: chain S residue 197 LEU Chi-restraints excluded: chain S residue 205 MET Chi-restraints excluded: chain S residue 223 THR Chi-restraints excluded: chain S residue 234 LEU Chi-restraints excluded: chain S residue 236 VAL Chi-restraints excluded: chain S residue 237 THR Chi-restraints excluded: chain S residue 310 VAL Chi-restraints excluded: chain S residue 416 THR Chi-restraints excluded: chain S residue 422 SER Chi-restraints excluded: chain S residue 426 VAL Chi-restraints excluded: chain S residue 460 LEU Chi-restraints excluded: chain S residue 461 LEU Chi-restraints excluded: chain S residue 471 THR Chi-restraints excluded: chain T residue 18 THR Chi-restraints excluded: chain T residue 47 LEU Chi-restraints excluded: chain T residue 49 LEU Chi-restraints excluded: chain T residue 58 THR Chi-restraints excluded: chain T residue 66 LEU Chi-restraints excluded: chain U residue 7 SER Chi-restraints excluded: chain U residue 43 LYS Chi-restraints excluded: chain U residue 56 ASN Chi-restraints excluded: chain U residue 62 ASP Chi-restraints excluded: chain U residue 87 THR Chi-restraints excluded: chain U residue 102 VAL Chi-restraints excluded: chain U residue 107 TRP Chi-restraints excluded: chain V residue 53 LEU Chi-restraints excluded: chain V residue 62 SER Chi-restraints excluded: chain V residue 95 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 196 optimal weight: 5.9990 chunk 4 optimal weight: 6.9990 chunk 190 optimal weight: 20.0000 chunk 283 optimal weight: 1.9990 chunk 271 optimal weight: 9.9990 chunk 347 optimal weight: 20.0000 chunk 157 optimal weight: 8.9990 chunk 337 optimal weight: 0.0470 chunk 94 optimal weight: 2.9990 chunk 233 optimal weight: 8.9990 chunk 152 optimal weight: 6.9990 overall best weight: 3.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 201 ASN ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 77 GLN ** P 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 201 ASN ** R 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 492 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.091127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.078920 restraints weight = 72222.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.081076 restraints weight = 36827.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.082484 restraints weight = 23119.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.083393 restraints weight = 16706.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.083995 restraints weight = 13363.958| |-----------------------------------------------------------------------------| r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.3463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 30908 Z= 0.147 Angle : 0.613 8.657 41992 Z= 0.311 Chirality : 0.044 0.231 4938 Planarity : 0.004 0.123 5192 Dihedral : 7.341 59.968 4914 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 4.93 % Allowed : 18.56 % Favored : 76.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.91 (0.13), residues: 3846 helix: 1.71 (0.18), residues: 866 sheet: -1.01 (0.16), residues: 1014 loop : -1.44 (0.13), residues: 1966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 2 TYR 0.013 0.001 TYR Q 176 PHE 0.020 0.001 PHE S 475 TRP 0.010 0.001 TRP E 451 HIS 0.003 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00342 (30836) covalent geometry : angle 0.60284 (41806) SS BOND : bond 0.00305 ( 30) SS BOND : angle 1.04666 ( 60) hydrogen bonds : bond 0.03880 ( 1180) hydrogen bonds : angle 5.11180 ( 3216) link_ALPHA1-3 : bond 0.01105 ( 4) link_ALPHA1-3 : angle 1.37205 ( 12) link_BETA1-4 : bond 0.00391 ( 22) link_BETA1-4 : angle 2.25091 ( 66) link_BETA1-6 : bond 0.00682 ( 4) link_BETA1-6 : angle 1.81631 ( 12) link_NAG-ASN : bond 0.00462 ( 12) link_NAG-ASN : angle 1.80842 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 633 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 474 time to evaluate : 1.152 Fit side-chains revert: symmetry clash REVERT: A 13 GLU cc_start: 0.7495 (tm-30) cc_final: 0.6832 (tm-30) REVERT: A 130 VAL cc_start: 0.9326 (OUTLIER) cc_final: 0.9107 (p) REVERT: A 430 LEU cc_start: 0.8860 (mt) cc_final: 0.8577 (mt) REVERT: B 30 GLU cc_start: 0.7153 (pt0) cc_final: 0.6807 (pt0) REVERT: B 47 LEU cc_start: 0.9030 (mt) cc_final: 0.8811 (mt) REVERT: B 70 VAL cc_start: 0.9189 (t) cc_final: 0.8812 (p) REVERT: C 415 ASP cc_start: 0.7925 (t0) cc_final: 0.7666 (m-30) REVERT: C 438 PHE cc_start: 0.7885 (m-10) cc_final: 0.7617 (m-10) REVERT: C 473 MET cc_start: 0.7489 (mmp) cc_final: 0.7053 (mtt) REVERT: D 10 MET cc_start: 0.8156 (tpp) cc_final: 0.7577 (mpp) REVERT: D 27 ARG cc_start: 0.8283 (ttp-110) cc_final: 0.8058 (ttp-110) REVERT: D 49 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8427 (mt) REVERT: D 59 GLN cc_start: 0.8841 (mm-40) cc_final: 0.8008 (mt0) REVERT: D 63 ILE cc_start: 0.8690 (mm) cc_final: 0.8471 (mt) REVERT: D 74 MET cc_start: 0.8726 (tpp) cc_final: 0.8342 (mmm) REVERT: E 234 LEU cc_start: 0.8126 (OUTLIER) cc_final: 0.7544 (pp) REVERT: F 10 MET cc_start: 0.8604 (ppp) cc_final: 0.8336 (ppp) REVERT: H 62 ASP cc_start: 0.8138 (OUTLIER) cc_final: 0.7841 (t0) REVERT: H 73 ASP cc_start: 0.7733 (t0) cc_final: 0.7319 (t0) REVERT: H 107 TRP cc_start: 0.8357 (OUTLIER) cc_final: 0.7307 (p90) REVERT: L 24 LYS cc_start: 0.8918 (tptp) cc_final: 0.8406 (mtpp) REVERT: L 80 LYS cc_start: 0.8615 (mptt) cc_final: 0.8320 (mmtm) REVERT: O 13 GLU cc_start: 0.7484 (tm-30) cc_final: 0.6830 (tm-30) REVERT: O 130 VAL cc_start: 0.9368 (OUTLIER) cc_final: 0.9162 (p) REVERT: O 199 MET cc_start: 0.8394 (ptp) cc_final: 0.8041 (ptm) REVERT: O 430 LEU cc_start: 0.8874 (mt) cc_final: 0.8583 (mt) REVERT: P 30 GLU cc_start: 0.7166 (pt0) cc_final: 0.6808 (pt0) REVERT: P 47 LEU cc_start: 0.9067 (mt) cc_final: 0.8830 (mt) REVERT: P 70 VAL cc_start: 0.9205 (t) cc_final: 0.8825 (p) REVERT: Q 415 ASP cc_start: 0.7926 (t0) cc_final: 0.7672 (m-30) REVERT: Q 473 MET cc_start: 0.7161 (mmp) cc_final: 0.6867 (mtt) REVERT: R 10 MET cc_start: 0.8166 (tpp) cc_final: 0.7587 (mpp) REVERT: R 27 ARG cc_start: 0.8280 (ttp-110) cc_final: 0.8044 (ttp-110) REVERT: R 49 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8456 (mt) REVERT: R 59 GLN cc_start: 0.8814 (mm-40) cc_final: 0.7949 (mt0) REVERT: R 63 ILE cc_start: 0.8682 (mm) cc_final: 0.8455 (mt) REVERT: R 74 MET cc_start: 0.8736 (tpp) cc_final: 0.8347 (mmm) REVERT: S 234 LEU cc_start: 0.8144 (OUTLIER) cc_final: 0.7569 (pp) REVERT: T 10 MET cc_start: 0.8589 (ppp) cc_final: 0.8318 (ppp) REVERT: U 3 GLU cc_start: 0.6816 (mm-30) cc_final: 0.6556 (mm-30) REVERT: U 62 ASP cc_start: 0.8149 (OUTLIER) cc_final: 0.7847 (t0) REVERT: U 107 TRP cc_start: 0.8298 (OUTLIER) cc_final: 0.7068 (p90) REVERT: V 24 LYS cc_start: 0.8975 (tptp) cc_final: 0.8324 (mtpp) REVERT: V 80 LYS cc_start: 0.8559 (mptt) cc_final: 0.8076 (mmtm) REVERT: V 83 ARG cc_start: 0.7842 (mtm110) cc_final: 0.7177 (mpp80) outliers start: 159 outliers final: 126 residues processed: 586 average time/residue: 0.1891 time to fit residues: 183.3269 Evaluate side-chains 594 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 458 time to evaluate : 1.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 60 CYS Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 183 CYS Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain C residue 271 SER Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 371 PHE Chi-restraints excluded: chain C residue 388 ASN Chi-restraints excluded: chain C residue 400 PHE Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 426 VAL Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 464 ILE Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 141 ILE Chi-restraints excluded: chain E residue 197 LEU Chi-restraints excluded: chain E residue 205 MET Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 237 THR Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain E residue 416 THR Chi-restraints excluded: chain E residue 422 SER Chi-restraints excluded: chain E residue 426 VAL Chi-restraints excluded: chain E residue 460 LEU Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain E residue 471 THR Chi-restraints excluded: chain F residue 18 THR Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain H residue 56 ASN Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 107 TRP Chi-restraints excluded: chain L residue 53 LEU Chi-restraints excluded: chain L residue 62 SER Chi-restraints excluded: chain L residue 88 ASP Chi-restraints excluded: chain L residue 95 MET Chi-restraints excluded: chain O residue 33 THR Chi-restraints excluded: chain O residue 41 LEU Chi-restraints excluded: chain O residue 60 CYS Chi-restraints excluded: chain O residue 70 THR Chi-restraints excluded: chain O residue 91 VAL Chi-restraints excluded: chain O residue 95 THR Chi-restraints excluded: chain O residue 130 VAL Chi-restraints excluded: chain O residue 163 THR Chi-restraints excluded: chain O residue 233 GLU Chi-restraints excluded: chain O residue 314 GLN Chi-restraints excluded: chain O residue 337 THR Chi-restraints excluded: chain O residue 376 ILE Chi-restraints excluded: chain O residue 476 SER Chi-restraints excluded: chain P residue 17 GLN Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain P residue 58 THR Chi-restraints excluded: chain Q residue 10 ASP Chi-restraints excluded: chain Q residue 41 LEU Chi-restraints excluded: chain Q residue 61 ILE Chi-restraints excluded: chain Q residue 183 CYS Chi-restraints excluded: chain Q residue 266 THR Chi-restraints excluded: chain Q residue 271 SER Chi-restraints excluded: chain Q residue 363 VAL Chi-restraints excluded: chain Q residue 371 PHE Chi-restraints excluded: chain Q residue 388 ASN Chi-restraints excluded: chain Q residue 400 PHE Chi-restraints excluded: chain Q residue 452 VAL Chi-restraints excluded: chain Q residue 461 LEU Chi-restraints excluded: chain Q residue 464 ILE Chi-restraints excluded: chain R residue 49 LEU Chi-restraints excluded: chain R residue 66 LEU Chi-restraints excluded: chain S residue 15 LEU Chi-restraints excluded: chain S residue 48 THR Chi-restraints excluded: chain S residue 49 GLU Chi-restraints excluded: chain S residue 91 VAL Chi-restraints excluded: chain S residue 107 LEU Chi-restraints excluded: chain S residue 141 ILE Chi-restraints excluded: chain S residue 197 LEU Chi-restraints excluded: chain S residue 205 MET Chi-restraints excluded: chain S residue 223 THR Chi-restraints excluded: chain S residue 234 LEU Chi-restraints excluded: chain S residue 236 VAL Chi-restraints excluded: chain S residue 237 THR Chi-restraints excluded: chain S residue 310 VAL Chi-restraints excluded: chain S residue 416 THR Chi-restraints excluded: chain S residue 422 SER Chi-restraints excluded: chain S residue 426 VAL Chi-restraints excluded: chain S residue 461 LEU Chi-restraints excluded: chain S residue 471 THR Chi-restraints excluded: chain S residue 483 ILE Chi-restraints excluded: chain T residue 18 THR Chi-restraints excluded: chain T residue 37 LEU Chi-restraints excluded: chain T residue 47 LEU Chi-restraints excluded: chain T residue 49 LEU Chi-restraints excluded: chain T residue 58 THR Chi-restraints excluded: chain T residue 66 LEU Chi-restraints excluded: chain U residue 7 SER Chi-restraints excluded: chain U residue 12 VAL Chi-restraints excluded: chain U residue 43 LYS Chi-restraints excluded: chain U residue 56 ASN Chi-restraints excluded: chain U residue 62 ASP Chi-restraints excluded: chain U residue 87 THR Chi-restraints excluded: chain U residue 102 VAL Chi-restraints excluded: chain U residue 107 TRP Chi-restraints excluded: chain V residue 53 LEU Chi-restraints excluded: chain V residue 62 SER Chi-restraints excluded: chain V residue 88 ASP Chi-restraints excluded: chain V residue 95 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 208 optimal weight: 3.9990 chunk 264 optimal weight: 8.9990 chunk 94 optimal weight: 20.0000 chunk 58 optimal weight: 9.9990 chunk 146 optimal weight: 30.0000 chunk 251 optimal weight: 4.9990 chunk 104 optimal weight: 20.0000 chunk 180 optimal weight: 4.9990 chunk 72 optimal weight: 0.1980 chunk 234 optimal weight: 6.9990 chunk 167 optimal weight: 10.0000 overall best weight: 4.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 201 ASN ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 201 ASN ** R 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.090882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.078612 restraints weight = 72707.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.080810 restraints weight = 36690.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.082236 restraints weight = 22827.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.083165 restraints weight = 16408.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.083775 restraints weight = 13060.254| |-----------------------------------------------------------------------------| r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.3572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 30908 Z= 0.158 Angle : 0.626 8.621 41992 Z= 0.315 Chirality : 0.045 0.196 4938 Planarity : 0.004 0.075 5192 Dihedral : 7.186 59.422 4914 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 5.34 % Allowed : 18.50 % Favored : 76.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.90 (0.13), residues: 3846 helix: 1.71 (0.18), residues: 866 sheet: -0.99 (0.16), residues: 1014 loop : -1.44 (0.13), residues: 1966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG U 19 TYR 0.010 0.001 TYR D 52 PHE 0.026 0.002 PHE P 48 TRP 0.010 0.001 TRP E 451 HIS 0.004 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00371 (30836) covalent geometry : angle 0.61592 (41806) SS BOND : bond 0.00311 ( 30) SS BOND : angle 1.03489 ( 60) hydrogen bonds : bond 0.03863 ( 1180) hydrogen bonds : angle 5.06859 ( 3216) link_ALPHA1-3 : bond 0.01113 ( 4) link_ALPHA1-3 : angle 1.49580 ( 12) link_BETA1-4 : bond 0.00379 ( 22) link_BETA1-4 : angle 2.22632 ( 66) link_BETA1-6 : bond 0.00606 ( 4) link_BETA1-6 : angle 1.73001 ( 12) link_NAG-ASN : bond 0.00480 ( 12) link_NAG-ASN : angle 1.79607 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 645 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 172 poor density : 473 time to evaluate : 1.260 Fit side-chains revert: symmetry clash REVERT: A 13 GLU cc_start: 0.7501 (tm-30) cc_final: 0.6825 (tm-30) REVERT: A 130 VAL cc_start: 0.9328 (OUTLIER) cc_final: 0.9126 (p) REVERT: A 285 LEU cc_start: 0.9535 (OUTLIER) cc_final: 0.9082 (mt) REVERT: A 430 LEU cc_start: 0.8867 (mt) cc_final: 0.8579 (mt) REVERT: B 30 GLU cc_start: 0.7158 (pt0) cc_final: 0.6800 (pt0) REVERT: B 47 LEU cc_start: 0.9022 (mt) cc_final: 0.8812 (mt) REVERT: B 70 VAL cc_start: 0.9188 (t) cc_final: 0.8817 (p) REVERT: C 415 ASP cc_start: 0.7923 (t0) cc_final: 0.7660 (m-30) REVERT: C 438 PHE cc_start: 0.7865 (m-10) cc_final: 0.7613 (m-10) REVERT: C 473 MET cc_start: 0.7531 (mmp) cc_final: 0.7171 (mtt) REVERT: D 27 ARG cc_start: 0.8284 (ttp-110) cc_final: 0.8082 (ttp-110) REVERT: D 49 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8472 (mt) REVERT: D 59 GLN cc_start: 0.8795 (mm-40) cc_final: 0.8048 (mt0) REVERT: D 63 ILE cc_start: 0.8673 (mm) cc_final: 0.8439 (mt) REVERT: D 74 MET cc_start: 0.8744 (tpp) cc_final: 0.8378 (mmm) REVERT: E 234 LEU cc_start: 0.8175 (OUTLIER) cc_final: 0.7595 (pp) REVERT: F 10 MET cc_start: 0.8612 (ppp) cc_final: 0.8352 (ppp) REVERT: H 62 ASP cc_start: 0.8153 (OUTLIER) cc_final: 0.7862 (t0) REVERT: H 107 TRP cc_start: 0.8397 (OUTLIER) cc_final: 0.7358 (p90) REVERT: L 80 LYS cc_start: 0.8627 (mptt) cc_final: 0.8322 (mmtm) REVERT: L 83 ARG cc_start: 0.7861 (mtm110) cc_final: 0.7188 (mpp80) REVERT: O 13 GLU cc_start: 0.7498 (tm-30) cc_final: 0.6826 (tm-30) REVERT: O 130 VAL cc_start: 0.9371 (OUTLIER) cc_final: 0.9169 (p) REVERT: O 199 MET cc_start: 0.8400 (ptp) cc_final: 0.8093 (ptm) REVERT: O 285 LEU cc_start: 0.9535 (OUTLIER) cc_final: 0.9081 (mt) REVERT: O 430 LEU cc_start: 0.8881 (mt) cc_final: 0.8585 (mt) REVERT: P 47 LEU cc_start: 0.9051 (mt) cc_final: 0.8826 (mt) REVERT: P 70 VAL cc_start: 0.9202 (t) cc_final: 0.8823 (p) REVERT: Q 415 ASP cc_start: 0.7925 (t0) cc_final: 0.7674 (m-30) REVERT: Q 473 MET cc_start: 0.7243 (mmp) cc_final: 0.7022 (mtt) REVERT: R 27 ARG cc_start: 0.8281 (ttp-110) cc_final: 0.8030 (ttp-110) REVERT: R 49 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8417 (mt) REVERT: R 59 GLN cc_start: 0.8760 (mm-40) cc_final: 0.7980 (mt0) REVERT: R 63 ILE cc_start: 0.8685 (mm) cc_final: 0.8460 (mt) REVERT: R 74 MET cc_start: 0.8744 (tpp) cc_final: 0.8378 (mmm) REVERT: S 234 LEU cc_start: 0.8183 (OUTLIER) cc_final: 0.7606 (pp) REVERT: T 10 MET cc_start: 0.8607 (ppp) cc_final: 0.8344 (ppp) REVERT: U 3 GLU cc_start: 0.6842 (mm-30) cc_final: 0.6580 (mm-30) REVERT: U 62 ASP cc_start: 0.8166 (OUTLIER) cc_final: 0.7883 (t0) REVERT: U 107 TRP cc_start: 0.8319 (OUTLIER) cc_final: 0.7077 (p90) REVERT: V 24 LYS cc_start: 0.8840 (tptp) cc_final: 0.8151 (mtpp) REVERT: V 80 LYS cc_start: 0.8530 (mptt) cc_final: 0.8013 (mmtm) REVERT: V 83 ARG cc_start: 0.7866 (mtm110) cc_final: 0.7183 (mpp80) outliers start: 172 outliers final: 138 residues processed: 602 average time/residue: 0.1862 time to fit residues: 185.5709 Evaluate side-chains 604 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 454 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 60 CYS Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 399 MET Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 68 MET Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 183 CYS Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain C residue 271 SER Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 371 PHE Chi-restraints excluded: chain C residue 388 ASN Chi-restraints excluded: chain C residue 400 PHE Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 464 ILE Chi-restraints excluded: chain C residue 491 VAL Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 141 ILE Chi-restraints excluded: chain E residue 197 LEU Chi-restraints excluded: chain E residue 205 MET Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 237 THR Chi-restraints excluded: chain E residue 266 THR Chi-restraints excluded: chain E residue 416 THR Chi-restraints excluded: chain E residue 422 SER Chi-restraints excluded: chain E residue 426 VAL Chi-restraints excluded: chain E residue 460 LEU Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain E residue 471 THR Chi-restraints excluded: chain F residue 18 THR Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain H residue 56 ASN Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 107 TRP Chi-restraints excluded: chain L residue 14 THR Chi-restraints excluded: chain L residue 53 LEU Chi-restraints excluded: chain L residue 62 SER Chi-restraints excluded: chain L residue 95 MET Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain O residue 33 THR Chi-restraints excluded: chain O residue 41 LEU Chi-restraints excluded: chain O residue 60 CYS Chi-restraints excluded: chain O residue 70 THR Chi-restraints excluded: chain O residue 91 VAL Chi-restraints excluded: chain O residue 95 THR Chi-restraints excluded: chain O residue 130 VAL Chi-restraints excluded: chain O residue 163 THR Chi-restraints excluded: chain O residue 233 GLU Chi-restraints excluded: chain O residue 285 LEU Chi-restraints excluded: chain O residue 314 GLN Chi-restraints excluded: chain O residue 337 THR Chi-restraints excluded: chain O residue 385 LEU Chi-restraints excluded: chain O residue 399 MET Chi-restraints excluded: chain O residue 476 SER Chi-restraints excluded: chain P residue 17 GLN Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain P residue 58 THR Chi-restraints excluded: chain Q residue 10 ASP Chi-restraints excluded: chain Q residue 41 LEU Chi-restraints excluded: chain Q residue 61 ILE Chi-restraints excluded: chain Q residue 183 CYS Chi-restraints excluded: chain Q residue 266 THR Chi-restraints excluded: chain Q residue 271 SER Chi-restraints excluded: chain Q residue 363 VAL Chi-restraints excluded: chain Q residue 371 PHE Chi-restraints excluded: chain Q residue 388 ASN Chi-restraints excluded: chain Q residue 400 PHE Chi-restraints excluded: chain Q residue 423 VAL Chi-restraints excluded: chain Q residue 426 VAL Chi-restraints excluded: chain Q residue 452 VAL Chi-restraints excluded: chain Q residue 455 ILE Chi-restraints excluded: chain Q residue 461 LEU Chi-restraints excluded: chain Q residue 464 ILE Chi-restraints excluded: chain Q residue 491 VAL Chi-restraints excluded: chain R residue 12 LEU Chi-restraints excluded: chain R residue 49 LEU Chi-restraints excluded: chain R residue 66 LEU Chi-restraints excluded: chain S residue 15 LEU Chi-restraints excluded: chain S residue 49 GLU Chi-restraints excluded: chain S residue 91 VAL Chi-restraints excluded: chain S residue 107 LEU Chi-restraints excluded: chain S residue 141 ILE Chi-restraints excluded: chain S residue 197 LEU Chi-restraints excluded: chain S residue 205 MET Chi-restraints excluded: chain S residue 223 THR Chi-restraints excluded: chain S residue 234 LEU Chi-restraints excluded: chain S residue 236 VAL Chi-restraints excluded: chain S residue 237 THR Chi-restraints excluded: chain S residue 251 LEU Chi-restraints excluded: chain S residue 310 VAL Chi-restraints excluded: chain S residue 416 THR Chi-restraints excluded: chain S residue 422 SER Chi-restraints excluded: chain S residue 426 VAL Chi-restraints excluded: chain S residue 460 LEU Chi-restraints excluded: chain S residue 461 LEU Chi-restraints excluded: chain S residue 471 THR Chi-restraints excluded: chain S residue 483 ILE Chi-restraints excluded: chain S residue 485 LEU Chi-restraints excluded: chain T residue 18 THR Chi-restraints excluded: chain T residue 37 LEU Chi-restraints excluded: chain T residue 47 LEU Chi-restraints excluded: chain T residue 49 LEU Chi-restraints excluded: chain T residue 58 THR Chi-restraints excluded: chain T residue 66 LEU Chi-restraints excluded: chain U residue 7 SER Chi-restraints excluded: chain U residue 12 VAL Chi-restraints excluded: chain U residue 43 LYS Chi-restraints excluded: chain U residue 56 ASN Chi-restraints excluded: chain U residue 62 ASP Chi-restraints excluded: chain U residue 87 THR Chi-restraints excluded: chain U residue 102 VAL Chi-restraints excluded: chain U residue 107 TRP Chi-restraints excluded: chain V residue 53 LEU Chi-restraints excluded: chain V residue 62 SER Chi-restraints excluded: chain V residue 95 MET Chi-restraints excluded: chain V residue 102 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 104 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 315 optimal weight: 30.0000 chunk 232 optimal weight: 20.0000 chunk 317 optimal weight: 0.0010 chunk 162 optimal weight: 20.0000 chunk 121 optimal weight: 9.9990 chunk 290 optimal weight: 5.9990 chunk 305 optimal weight: 9.9990 chunk 183 optimal weight: 20.0000 chunk 280 optimal weight: 7.9990 overall best weight: 3.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 201 ASN C 246 GLN ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 492 GLN ** P 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 201 ASN Q 246 GLN ** R 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.091240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.079011 restraints weight = 72167.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.081204 restraints weight = 36388.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.082625 restraints weight = 22665.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.083531 restraints weight = 16277.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.084146 restraints weight = 13031.054| |-----------------------------------------------------------------------------| r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.3646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 30908 Z= 0.141 Angle : 0.609 8.730 41992 Z= 0.307 Chirality : 0.044 0.207 4938 Planarity : 0.004 0.066 5192 Dihedral : 6.984 58.605 4914 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 5.25 % Allowed : 18.53 % Favored : 76.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.89 (0.13), residues: 3846 helix: 1.73 (0.18), residues: 866 sheet: -1.07 (0.16), residues: 1056 loop : -1.39 (0.13), residues: 1924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG U 19 TYR 0.010 0.001 TYR V 38 PHE 0.024 0.001 PHE D 48 TRP 0.010 0.001 TRP E 451 HIS 0.004 0.001 HIS O 242 Details of bonding type rmsd covalent geometry : bond 0.00329 (30836) covalent geometry : angle 0.59940 (41806) SS BOND : bond 0.00296 ( 30) SS BOND : angle 0.98871 ( 60) hydrogen bonds : bond 0.03774 ( 1180) hydrogen bonds : angle 4.98933 ( 3216) link_ALPHA1-3 : bond 0.01103 ( 4) link_ALPHA1-3 : angle 1.48722 ( 12) link_BETA1-4 : bond 0.00396 ( 22) link_BETA1-4 : angle 2.18676 ( 66) link_BETA1-6 : bond 0.00592 ( 4) link_BETA1-6 : angle 1.65355 ( 12) link_NAG-ASN : bond 0.00423 ( 12) link_NAG-ASN : angle 1.75320 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 632 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 169 poor density : 463 time to evaluate : 1.289 Fit side-chains REVERT: A 13 GLU cc_start: 0.7497 (tm-30) cc_final: 0.6802 (tm-30) REVERT: A 130 VAL cc_start: 0.9344 (OUTLIER) cc_final: 0.9113 (p) REVERT: A 285 LEU cc_start: 0.9533 (OUTLIER) cc_final: 0.9057 (mt) REVERT: A 430 LEU cc_start: 0.8867 (mt) cc_final: 0.8582 (mt) REVERT: B 30 GLU cc_start: 0.7137 (pt0) cc_final: 0.6730 (pt0) REVERT: B 47 LEU cc_start: 0.9012 (mt) cc_final: 0.8806 (mt) REVERT: B 70 VAL cc_start: 0.9190 (t) cc_final: 0.8817 (p) REVERT: C 438 PHE cc_start: 0.7866 (m-10) cc_final: 0.7632 (m-10) REVERT: C 467 ASN cc_start: 0.6501 (m110) cc_final: 0.6094 (m110) REVERT: C 473 MET cc_start: 0.7357 (mmp) cc_final: 0.7015 (mtt) REVERT: D 49 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8406 (mt) REVERT: D 59 GLN cc_start: 0.8705 (mm-40) cc_final: 0.8154 (mt0) REVERT: D 63 ILE cc_start: 0.8649 (mm) cc_final: 0.8435 (mt) REVERT: D 74 MET cc_start: 0.8699 (tpp) cc_final: 0.8395 (mmm) REVERT: E 234 LEU cc_start: 0.8054 (OUTLIER) cc_final: 0.7491 (pp) REVERT: F 10 MET cc_start: 0.8580 (ppp) cc_final: 0.8297 (ppp) REVERT: H 62 ASP cc_start: 0.7921 (OUTLIER) cc_final: 0.7642 (t0) REVERT: H 73 ASP cc_start: 0.7735 (t70) cc_final: 0.7445 (t70) REVERT: H 107 TRP cc_start: 0.8388 (OUTLIER) cc_final: 0.7233 (p90) REVERT: L 80 LYS cc_start: 0.8633 (mptt) cc_final: 0.8355 (mmtm) REVERT: L 83 ARG cc_start: 0.7875 (mtm110) cc_final: 0.7186 (mpp80) REVERT: O 13 GLU cc_start: 0.7499 (tm-30) cc_final: 0.6805 (tm-30) REVERT: O 130 VAL cc_start: 0.9374 (OUTLIER) cc_final: 0.9168 (p) REVERT: O 199 MET cc_start: 0.8391 (ptp) cc_final: 0.8056 (ptm) REVERT: O 285 LEU cc_start: 0.9545 (OUTLIER) cc_final: 0.9100 (mt) REVERT: O 430 LEU cc_start: 0.8878 (mt) cc_final: 0.8586 (mt) REVERT: P 47 LEU cc_start: 0.9038 (mt) cc_final: 0.8813 (mt) REVERT: P 70 VAL cc_start: 0.9197 (t) cc_final: 0.8823 (p) REVERT: Q 467 ASN cc_start: 0.6491 (m110) cc_final: 0.6081 (m110) REVERT: R 49 LEU cc_start: 0.8635 (OUTLIER) cc_final: 0.8397 (mt) REVERT: R 59 GLN cc_start: 0.8704 (mm-40) cc_final: 0.8148 (mt0) REVERT: R 63 ILE cc_start: 0.8656 (mm) cc_final: 0.8436 (mt) REVERT: R 74 MET cc_start: 0.8708 (tpp) cc_final: 0.8400 (mmm) REVERT: S 234 LEU cc_start: 0.8055 (OUTLIER) cc_final: 0.7497 (pp) REVERT: T 10 MET cc_start: 0.8572 (ppp) cc_final: 0.8289 (ppp) REVERT: U 62 ASP cc_start: 0.8010 (OUTLIER) cc_final: 0.7744 (t0) REVERT: U 107 TRP cc_start: 0.8414 (OUTLIER) cc_final: 0.7134 (p90) REVERT: V 24 LYS cc_start: 0.8575 (tptp) cc_final: 0.8050 (mtpp) REVERT: V 80 LYS cc_start: 0.8536 (mptt) cc_final: 0.8001 (mmtm) REVERT: V 83 ARG cc_start: 0.7871 (mtm110) cc_final: 0.7179 (mpp80) outliers start: 169 outliers final: 139 residues processed: 591 average time/residue: 0.1805 time to fit residues: 177.6851 Evaluate side-chains 611 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 460 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 60 CYS Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 399 MET Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 183 CYS Chi-restraints excluded: chain C residue 246 GLN Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain C residue 271 SER Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 371 PHE Chi-restraints excluded: chain C residue 388 ASN Chi-restraints excluded: chain C residue 400 PHE Chi-restraints excluded: chain C residue 426 VAL Chi-restraints excluded: chain C residue 455 ILE Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 464 ILE Chi-restraints excluded: chain C residue 491 VAL Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain E residue 27 HIS Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 197 LEU Chi-restraints excluded: chain E residue 205 MET Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 237 THR Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain E residue 416 THR Chi-restraints excluded: chain E residue 422 SER Chi-restraints excluded: chain E residue 426 VAL Chi-restraints excluded: chain E residue 460 LEU Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain E residue 471 THR Chi-restraints excluded: chain E residue 485 LEU Chi-restraints excluded: chain F residue 18 THR Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain H residue 56 ASN Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 107 TRP Chi-restraints excluded: chain L residue 14 THR Chi-restraints excluded: chain L residue 36 LYS Chi-restraints excluded: chain L residue 53 LEU Chi-restraints excluded: chain L residue 62 SER Chi-restraints excluded: chain L residue 95 MET Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain O residue 33 THR Chi-restraints excluded: chain O residue 41 LEU Chi-restraints excluded: chain O residue 60 CYS Chi-restraints excluded: chain O residue 70 THR Chi-restraints excluded: chain O residue 91 VAL Chi-restraints excluded: chain O residue 130 VAL Chi-restraints excluded: chain O residue 163 THR Chi-restraints excluded: chain O residue 233 GLU Chi-restraints excluded: chain O residue 285 LEU Chi-restraints excluded: chain O residue 314 GLN Chi-restraints excluded: chain O residue 337 THR Chi-restraints excluded: chain O residue 385 LEU Chi-restraints excluded: chain O residue 399 MET Chi-restraints excluded: chain O residue 476 SER Chi-restraints excluded: chain P residue 17 GLN Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain P residue 58 THR Chi-restraints excluded: chain Q residue 10 ASP Chi-restraints excluded: chain Q residue 41 LEU Chi-restraints excluded: chain Q residue 61 ILE Chi-restraints excluded: chain Q residue 183 CYS Chi-restraints excluded: chain Q residue 246 GLN Chi-restraints excluded: chain Q residue 266 THR Chi-restraints excluded: chain Q residue 271 SER Chi-restraints excluded: chain Q residue 363 VAL Chi-restraints excluded: chain Q residue 371 PHE Chi-restraints excluded: chain Q residue 400 PHE Chi-restraints excluded: chain Q residue 423 VAL Chi-restraints excluded: chain Q residue 426 VAL Chi-restraints excluded: chain Q residue 461 LEU Chi-restraints excluded: chain Q residue 464 ILE Chi-restraints excluded: chain Q residue 491 VAL Chi-restraints excluded: chain R residue 49 LEU Chi-restraints excluded: chain R residue 66 LEU Chi-restraints excluded: chain S residue 15 LEU Chi-restraints excluded: chain S residue 27 HIS Chi-restraints excluded: chain S residue 49 GLU Chi-restraints excluded: chain S residue 91 VAL Chi-restraints excluded: chain S residue 107 LEU Chi-restraints excluded: chain S residue 141 ILE Chi-restraints excluded: chain S residue 197 LEU Chi-restraints excluded: chain S residue 205 MET Chi-restraints excluded: chain S residue 223 THR Chi-restraints excluded: chain S residue 234 LEU Chi-restraints excluded: chain S residue 236 VAL Chi-restraints excluded: chain S residue 237 THR Chi-restraints excluded: chain S residue 251 LEU Chi-restraints excluded: chain S residue 266 THR Chi-restraints excluded: chain S residue 310 VAL Chi-restraints excluded: chain S residue 356 VAL Chi-restraints excluded: chain S residue 416 THR Chi-restraints excluded: chain S residue 422 SER Chi-restraints excluded: chain S residue 426 VAL Chi-restraints excluded: chain S residue 460 LEU Chi-restraints excluded: chain S residue 461 LEU Chi-restraints excluded: chain S residue 471 THR Chi-restraints excluded: chain S residue 483 ILE Chi-restraints excluded: chain S residue 485 LEU Chi-restraints excluded: chain T residue 18 THR Chi-restraints excluded: chain T residue 37 LEU Chi-restraints excluded: chain T residue 47 LEU Chi-restraints excluded: chain T residue 49 LEU Chi-restraints excluded: chain T residue 58 THR Chi-restraints excluded: chain T residue 66 LEU Chi-restraints excluded: chain U residue 7 SER Chi-restraints excluded: chain U residue 12 VAL Chi-restraints excluded: chain U residue 43 LYS Chi-restraints excluded: chain U residue 50 VAL Chi-restraints excluded: chain U residue 56 ASN Chi-restraints excluded: chain U residue 62 ASP Chi-restraints excluded: chain U residue 87 THR Chi-restraints excluded: chain U residue 102 VAL Chi-restraints excluded: chain U residue 107 TRP Chi-restraints excluded: chain V residue 53 LEU Chi-restraints excluded: chain V residue 62 SER Chi-restraints excluded: chain V residue 95 MET Chi-restraints excluded: chain V residue 102 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 38 optimal weight: 10.0000 chunk 153 optimal weight: 9.9990 chunk 309 optimal weight: 9.9990 chunk 275 optimal weight: 20.0000 chunk 282 optimal weight: 9.9990 chunk 233 optimal weight: 7.9990 chunk 205 optimal weight: 8.9990 chunk 111 optimal weight: 5.9990 chunk 2 optimal weight: 10.0000 chunk 260 optimal weight: 5.9990 chunk 69 optimal weight: 9.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 ASN ** B 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 201 ASN ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 103 ASN ** P 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 77 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.089576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.077159 restraints weight = 72547.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.079331 restraints weight = 37048.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.080743 restraints weight = 23256.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.081667 restraints weight = 16834.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.082266 restraints weight = 13475.432| |-----------------------------------------------------------------------------| r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.3719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.122 30908 Z= 0.240 Angle : 0.680 8.761 41992 Z= 0.345 Chirality : 0.046 0.203 4938 Planarity : 0.004 0.074 5192 Dihedral : 7.149 59.160 4914 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 4.93 % Allowed : 18.99 % Favored : 76.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.96 (0.13), residues: 3846 helix: 1.64 (0.18), residues: 866 sheet: -1.03 (0.16), residues: 1020 loop : -1.48 (0.13), residues: 1960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 19 TYR 0.013 0.002 TYR T 52 PHE 0.026 0.002 PHE P 48 TRP 0.015 0.002 TRP C 418 HIS 0.006 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00566 (30836) covalent geometry : angle 0.67019 (41806) SS BOND : bond 0.00420 ( 30) SS BOND : angle 1.23593 ( 60) hydrogen bonds : bond 0.04209 ( 1180) hydrogen bonds : angle 5.14493 ( 3216) link_ALPHA1-3 : bond 0.01051 ( 4) link_ALPHA1-3 : angle 1.86881 ( 12) link_BETA1-4 : bond 0.00355 ( 22) link_BETA1-4 : angle 2.26539 ( 66) link_BETA1-6 : bond 0.00464 ( 4) link_BETA1-6 : angle 1.83935 ( 12) link_NAG-ASN : bond 0.00650 ( 12) link_NAG-ASN : angle 1.98342 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 619 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 460 time to evaluate : 1.223 Fit side-chains revert: symmetry clash REVERT: A 13 GLU cc_start: 0.7503 (tm-30) cc_final: 0.6831 (tm-30) REVERT: A 130 VAL cc_start: 0.9293 (OUTLIER) cc_final: 0.9060 (p) REVERT: B 70 VAL cc_start: 0.9127 (t) cc_final: 0.8763 (p) REVERT: C 467 ASN cc_start: 0.6553 (m110) cc_final: 0.6113 (m110) REVERT: C 473 MET cc_start: 0.7537 (mmp) cc_final: 0.7200 (mtt) REVERT: D 27 ARG cc_start: 0.8400 (ttp80) cc_final: 0.7938 (ttp-110) REVERT: D 74 MET cc_start: 0.8749 (tpp) cc_final: 0.8466 (mmm) REVERT: E 193 GLU cc_start: 0.7735 (mp0) cc_final: 0.7507 (mp0) REVERT: E 234 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.7892 (pp) REVERT: E 373 GLU cc_start: 0.6946 (OUTLIER) cc_final: 0.6337 (tp30) REVERT: F 10 MET cc_start: 0.8688 (ppp) cc_final: 0.8416 (ppp) REVERT: H 3 GLU cc_start: 0.7306 (mm-30) cc_final: 0.7083 (mm-30) REVERT: H 62 ASP cc_start: 0.8067 (OUTLIER) cc_final: 0.7821 (t0) REVERT: H 107 TRP cc_start: 0.8440 (OUTLIER) cc_final: 0.7394 (p90) REVERT: L 80 LYS cc_start: 0.8480 (mptt) cc_final: 0.8212 (mmtm) REVERT: L 83 ARG cc_start: 0.7918 (mtm110) cc_final: 0.7199 (mpp80) REVERT: O 13 GLU cc_start: 0.7501 (tm-30) cc_final: 0.6827 (tm-30) REVERT: O 130 VAL cc_start: 0.9342 (OUTLIER) cc_final: 0.9121 (p) REVERT: O 199 MET cc_start: 0.8462 (ptp) cc_final: 0.7986 (ptm) REVERT: O 285 LEU cc_start: 0.9556 (OUTLIER) cc_final: 0.9117 (mt) REVERT: P 47 LEU cc_start: 0.9060 (mt) cc_final: 0.8841 (mt) REVERT: P 70 VAL cc_start: 0.9135 (t) cc_final: 0.8764 (p) REVERT: R 27 ARG cc_start: 0.8392 (ttp80) cc_final: 0.7930 (ttp-110) REVERT: R 49 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8512 (mt) REVERT: R 74 MET cc_start: 0.8762 (tpp) cc_final: 0.8476 (mmm) REVERT: S 193 GLU cc_start: 0.7725 (mp0) cc_final: 0.7477 (mp0) REVERT: S 234 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.7902 (pp) REVERT: T 10 MET cc_start: 0.8683 (ppp) cc_final: 0.8408 (ppp) REVERT: U 62 ASP cc_start: 0.8075 (OUTLIER) cc_final: 0.7833 (t0) REVERT: U 107 TRP cc_start: 0.8367 (OUTLIER) cc_final: 0.7233 (p90) REVERT: V 24 LYS cc_start: 0.8703 (tptp) cc_final: 0.8250 (mtpp) REVERT: V 80 LYS cc_start: 0.8392 (mptt) cc_final: 0.7843 (mmtm) REVERT: V 83 ARG cc_start: 0.7916 (mtm110) cc_final: 0.7194 (mpp80) outliers start: 159 outliers final: 133 residues processed: 580 average time/residue: 0.1840 time to fit residues: 176.9812 Evaluate side-chains 592 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 448 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 60 CYS Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 399 MET Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 68 MET Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 183 CYS Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain C residue 271 SER Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 371 PHE Chi-restraints excluded: chain C residue 388 ASN Chi-restraints excluded: chain C residue 400 PHE Chi-restraints excluded: chain C residue 426 VAL Chi-restraints excluded: chain C residue 455 ILE Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 464 ILE Chi-restraints excluded: chain C residue 491 VAL Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain E residue 27 HIS Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 197 LEU Chi-restraints excluded: chain E residue 205 MET Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 237 THR Chi-restraints excluded: chain E residue 266 THR Chi-restraints excluded: chain E residue 373 GLU Chi-restraints excluded: chain E residue 416 THR Chi-restraints excluded: chain E residue 422 SER Chi-restraints excluded: chain E residue 426 VAL Chi-restraints excluded: chain E residue 460 LEU Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain E residue 471 THR Chi-restraints excluded: chain E residue 485 LEU Chi-restraints excluded: chain F residue 18 THR Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 56 ASN Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 107 TRP Chi-restraints excluded: chain L residue 14 THR Chi-restraints excluded: chain L residue 53 LEU Chi-restraints excluded: chain L residue 62 SER Chi-restraints excluded: chain L residue 95 MET Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain O residue 41 LEU Chi-restraints excluded: chain O residue 60 CYS Chi-restraints excluded: chain O residue 70 THR Chi-restraints excluded: chain O residue 91 VAL Chi-restraints excluded: chain O residue 95 THR Chi-restraints excluded: chain O residue 130 VAL Chi-restraints excluded: chain O residue 163 THR Chi-restraints excluded: chain O residue 233 GLU Chi-restraints excluded: chain O residue 285 LEU Chi-restraints excluded: chain O residue 314 GLN Chi-restraints excluded: chain O residue 337 THR Chi-restraints excluded: chain O residue 385 LEU Chi-restraints excluded: chain O residue 399 MET Chi-restraints excluded: chain O residue 476 SER Chi-restraints excluded: chain P residue 17 GLN Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain P residue 58 THR Chi-restraints excluded: chain Q residue 10 ASP Chi-restraints excluded: chain Q residue 41 LEU Chi-restraints excluded: chain Q residue 61 ILE Chi-restraints excluded: chain Q residue 183 CYS Chi-restraints excluded: chain Q residue 266 THR Chi-restraints excluded: chain Q residue 271 SER Chi-restraints excluded: chain Q residue 363 VAL Chi-restraints excluded: chain Q residue 371 PHE Chi-restraints excluded: chain Q residue 388 ASN Chi-restraints excluded: chain Q residue 400 PHE Chi-restraints excluded: chain Q residue 423 VAL Chi-restraints excluded: chain Q residue 426 VAL Chi-restraints excluded: chain Q residue 461 LEU Chi-restraints excluded: chain Q residue 464 ILE Chi-restraints excluded: chain Q residue 491 VAL Chi-restraints excluded: chain R residue 49 LEU Chi-restraints excluded: chain R residue 66 LEU Chi-restraints excluded: chain S residue 15 LEU Chi-restraints excluded: chain S residue 27 HIS Chi-restraints excluded: chain S residue 49 GLU Chi-restraints excluded: chain S residue 91 VAL Chi-restraints excluded: chain S residue 107 LEU Chi-restraints excluded: chain S residue 141 ILE Chi-restraints excluded: chain S residue 197 LEU Chi-restraints excluded: chain S residue 205 MET Chi-restraints excluded: chain S residue 223 THR Chi-restraints excluded: chain S residue 234 LEU Chi-restraints excluded: chain S residue 236 VAL Chi-restraints excluded: chain S residue 237 THR Chi-restraints excluded: chain S residue 263 THR Chi-restraints excluded: chain S residue 266 THR Chi-restraints excluded: chain S residue 310 VAL Chi-restraints excluded: chain S residue 356 VAL Chi-restraints excluded: chain S residue 416 THR Chi-restraints excluded: chain S residue 422 SER Chi-restraints excluded: chain S residue 426 VAL Chi-restraints excluded: chain S residue 460 LEU Chi-restraints excluded: chain S residue 471 THR Chi-restraints excluded: chain S residue 483 ILE Chi-restraints excluded: chain S residue 485 LEU Chi-restraints excluded: chain T residue 18 THR Chi-restraints excluded: chain T residue 47 LEU Chi-restraints excluded: chain T residue 49 LEU Chi-restraints excluded: chain T residue 58 THR Chi-restraints excluded: chain T residue 66 LEU Chi-restraints excluded: chain U residue 7 SER Chi-restraints excluded: chain U residue 12 VAL Chi-restraints excluded: chain U residue 43 LYS Chi-restraints excluded: chain U residue 50 VAL Chi-restraints excluded: chain U residue 56 ASN Chi-restraints excluded: chain U residue 62 ASP Chi-restraints excluded: chain U residue 87 THR Chi-restraints excluded: chain U residue 102 VAL Chi-restraints excluded: chain U residue 107 TRP Chi-restraints excluded: chain V residue 14 THR Chi-restraints excluded: chain V residue 53 LEU Chi-restraints excluded: chain V residue 62 SER Chi-restraints excluded: chain V residue 102 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 89 optimal weight: 10.0000 chunk 177 optimal weight: 20.0000 chunk 300 optimal weight: 4.9990 chunk 285 optimal weight: 20.0000 chunk 281 optimal weight: 20.0000 chunk 143 optimal weight: 6.9990 chunk 134 optimal weight: 0.7980 chunk 348 optimal weight: 7.9990 chunk 357 optimal weight: 30.0000 chunk 358 optimal weight: 3.9990 chunk 67 optimal weight: 6.9990 overall best weight: 4.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 201 ASN ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 201 ASN ** R 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.090276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.077906 restraints weight = 72792.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.080094 restraints weight = 36828.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.081521 restraints weight = 22965.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.082464 restraints weight = 16523.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.083065 restraints weight = 13169.373| |-----------------------------------------------------------------------------| r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.3753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.096 30908 Z= 0.170 Angle : 0.636 8.695 41992 Z= 0.323 Chirality : 0.045 0.203 4938 Planarity : 0.004 0.072 5192 Dihedral : 7.019 59.388 4914 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 4.72 % Allowed : 18.96 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.92 (0.13), residues: 3846 helix: 1.65 (0.18), residues: 866 sheet: -0.98 (0.16), residues: 1020 loop : -1.45 (0.13), residues: 1960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG U 19 TYR 0.010 0.001 TYR U 80 PHE 0.021 0.002 PHE D 48 TRP 0.012 0.001 TRP Q 418 HIS 0.004 0.001 HIS O 207 Details of bonding type rmsd covalent geometry : bond 0.00399 (30836) covalent geometry : angle 0.62622 (41806) SS BOND : bond 0.00337 ( 30) SS BOND : angle 1.08239 ( 60) hydrogen bonds : bond 0.03951 ( 1180) hydrogen bonds : angle 5.10466 ( 3216) link_ALPHA1-3 : bond 0.01009 ( 4) link_ALPHA1-3 : angle 1.57388 ( 12) link_BETA1-4 : bond 0.00370 ( 22) link_BETA1-4 : angle 2.20211 ( 66) link_BETA1-6 : bond 0.00500 ( 4) link_BETA1-6 : angle 1.75146 ( 12) link_NAG-ASN : bond 0.00519 ( 12) link_NAG-ASN : angle 1.84720 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5625.92 seconds wall clock time: 98 minutes 21.09 seconds (5901.09 seconds total)