Starting phenix.real_space_refine on Wed Jun 25 22:54:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jn4_36432/06_2025/8jn4_36432.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jn4_36432/06_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_36432/06_2025/8jn4_36432.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jn4_36432/06_2025/8jn4_36432.map" model { file = "/net/cci-nas-00/data/ceres_data/8jn4_36432/06_2025/8jn4_36432.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jn4_36432/06_2025/8jn4_36432.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 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): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 17.29, per 1000 atoms: 0.57 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: 8.27 Conformation dependent library (CDL) restraints added in 3.9 seconds 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: 4.00 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: 11.20 Time building geometry restraints manager: 9.48 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: 0.01 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: 0.010 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: 1.110 Check model and map are aligned: 0.210 Set scattering table: 0.300 Process input model: 66.880 Find NCS groups from input model: 1.040 Set up NCS constraints: 0.210 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.920 ------------------------------------------------------------------------------- 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 : 11.44 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (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 TRP 0.019 0.001 TRP P 26 HIS 0.006 0.001 HIS O 345 PHE 0.021 0.002 PHE P 42 TYR 0.014 0.001 TYR Q 486 ARG 0.004 0.001 ARG A 9 Details of bonding type rmsd link_NAG-ASN : bond 0.00462 ( 12) link_NAG-ASN : angle 1.98297 ( 36) link_BETA1-4 : bond 0.00427 ( 22) link_BETA1-4 : angle 2.55805 ( 66) link_ALPHA1-3 : bond 0.00441 ( 4) link_ALPHA1-3 : angle 2.19127 ( 12) hydrogen bonds : bond 0.21172 ( 1180) hydrogen bonds : angle 8.38563 ( 3216) link_BETA1-6 : bond 0.00657 ( 4) link_BETA1-6 : angle 1.20716 ( 12) SS BOND : bond 0.00376 ( 30) SS BOND : angle 1.39343 ( 60) covalent geometry : bond 0.00407 (30836) covalent geometry : angle 0.73552 (41806) *********************** 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 : 3.260 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: 0.4576 time to fit residues: 603.6595 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 : 3.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 322 optimal weight: 9.9990 chunk 289 optimal weight: 30.0000 chunk 160 optimal weight: 5.9990 chunk 98 optimal weight: 30.0000 chunk 195 optimal weight: 2.9990 chunk 154 optimal weight: 20.0000 chunk 299 optimal weight: 9.9990 chunk 115 optimal weight: 8.9990 chunk 182 optimal weight: 50.0000 chunk 222 optimal weight: 5.9990 chunk 346 optimal weight: 7.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- 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 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 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 201 ASN S 314 GLN ** U 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 1 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.090750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.078948 restraints weight = 71638.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.081007 restraints weight = 37106.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.082334 restraints weight = 23485.997| |-----------------------------------------------------------------------------| r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 30908 Z= 0.222 Angle : 0.728 8.669 41992 Z= 0.372 Chirality : 0.048 0.177 4938 Planarity : 0.004 0.040 5192 Dihedral : 12.384 80.288 4914 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 2.86 % Allowed : 12.01 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.13), residues: 3846 helix: 1.23 (0.18), residues: 874 sheet: -1.26 (0.16), residues: 1054 loop : -1.53 (0.13), residues: 1918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 20 HIS 0.006 0.001 HIS O 207 PHE 0.025 0.002 PHE S 475 TYR 0.019 0.002 TYR Q 486 ARG 0.006 0.001 ARG V 67 Details of bonding type rmsd link_NAG-ASN : bond 0.00609 ( 12) link_NAG-ASN : angle 2.15219 ( 36) link_BETA1-4 : bond 0.00470 ( 22) link_BETA1-4 : angle 2.65273 ( 66) link_ALPHA1-3 : bond 0.01253 ( 4) link_ALPHA1-3 : angle 1.16037 ( 12) hydrogen bonds : bond 0.05109 ( 1180) hydrogen bonds : angle 6.15646 ( 3216) link_BETA1-6 : bond 0.00996 ( 4) link_BETA1-6 : angle 2.64770 ( 12) SS BOND : bond 0.00436 ( 30) SS BOND : angle 1.25609 ( 60) covalent geometry : bond 0.00518 (30836) covalent geometry : angle 0.71564 (41806) *********************** 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: 92 poor density : 558 time to evaluate : 3.437 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 GLU cc_start: 0.7508 (tm-30) cc_final: 0.7046 (tm-30) REVERT: A 36 LYS cc_start: 0.8354 (tptp) cc_final: 0.7815 (tptp) REVERT: A 37 ASN cc_start: 0.7847 (m110) cc_final: 0.7356 (m110) REVERT: A 56 LEU cc_start: 0.9319 (tp) cc_final: 0.9059 (tt) REVERT: A 176 TYR cc_start: 0.8770 (m-80) cc_final: 0.8343 (m-80) REVERT: A 199 MET cc_start: 0.8586 (ptp) cc_final: 0.8371 (ptm) REVERT: B 70 VAL cc_start: 0.9110 (t) cc_final: 0.8572 (p) REVERT: B 73 SER cc_start: 0.8307 (m) cc_final: 0.7806 (p) REVERT: C 438 PHE cc_start: 0.8233 (m-10) cc_final: 0.7755 (m-10) REVERT: C 473 MET cc_start: 0.7443 (mmp) cc_final: 0.7010 (mtt) REVERT: C 486 TYR cc_start: 0.7994 (t80) cc_final: 0.7372 (t80) REVERT: D 10 MET cc_start: 0.7910 (OUTLIER) cc_final: 0.7632 (mpp) REVERT: D 27 ARG cc_start: 0.8066 (ttp80) cc_final: 0.7728 (ttp-110) REVERT: D 59 GLN cc_start: 0.7501 (mt0) cc_final: 0.6999 (mt0) REVERT: D 74 MET cc_start: 0.8492 (tpp) cc_final: 0.7793 (mmm) REVERT: D 75 THR cc_start: 0.7803 (p) cc_final: 0.7519 (p) REVERT: F 64 PHE cc_start: 0.9169 (t80) cc_final: 0.8958 (t80) REVERT: H 65 LYS cc_start: 0.8434 (tttp) cc_final: 0.8190 (tttp) REVERT: H 109 PHE cc_start: 0.8275 (m-10) cc_final: 0.7844 (m-10) REVERT: H 111 TYR cc_start: 0.8200 (m-80) cc_final: 0.7981 (m-10) REVERT: L 24 LYS cc_start: 0.8794 (tptp) cc_final: 0.8254 (mtpp) REVERT: L 31 TRP cc_start: 0.7274 (t60) cc_final: 0.7030 (t60) REVERT: L 85 GLN cc_start: 0.7996 (mp10) cc_final: 0.7488 (mp10) REVERT: O 13 GLU cc_start: 0.7509 (tm-30) cc_final: 0.7040 (tm-30) REVERT: O 36 LYS cc_start: 0.8345 (tptp) cc_final: 0.7817 (tptp) REVERT: O 37 ASN cc_start: 0.7849 (m110) cc_final: 0.7362 (m110) REVERT: O 56 LEU cc_start: 0.9320 (tp) cc_final: 0.9058 (tt) REVERT: O 176 TYR cc_start: 0.8762 (m-80) cc_final: 0.8338 (m-80) REVERT: O 199 MET cc_start: 0.8586 (ptp) cc_final: 0.8356 (ptm) REVERT: P 70 VAL cc_start: 0.9099 (t) cc_final: 0.8563 (p) REVERT: P 73 SER cc_start: 0.8311 (m) cc_final: 0.7818 (p) REVERT: Q 438 PHE cc_start: 0.8228 (m-10) cc_final: 0.7748 (m-10) REVERT: Q 473 MET cc_start: 0.7425 (mmp) cc_final: 0.7009 (mtt) REVERT: Q 486 TYR cc_start: 0.7999 (t80) cc_final: 0.7375 (t80) REVERT: R 10 MET cc_start: 0.7896 (OUTLIER) cc_final: 0.7629 (mpp) REVERT: R 27 ARG cc_start: 0.8062 (ttp80) cc_final: 0.7722 (ttp-110) REVERT: R 59 GLN cc_start: 0.7496 (mt0) cc_final: 0.6995 (mt0) REVERT: R 74 MET cc_start: 0.8490 (tpp) cc_final: 0.7801 (mmm) REVERT: R 75 THR cc_start: 0.7771 (p) cc_final: 0.7510 (p) REVERT: T 64 PHE cc_start: 0.9173 (t80) cc_final: 0.8956 (t80) REVERT: U 34 MET cc_start: 0.8315 (mmm) cc_final: 0.8109 (mmm) REVERT: U 65 LYS cc_start: 0.8448 (tttp) cc_final: 0.8199 (tttp) REVERT: U 109 PHE cc_start: 0.8293 (m-10) cc_final: 0.7864 (m-10) REVERT: U 111 TYR cc_start: 0.8212 (m-80) cc_final: 0.7993 (m-10) REVERT: V 24 LYS cc_start: 0.8781 (tptp) cc_final: 0.8262 (mtpp) REVERT: V 85 GLN cc_start: 0.8003 (mp10) cc_final: 0.7506 (mp10) outliers start: 92 outliers final: 64 residues processed: 607 average time/residue: 0.3929 time to fit residues: 385.2566 Evaluate side-chains 563 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 497 time to evaluate : 3.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 392 LYS Chi-restraints excluded: chain A residue 410 MET Chi-restraints excluded: chain A residue 466 LEU 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 65 ILE Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 371 PHE 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 15 LEU Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 197 LEU Chi-restraints excluded: chain E residue 237 THR Chi-restraints excluded: chain E residue 426 VAL Chi-restraints excluded: chain E residue 457 ILE 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 30 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 247 GLU Chi-restraints excluded: chain O residue 314 GLN Chi-restraints excluded: chain O residue 392 LYS Chi-restraints excluded: chain O residue 410 MET Chi-restraints excluded: chain O residue 466 LEU 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 65 ILE Chi-restraints excluded: chain Q residue 10 ASP Chi-restraints excluded: chain Q residue 363 VAL Chi-restraints excluded: chain Q residue 371 PHE 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 15 LEU Chi-restraints excluded: chain S residue 107 LEU Chi-restraints excluded: chain S residue 197 LEU Chi-restraints excluded: chain S residue 237 THR Chi-restraints excluded: chain S residue 426 VAL Chi-restraints excluded: chain S residue 457 ILE 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 30 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 332 optimal weight: 10.0000 chunk 60 optimal weight: 6.9990 chunk 342 optimal weight: 20.0000 chunk 295 optimal weight: 10.0000 chunk 205 optimal weight: 9.9990 chunk 310 optimal weight: 10.0000 chunk 263 optimal weight: 20.0000 chunk 245 optimal weight: 10.0000 chunk 235 optimal weight: 9.9990 chunk 182 optimal weight: 8.9990 chunk 351 optimal weight: 9.9990 overall best weight: 9.1990 ------------------------------------------------------------------------------- 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** ** D 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 1 HIS ** P 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 27 HIS Q 201 ASN ** R 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 59 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** ** U 100 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 = 0.3272 r_free = 0.3272 target = 0.088594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.076385 restraints weight = 73406.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.078474 restraints weight = 37865.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.079836 restraints weight = 23929.425| |-----------------------------------------------------------------------------| r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.2934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.124 30908 Z= 0.282 Angle : 0.755 9.275 41992 Z= 0.384 Chirality : 0.049 0.188 4938 Planarity : 0.004 0.050 5192 Dihedral : 10.152 63.473 4914 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 4.84 % Allowed : 14.77 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.13), residues: 3846 helix: 1.23 (0.18), residues: 874 sheet: -1.19 (0.16), residues: 986 loop : -1.66 (0.13), residues: 1986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP V 31 HIS 0.008 0.001 HIS O 207 PHE 0.028 0.002 PHE E 475 TYR 0.021 0.002 TYR Q 486 ARG 0.005 0.001 ARG E 231 Details of bonding type rmsd link_NAG-ASN : bond 0.00825 ( 12) link_NAG-ASN : angle 2.26689 ( 36) link_BETA1-4 : bond 0.00510 ( 22) link_BETA1-4 : angle 2.61694 ( 66) link_ALPHA1-3 : bond 0.01038 ( 4) link_ALPHA1-3 : angle 1.39213 ( 12) hydrogen bonds : bond 0.05044 ( 1180) hydrogen bonds : angle 5.77266 ( 3216) link_BETA1-6 : bond 0.00857 ( 4) link_BETA1-6 : angle 2.52969 ( 12) SS BOND : bond 0.00513 ( 30) SS BOND : angle 1.39901 ( 60) covalent geometry : bond 0.00663 (30836) covalent geometry : angle 0.74354 (41806) *********************** 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 670 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 514 time to evaluate : 3.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 GLU cc_start: 0.7640 (tm-30) cc_final: 0.6996 (tm-30) REVERT: A 36 LYS cc_start: 0.8406 (tptp) cc_final: 0.8198 (tptm) REVERT: B 70 VAL cc_start: 0.9143 (t) cc_final: 0.8633 (p) REVERT: B 73 SER cc_start: 0.8359 (m) cc_final: 0.7795 (p) REVERT: B 74 MET cc_start: 0.7131 (tpp) cc_final: 0.6544 (tpp) REVERT: C 438 PHE cc_start: 0.8154 (m-10) cc_final: 0.7952 (m-10) REVERT: C 473 MET cc_start: 0.7468 (mmp) cc_final: 0.6981 (mtt) REVERT: C 478 ILE cc_start: 0.9127 (mt) cc_final: 0.8919 (mm) REVERT: C 482 ILE cc_start: 0.9103 (mm) cc_final: 0.8811 (mt) REVERT: C 486 TYR cc_start: 0.8376 (t80) cc_final: 0.7984 (t80) REVERT: D 10 MET cc_start: 0.8145 (tpp) cc_final: 0.7642 (mpp) REVERT: D 27 ARG cc_start: 0.8285 (ttp80) cc_final: 0.7864 (ttp-110) REVERT: D 74 MET cc_start: 0.8682 (tpp) cc_final: 0.8218 (mmm) REVERT: E 373 GLU cc_start: 0.7145 (OUTLIER) cc_final: 0.6416 (tp30) REVERT: H 3 GLU cc_start: 0.7184 (mm-30) cc_final: 0.6974 (mm-30) REVERT: H 62 ASP cc_start: 0.8267 (OUTLIER) cc_final: 0.7979 (t0) REVERT: H 65 LYS cc_start: 0.8578 (tttp) cc_final: 0.8295 (tttp) REVERT: L 24 LYS cc_start: 0.8813 (tptp) cc_final: 0.8323 (mtpp) REVERT: O 13 GLU cc_start: 0.7638 (tm-30) cc_final: 0.6982 (tm-30) REVERT: O 36 LYS cc_start: 0.8396 (tptp) cc_final: 0.8195 (tptm) REVERT: O 445 LEU cc_start: 0.9149 (tt) cc_final: 0.8939 (tt) REVERT: P 70 VAL cc_start: 0.9136 (t) cc_final: 0.8628 (p) REVERT: P 73 SER cc_start: 0.8375 (m) cc_final: 0.7889 (p) REVERT: Q 473 MET cc_start: 0.7456 (mmp) cc_final: 0.6981 (mtt) REVERT: Q 478 ILE cc_start: 0.9130 (mt) cc_final: 0.8923 (mm) REVERT: Q 482 ILE cc_start: 0.9098 (mm) cc_final: 0.8806 (mt) REVERT: Q 486 TYR cc_start: 0.8381 (t80) cc_final: 0.7990 (t80) REVERT: R 10 MET cc_start: 0.8154 (tpp) cc_final: 0.7640 (mpp) REVERT: R 27 ARG cc_start: 0.8278 (ttp80) cc_final: 0.7856 (ttp-110) REVERT: R 74 MET cc_start: 0.8688 (tpp) cc_final: 0.8215 (mmm) REVERT: S 373 GLU cc_start: 0.7153 (OUTLIER) cc_final: 0.6422 (tp30) REVERT: T 10 MET cc_start: 0.8672 (ppp) cc_final: 0.8443 (ppp) REVERT: U 3 GLU cc_start: 0.7208 (mm-30) cc_final: 0.6985 (mm-30) REVERT: U 62 ASP cc_start: 0.8271 (OUTLIER) cc_final: 0.7983 (t0) REVERT: U 65 LYS cc_start: 0.8566 (tttp) cc_final: 0.8350 (tttp) REVERT: V 24 LYS cc_start: 0.8803 (tptp) cc_final: 0.8342 (mtpp) outliers start: 156 outliers final: 98 residues processed: 614 average time/residue: 0.3867 time to fit residues: 387.0091 Evaluate side-chains 567 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 465 time to evaluate : 3.083 ------------------------------------------------------------------------------- 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 233 GLU Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 466 LEU 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 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 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 8 VAL 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 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 426 VAL Chi-restraints excluded: chain E residue 457 ILE Chi-restraints excluded: chain F residue 14 THR 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 30 THR 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 102 VAL Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 62 SER Chi-restraints excluded: chain L residue 112 ILE Chi-restraints excluded: chain O residue 60 CYS Chi-restraints excluded: chain O residue 95 THR Chi-restraints excluded: chain O residue 233 GLU Chi-restraints excluded: chain O residue 247 GLU Chi-restraints excluded: chain O residue 314 GLN Chi-restraints excluded: chain O residue 466 LEU Chi-restraints excluded: chain O residue 473 MET 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 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 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 8 VAL 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 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 426 VAL Chi-restraints excluded: chain S residue 457 ILE Chi-restraints excluded: chain T residue 14 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 55 THR Chi-restraints excluded: chain T residue 58 THR Chi-restraints excluded: chain T residue 61 VAL Chi-restraints excluded: chain U residue 30 THR 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 86 LEU 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 112 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 180 optimal weight: 30.0000 chunk 17 optimal weight: 8.9990 chunk 28 optimal weight: 9.9990 chunk 276 optimal weight: 20.0000 chunk 267 optimal weight: 0.4980 chunk 18 optimal weight: 6.9990 chunk 347 optimal weight: 6.9990 chunk 134 optimal weight: 6.9990 chunk 162 optimal weight: 9.9990 chunk 161 optimal weight: 2.9990 chunk 252 optimal weight: 5.9990 overall best weight: 4.6988 ------------------------------------------------------------------------------- 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** ** D 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 314 GLN L 1 HIS O 8 ASN ** 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 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 314 GLN V 1 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.090137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.077921 restraints weight = 72667.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.080043 restraints weight = 37106.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.081430 restraints weight = 23287.483| |-----------------------------------------------------------------------------| r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.3106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 30908 Z= 0.172 Angle : 0.657 8.796 41992 Z= 0.331 Chirality : 0.046 0.201 4938 Planarity : 0.004 0.040 5192 Dihedral : 8.759 59.877 4914 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 4.19 % Allowed : 17.94 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.13), residues: 3846 helix: 1.45 (0.18), residues: 866 sheet: -1.22 (0.16), residues: 996 loop : -1.58 (0.13), residues: 1984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 26 HIS 0.005 0.001 HIS F 7 PHE 0.021 0.002 PHE B 48 TYR 0.013 0.001 TYR Q 486 ARG 0.004 0.000 ARG B 27 Details of bonding type rmsd link_NAG-ASN : bond 0.00538 ( 12) link_NAG-ASN : angle 1.97449 ( 36) link_BETA1-4 : bond 0.00424 ( 22) link_BETA1-4 : angle 2.46349 ( 66) link_ALPHA1-3 : bond 0.01179 ( 4) link_ALPHA1-3 : angle 1.24066 ( 12) hydrogen bonds : bond 0.04306 ( 1180) hydrogen bonds : angle 5.43040 ( 3216) link_BETA1-6 : bond 0.00869 ( 4) link_BETA1-6 : angle 2.37798 ( 12) SS BOND : bond 0.00327 ( 30) SS BOND : angle 1.00251 ( 60) covalent geometry : bond 0.00401 (30836) covalent geometry : angle 0.64593 (41806) *********************** 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 626 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 491 time to evaluate : 3.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 GLU cc_start: 0.7712 (tm-30) cc_final: 0.6945 (tm-30) REVERT: A 36 LYS cc_start: 0.8437 (tptp) cc_final: 0.8169 (tmtt) REVERT: B 27 ARG cc_start: 0.7385 (ptt-90) cc_final: 0.6913 (ptt-90) REVERT: B 30 GLU cc_start: 0.7260 (pt0) cc_final: 0.6884 (pt0) REVERT: B 70 VAL cc_start: 0.9128 (t) cc_final: 0.8603 (p) REVERT: B 74 MET cc_start: 0.6960 (tpp) cc_final: 0.6730 (tpp) REVERT: C 438 PHE cc_start: 0.8110 (m-10) cc_final: 0.7900 (m-10) REVERT: C 473 MET cc_start: 0.7539 (mmp) cc_final: 0.6934 (mtt) REVERT: C 482 ILE cc_start: 0.9090 (mm) cc_final: 0.8827 (mt) REVERT: C 486 TYR cc_start: 0.8249 (t80) cc_final: 0.7880 (t80) REVERT: D 10 MET cc_start: 0.8166 (tpp) cc_final: 0.7655 (mpp) REVERT: D 27 ARG cc_start: 0.8348 (ttp80) cc_final: 0.7898 (ttp-170) REVERT: D 64 PHE cc_start: 0.8954 (t80) cc_final: 0.8679 (t80) REVERT: D 74 MET cc_start: 0.8674 (tpp) cc_final: 0.8256 (mmm) REVERT: E 234 LEU cc_start: 0.8287 (OUTLIER) cc_final: 0.7659 (pp) REVERT: E 410 MET cc_start: 0.8294 (ttm) cc_final: 0.8059 (ttm) REVERT: E 480 ILE cc_start: 0.8135 (mm) cc_final: 0.7925 (mm) REVERT: F 10 MET cc_start: 0.8276 (ppp) cc_final: 0.8072 (ppp) REVERT: H 6 GLU cc_start: 0.7586 (mm-30) cc_final: 0.6581 (mp0) REVERT: H 62 ASP cc_start: 0.8256 (OUTLIER) cc_final: 0.7945 (t0) REVERT: H 80 TYR cc_start: 0.7616 (m-10) cc_final: 0.7334 (m-80) REVERT: H 89 GLU cc_start: 0.7270 (tm-30) cc_final: 0.7052 (tm-30) REVERT: H 107 TRP cc_start: 0.8572 (OUTLIER) cc_final: 0.7598 (p90) REVERT: L 24 LYS cc_start: 0.8775 (tptp) cc_final: 0.8329 (mtpp) REVERT: O 13 GLU cc_start: 0.7688 (tm-30) cc_final: 0.6930 (tm-30) REVERT: O 36 LYS cc_start: 0.8424 (tptp) cc_final: 0.8198 (tmtt) REVERT: P 30 GLU cc_start: 0.7297 (pt0) cc_final: 0.6833 (pt0) REVERT: P 70 VAL cc_start: 0.9119 (t) cc_final: 0.8604 (p) REVERT: Q 473 MET cc_start: 0.7517 (mmp) cc_final: 0.6934 (mtt) REVERT: Q 482 ILE cc_start: 0.9085 (mm) cc_final: 0.8820 (mt) REVERT: Q 486 TYR cc_start: 0.8255 (t80) cc_final: 0.7888 (t80) REVERT: R 10 MET cc_start: 0.8171 (tpp) cc_final: 0.7660 (mpp) REVERT: R 27 ARG cc_start: 0.8344 (ttp80) cc_final: 0.7893 (ttp-170) REVERT: R 64 PHE cc_start: 0.8954 (t80) cc_final: 0.8679 (t80) REVERT: R 74 MET cc_start: 0.8680 (tpp) cc_final: 0.8260 (mmm) REVERT: S 234 LEU cc_start: 0.8294 (OUTLIER) cc_final: 0.7668 (pp) REVERT: S 399 MET cc_start: 0.7676 (tpp) cc_final: 0.7403 (tpp) REVERT: S 410 MET cc_start: 0.8306 (ttm) cc_final: 0.8068 (ttm) REVERT: S 480 ILE cc_start: 0.8129 (mm) cc_final: 0.7919 (mm) REVERT: U 6 GLU cc_start: 0.7586 (mm-30) cc_final: 0.6577 (mp0) REVERT: U 62 ASP cc_start: 0.8257 (OUTLIER) cc_final: 0.7939 (t0) REVERT: U 80 TYR cc_start: 0.7606 (m-10) cc_final: 0.7336 (m-80) REVERT: U 86 LEU cc_start: 0.7605 (mt) cc_final: 0.7368 (mp) REVERT: U 89 GLU cc_start: 0.7225 (tm-30) cc_final: 0.7018 (tm-30) REVERT: U 107 TRP cc_start: 0.8568 (OUTLIER) cc_final: 0.7586 (p90) REVERT: V 24 LYS cc_start: 0.8768 (tptp) cc_final: 0.8347 (mtpp) outliers start: 135 outliers final: 97 residues processed: 582 average time/residue: 0.3935 time to fit residues: 372.2893 Evaluate side-chains 568 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 465 time to evaluate : 3.546 ------------------------------------------------------------------------------- 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 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 476 SER Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 183 CYS 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 453 MET 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 66 LEU Chi-restraints excluded: chain D residue 70 VAL 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 234 LEU Chi-restraints excluded: chain E residue 237 THR Chi-restraints excluded: chain E residue 426 VAL Chi-restraints excluded: chain E residue 460 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 61 VAL Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 30 THR 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 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 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 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 49 LEU Chi-restraints excluded: chain P residue 58 THR Chi-restraints excluded: chain Q residue 10 ASP Chi-restraints excluded: chain Q residue 183 CYS 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 453 MET 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 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 234 LEU Chi-restraints excluded: chain S residue 237 THR 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 61 VAL Chi-restraints excluded: chain U residue 7 SER Chi-restraints excluded: chain U residue 30 THR 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 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 95 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 71 optimal weight: 10.0000 chunk 338 optimal weight: 30.0000 chunk 118 optimal weight: 10.0000 chunk 378 optimal weight: 10.0000 chunk 151 optimal weight: 20.0000 chunk 83 optimal weight: 20.0000 chunk 194 optimal weight: 30.0000 chunk 28 optimal weight: 9.9990 chunk 141 optimal weight: 20.0000 chunk 299 optimal weight: 10.0000 chunk 212 optimal weight: 0.8980 overall best weight: 8.1794 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 150 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** ** S 150 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 = 0.3270 r_free = 0.3270 target = 0.088585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.076311 restraints weight = 73092.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.078406 restraints weight = 37554.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.079759 restraints weight = 23722.417| |-----------------------------------------------------------------------------| r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.3384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.125 30908 Z= 0.254 Angle : 0.705 8.728 41992 Z= 0.356 Chirality : 0.047 0.180 4938 Planarity : 0.004 0.047 5192 Dihedral : 8.207 59.226 4914 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 5.90 % Allowed : 17.94 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.13), residues: 3846 helix: 1.35 (0.18), residues: 874 sheet: -1.32 (0.16), residues: 1002 loop : -1.67 (0.13), residues: 1970 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 418 HIS 0.007 0.001 HIS T 7 PHE 0.024 0.002 PHE E 475 TYR 0.018 0.002 TYR C 486 ARG 0.007 0.001 ARG P 27 Details of bonding type rmsd link_NAG-ASN : bond 0.00779 ( 12) link_NAG-ASN : angle 2.21682 ( 36) link_BETA1-4 : bond 0.00391 ( 22) link_BETA1-4 : angle 2.40201 ( 66) link_ALPHA1-3 : bond 0.01081 ( 4) link_ALPHA1-3 : angle 1.62632 ( 12) hydrogen bonds : bond 0.04565 ( 1180) hydrogen bonds : angle 5.47135 ( 3216) link_BETA1-6 : bond 0.00753 ( 4) link_BETA1-6 : angle 2.31147 ( 12) SS BOND : bond 0.00428 ( 30) SS BOND : angle 1.18927 ( 60) covalent geometry : bond 0.00600 (30836) covalent geometry : angle 0.69381 (41806) *********************** 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 672 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 190 poor density : 482 time to evaluate : 3.203 Fit side-chains revert: symmetry clash REVERT: A 13 GLU cc_start: 0.7710 (tm-30) cc_final: 0.6881 (tm-30) REVERT: A 36 LYS cc_start: 0.8366 (tptp) cc_final: 0.8155 (tmtt) REVERT: A 236 VAL cc_start: 0.9430 (OUTLIER) cc_final: 0.9228 (p) REVERT: B 47 LEU cc_start: 0.9047 (mt) cc_final: 0.8774 (mt) REVERT: B 70 VAL cc_start: 0.9086 (t) cc_final: 0.8717 (p) REVERT: B 74 MET cc_start: 0.7175 (tpp) cc_final: 0.6684 (tpp) REVERT: C 473 MET cc_start: 0.7653 (mmp) cc_final: 0.7205 (mtt) REVERT: C 482 ILE cc_start: 0.9111 (mm) cc_final: 0.8827 (mt) REVERT: C 486 TYR cc_start: 0.8367 (t80) cc_final: 0.8060 (t80) REVERT: D 27 ARG cc_start: 0.8396 (ttp80) cc_final: 0.7948 (ttp-110) REVERT: D 74 MET cc_start: 0.8737 (tpp) cc_final: 0.8394 (mmm) REVERT: E 234 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8092 (pp) REVERT: E 373 GLU cc_start: 0.7081 (OUTLIER) cc_final: 0.6483 (tp30) REVERT: E 410 MET cc_start: 0.8360 (ttm) cc_final: 0.8105 (ttm) REVERT: H 62 ASP cc_start: 0.8189 (OUTLIER) cc_final: 0.7868 (t0) REVERT: H 107 TRP cc_start: 0.8446 (OUTLIER) cc_final: 0.7573 (p90) REVERT: L 24 LYS cc_start: 0.8772 (tptp) cc_final: 0.8345 (mtpp) REVERT: O 13 GLU cc_start: 0.7700 (tm-30) cc_final: 0.6865 (tm-30) REVERT: O 36 LYS cc_start: 0.8367 (tptp) cc_final: 0.8156 (tmtt) REVERT: P 47 LEU cc_start: 0.9041 (mt) cc_final: 0.8771 (mt) REVERT: P 70 VAL cc_start: 0.9078 (t) cc_final: 0.8710 (p) REVERT: P 74 MET cc_start: 0.7638 (tpp) cc_final: 0.7381 (tpp) REVERT: Q 473 MET cc_start: 0.7641 (mmp) cc_final: 0.7212 (mtt) REVERT: Q 482 ILE cc_start: 0.9107 (mm) cc_final: 0.8820 (mt) REVERT: Q 486 TYR cc_start: 0.8369 (t80) cc_final: 0.8065 (t80) REVERT: R 27 ARG cc_start: 0.8394 (ttp80) cc_final: 0.7941 (ttp-110) REVERT: R 74 MET cc_start: 0.8743 (tpp) cc_final: 0.8405 (mmm) REVERT: S 175 GLU cc_start: 0.7629 (tp30) cc_final: 0.7384 (tp30) REVERT: S 234 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8102 (pp) REVERT: S 373 GLU cc_start: 0.7087 (OUTLIER) cc_final: 0.6522 (tp30) REVERT: S 399 MET cc_start: 0.7659 (tpp) cc_final: 0.7425 (tpp) REVERT: S 410 MET cc_start: 0.8371 (ttm) cc_final: 0.8131 (ttm) REVERT: T 10 MET cc_start: 0.8437 (ppp) cc_final: 0.8193 (ppp) REVERT: U 62 ASP cc_start: 0.8196 (OUTLIER) cc_final: 0.7874 (t0) REVERT: U 107 TRP cc_start: 0.8442 (OUTLIER) cc_final: 0.7566 (p90) REVERT: V 24 LYS cc_start: 0.8766 (tptp) cc_final: 0.8364 (mtpp) outliers start: 190 outliers final: 144 residues processed: 616 average time/residue: 0.3923 time to fit residues: 396.8418 Evaluate side-chains 610 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 457 time to evaluate : 3.298 ------------------------------------------------------------------------------- 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 195 ILE Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 236 VAL 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 399 MET Chi-restraints excluded: chain A residue 466 LEU 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 49 LEU 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 187 THR Chi-restraints excluded: chain C residue 196 LEU 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 66 LEU Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain E residue 62 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 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 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 61 VAL 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 30 THR 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 H residue 116 THR 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 112 ILE 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 95 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 399 MET Chi-restraints excluded: chain O residue 466 LEU Chi-restraints excluded: chain O residue 473 MET Chi-restraints excluded: chain O residue 476 SER Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain P residue 49 LEU 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 187 THR 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 66 LEU Chi-restraints excluded: chain R residue 70 VAL Chi-restraints excluded: chain S residue 49 GLU Chi-restraints excluded: chain S residue 62 GLU Chi-restraints excluded: chain S residue 91 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 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 305 VAL Chi-restraints excluded: chain S residue 373 GLU Chi-restraints excluded: chain S residue 416 THR 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 61 VAL 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 30 THR 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 U residue 116 THR 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 95 MET Chi-restraints excluded: chain V residue 112 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 110 optimal weight: 20.0000 chunk 207 optimal weight: 0.7980 chunk 366 optimal weight: 10.0000 chunk 273 optimal weight: 10.0000 chunk 230 optimal weight: 3.9990 chunk 128 optimal weight: 8.9990 chunk 17 optimal weight: 4.9990 chunk 278 optimal weight: 20.0000 chunk 118 optimal weight: 9.9990 chunk 81 optimal weight: 6.9990 chunk 37 optimal weight: 20.0000 overall best weight: 5.1588 ------------------------------------------------------------------------------- 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 467 ASN ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 280 HIS ** P 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 201 ASN Q 467 ASN ** R 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 280 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.089659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.077412 restraints weight = 72784.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.079518 restraints weight = 37199.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.080905 restraints weight = 23402.841| |-----------------------------------------------------------------------------| r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.3481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.099 30908 Z= 0.180 Angle : 0.648 8.417 41992 Z= 0.329 Chirality : 0.045 0.184 4938 Planarity : 0.004 0.123 5192 Dihedral : 7.785 59.224 4914 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 5.52 % Allowed : 19.34 % Favored : 75.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.13), residues: 3846 helix: 1.49 (0.18), residues: 866 sheet: -1.23 (0.16), residues: 1002 loop : -1.59 (0.13), residues: 1978 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP S 451 HIS 0.004 0.001 HIS O 207 PHE 0.023 0.002 PHE B 48 TYR 0.012 0.001 TYR Q 486 ARG 0.004 0.000 ARG H 19 Details of bonding type rmsd link_NAG-ASN : bond 0.00586 ( 12) link_NAG-ASN : angle 1.90976 ( 36) link_BETA1-4 : bond 0.00392 ( 22) link_BETA1-4 : angle 2.33040 ( 66) link_ALPHA1-3 : bond 0.01147 ( 4) link_ALPHA1-3 : angle 1.37086 ( 12) hydrogen bonds : bond 0.04176 ( 1180) hydrogen bonds : angle 5.32042 ( 3216) link_BETA1-6 : bond 0.00711 ( 4) link_BETA1-6 : angle 2.11054 ( 12) SS BOND : bond 0.00341 ( 30) SS BOND : angle 1.11010 ( 60) covalent geometry : bond 0.00422 (30836) covalent geometry : angle 0.63788 (41806) *********************** 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 660 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 178 poor density : 482 time to evaluate : 3.382 Fit side-chains REVERT: A 13 GLU cc_start: 0.7532 (tm-30) cc_final: 0.6711 (tm-30) REVERT: A 130 VAL cc_start: 0.9385 (OUTLIER) cc_final: 0.9162 (p) REVERT: A 236 VAL cc_start: 0.9400 (OUTLIER) cc_final: 0.9184 (p) REVERT: B 30 GLU cc_start: 0.7295 (pt0) cc_final: 0.6919 (pt0) REVERT: B 70 VAL cc_start: 0.9092 (t) cc_final: 0.8722 (p) REVERT: B 74 MET cc_start: 0.7462 (tpp) cc_final: 0.6801 (tpp) REVERT: C 473 MET cc_start: 0.7413 (mmp) cc_final: 0.6985 (mtt) REVERT: C 482 ILE cc_start: 0.9171 (mm) cc_final: 0.8836 (mt) REVERT: C 486 TYR cc_start: 0.8252 (t80) cc_final: 0.7821 (t80) REVERT: D 27 ARG cc_start: 0.8347 (ttp80) cc_final: 0.7912 (ttp-110) REVERT: D 74 MET cc_start: 0.8714 (tpp) cc_final: 0.8387 (mmm) REVERT: E 65 ILE cc_start: 0.9214 (OUTLIER) cc_final: 0.8849 (tp) REVERT: E 234 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.7946 (pp) REVERT: E 410 MET cc_start: 0.8325 (ttm) cc_final: 0.8032 (ttm) REVERT: F 10 MET cc_start: 0.8425 (ppp) cc_final: 0.8051 (ppp) REVERT: H 107 TRP cc_start: 0.8454 (OUTLIER) cc_final: 0.7461 (p90) REVERT: L 80 LYS cc_start: 0.8550 (mptt) cc_final: 0.8124 (mmtm) REVERT: O 13 GLU cc_start: 0.7520 (tm-30) cc_final: 0.6703 (tm-30) REVERT: O 205 MET cc_start: 0.8095 (ttm) cc_final: 0.7766 (mtp) REVERT: P 28 GLN cc_start: 0.7283 (tp-100) cc_final: 0.6539 (tp-100) REVERT: P 30 GLU cc_start: 0.7346 (pt0) cc_final: 0.6982 (pt0) REVERT: P 70 VAL cc_start: 0.9086 (t) cc_final: 0.8745 (p) REVERT: Q 473 MET cc_start: 0.7404 (mmp) cc_final: 0.6992 (mtt) REVERT: Q 482 ILE cc_start: 0.9170 (mm) cc_final: 0.8831 (mt) REVERT: Q 486 TYR cc_start: 0.8261 (t80) cc_final: 0.7832 (t80) REVERT: R 27 ARG cc_start: 0.8341 (ttp80) cc_final: 0.7905 (ttp-110) REVERT: R 74 MET cc_start: 0.8724 (tpp) cc_final: 0.8398 (mmm) REVERT: S 65 ILE cc_start: 0.9221 (OUTLIER) cc_final: 0.8852 (tp) REVERT: S 234 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.7966 (pp) REVERT: S 410 MET cc_start: 0.8350 (ttm) cc_final: 0.8062 (ttm) REVERT: U 73 ASP cc_start: 0.7755 (t0) cc_final: 0.7451 (t0) REVERT: U 107 TRP cc_start: 0.8455 (OUTLIER) cc_final: 0.7460 (p90) REVERT: V 24 LYS cc_start: 0.8830 (tptp) cc_final: 0.8390 (mtpp) REVERT: V 80 LYS cc_start: 0.8546 (mptt) cc_final: 0.8119 (mmtm) outliers start: 178 outliers final: 134 residues processed: 611 average time/residue: 0.3834 time to fit residues: 383.9339 Evaluate side-chains 598 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 456 time to evaluate : 3.202 ------------------------------------------------------------------------------- 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 122 LEU 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 236 VAL 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 399 MET Chi-restraints excluded: chain A residue 466 LEU 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 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 461 LEU Chi-restraints excluded: chain C residue 464 ILE 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 15 LEU Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 65 ILE 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 206 VAL 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 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 61 VAL Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 56 ASN 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 195 ILE 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 399 MET Chi-restraints excluded: chain O residue 466 LEU Chi-restraints excluded: chain O residue 473 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 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 461 LEU Chi-restraints excluded: chain Q residue 464 ILE Chi-restraints excluded: chain R residue 12 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 62 GLU Chi-restraints excluded: chain S residue 65 ILE 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 266 THR 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 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 61 VAL Chi-restraints excluded: chain T residue 66 LEU Chi-restraints excluded: chain U residue 7 SER Chi-restraints excluded: chain U residue 30 THR Chi-restraints excluded: chain U residue 56 ASN 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 95 MET Chi-restraints excluded: chain V residue 102 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 35 optimal weight: 9.9990 chunk 243 optimal weight: 4.9990 chunk 309 optimal weight: 10.0000 chunk 168 optimal weight: 30.0000 chunk 249 optimal weight: 20.0000 chunk 68 optimal weight: 10.0000 chunk 220 optimal weight: 5.9990 chunk 297 optimal weight: 20.0000 chunk 45 optimal weight: 7.9990 chunk 70 optimal weight: 20.0000 chunk 319 optimal weight: 10.0000 overall best weight: 7.7992 ------------------------------------------------------------------------------- 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** ** D 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 103 ASN ** 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 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.088727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.076437 restraints weight = 72844.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.078537 restraints weight = 37478.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.079922 restraints weight = 23687.711| |-----------------------------------------------------------------------------| r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.3664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.124 30908 Z= 0.244 Angle : 0.696 9.321 41992 Z= 0.354 Chirality : 0.047 0.191 4938 Planarity : 0.004 0.065 5192 Dihedral : 7.727 58.526 4914 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 5.93 % Allowed : 19.21 % Favored : 74.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.13), residues: 3846 helix: 1.41 (0.18), residues: 874 sheet: -1.29 (0.16), residues: 1002 loop : -1.67 (0.13), residues: 1970 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP Q 418 HIS 0.006 0.001 HIS O 207 PHE 0.025 0.002 PHE S 475 TYR 0.016 0.002 TYR Q 486 ARG 0.004 0.001 ARG Q 2 Details of bonding type rmsd link_NAG-ASN : bond 0.00754 ( 12) link_NAG-ASN : angle 2.09037 ( 36) link_BETA1-4 : bond 0.00346 ( 22) link_BETA1-4 : angle 2.33811 ( 66) link_ALPHA1-3 : bond 0.01071 ( 4) link_ALPHA1-3 : angle 1.84329 ( 12) hydrogen bonds : bond 0.04445 ( 1180) hydrogen bonds : angle 5.35502 ( 3216) link_BETA1-6 : bond 0.00583 ( 4) link_BETA1-6 : angle 1.96023 ( 12) SS BOND : bond 0.00449 ( 30) SS BOND : angle 1.26183 ( 60) covalent geometry : bond 0.00575 (30836) covalent geometry : angle 0.68498 (41806) *********************** 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 651 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 191 poor density : 460 time to evaluate : 3.334 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 GLU cc_start: 0.7531 (tm-30) cc_final: 0.6711 (tm-30) REVERT: A 130 VAL cc_start: 0.9347 (OUTLIER) cc_final: 0.9109 (p) REVERT: A 236 VAL cc_start: 0.9429 (OUTLIER) cc_final: 0.9208 (p) REVERT: B 10 MET cc_start: 0.7962 (OUTLIER) cc_final: 0.7125 (mmm) REVERT: B 30 GLU cc_start: 0.7338 (pt0) cc_final: 0.6958 (pt0) REVERT: B 70 VAL cc_start: 0.9112 (t) cc_final: 0.8746 (p) REVERT: C 473 MET cc_start: 0.7417 (mmp) cc_final: 0.6995 (mtt) REVERT: C 482 ILE cc_start: 0.9176 (mm) cc_final: 0.8836 (mt) REVERT: C 486 TYR cc_start: 0.8347 (t80) cc_final: 0.8075 (t80) REVERT: D 27 ARG cc_start: 0.8365 (ttp80) cc_final: 0.7933 (ttp-110) REVERT: D 74 MET cc_start: 0.8756 (tpp) cc_final: 0.8369 (mmm) REVERT: E 65 ILE cc_start: 0.9230 (OUTLIER) cc_final: 0.8856 (tp) REVERT: E 234 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.7973 (pp) REVERT: E 373 GLU cc_start: 0.7013 (OUTLIER) cc_final: 0.6288 (tp30) REVERT: E 410 MET cc_start: 0.8410 (ttm) cc_final: 0.8124 (ttm) REVERT: H 62 ASP cc_start: 0.8340 (OUTLIER) cc_final: 0.8113 (t0) REVERT: H 107 TRP cc_start: 0.8474 (OUTLIER) cc_final: 0.7620 (p90) REVERT: L 24 LYS cc_start: 0.8796 (tptp) cc_final: 0.8296 (mtpp) REVERT: L 80 LYS cc_start: 0.8534 (mptt) cc_final: 0.8063 (mmtm) REVERT: O 13 GLU cc_start: 0.7523 (tm-30) cc_final: 0.6696 (tm-30) REVERT: P 10 MET cc_start: 0.7892 (OUTLIER) cc_final: 0.7073 (mmm) REVERT: P 30 GLU cc_start: 0.7368 (pt0) cc_final: 0.6986 (pt0) REVERT: P 70 VAL cc_start: 0.9100 (t) cc_final: 0.8729 (p) REVERT: Q 473 MET cc_start: 0.7386 (mmp) cc_final: 0.6994 (mtt) REVERT: Q 482 ILE cc_start: 0.9170 (mm) cc_final: 0.8828 (mt) REVERT: Q 486 TYR cc_start: 0.8354 (t80) cc_final: 0.8080 (t80) REVERT: R 27 ARG cc_start: 0.8357 (ttp80) cc_final: 0.7933 (ttp-110) REVERT: R 74 MET cc_start: 0.8773 (tpp) cc_final: 0.8378 (mmm) REVERT: S 65 ILE cc_start: 0.9233 (OUTLIER) cc_final: 0.8858 (tp) REVERT: S 193 GLU cc_start: 0.7636 (mp0) cc_final: 0.7089 (mp0) REVERT: S 234 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.7985 (pp) REVERT: S 373 GLU cc_start: 0.7021 (OUTLIER) cc_final: 0.6312 (tp30) REVERT: S 410 MET cc_start: 0.8421 (ttm) cc_final: 0.8137 (ttm) REVERT: U 62 ASP cc_start: 0.8341 (OUTLIER) cc_final: 0.8114 (t0) REVERT: U 107 TRP cc_start: 0.8476 (OUTLIER) cc_final: 0.7619 (p90) REVERT: V 80 LYS cc_start: 0.8523 (mptt) cc_final: 0.8056 (mmtm) outliers start: 191 outliers final: 156 residues processed: 600 average time/residue: 0.4209 time to fit residues: 419.1953 Evaluate side-chains 613 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 170 poor density : 443 time to evaluate : 3.563 ------------------------------------------------------------------------------- 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 122 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 236 VAL 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 385 LEU Chi-restraints excluded: chain A residue 399 MET Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 473 MET Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain B residue 10 MET 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 65 ILE Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 41 LEU 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 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 66 LEU Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain E residue 27 HIS Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 65 ILE 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 206 VAL 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 263 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 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 61 VAL 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 30 THR 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 H residue 116 THR 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 95 THR Chi-restraints excluded: chain O residue 163 THR Chi-restraints excluded: chain O residue 194 MET Chi-restraints excluded: chain O residue 195 ILE 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 385 LEU Chi-restraints excluded: chain O residue 399 MET Chi-restraints excluded: chain O residue 466 LEU Chi-restraints excluded: chain O residue 473 MET Chi-restraints excluded: chain O residue 476 SER Chi-restraints excluded: chain P residue 10 MET 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 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 41 LEU 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 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 66 LEU Chi-restraints excluded: chain R residue 70 VAL 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 62 GLU Chi-restraints excluded: chain S residue 65 ILE 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 206 VAL 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 356 VAL Chi-restraints excluded: chain S residue 373 GLU Chi-restraints excluded: chain S residue 416 THR 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 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 61 VAL 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 30 THR 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 U residue 116 THR 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 95 MET Chi-restraints excluded: chain V residue 102 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 242 optimal weight: 5.9990 chunk 212 optimal weight: 7.9990 chunk 338 optimal weight: 8.9990 chunk 243 optimal weight: 9.9990 chunk 305 optimal weight: 5.9990 chunk 135 optimal weight: 9.9990 chunk 30 optimal weight: 9.9990 chunk 206 optimal weight: 5.9990 chunk 148 optimal weight: 8.9990 chunk 68 optimal weight: 5.9990 chunk 119 optimal weight: 0.5980 overall best weight: 4.9188 ------------------------------------------------------------------------------- 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** ** S 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 492 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.089465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.077282 restraints weight = 72723.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.079397 restraints weight = 37186.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.080796 restraints weight = 23421.728| |-----------------------------------------------------------------------------| r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.3707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 30908 Z= 0.174 Angle : 0.653 10.711 41992 Z= 0.330 Chirality : 0.045 0.198 4938 Planarity : 0.004 0.055 5192 Dihedral : 7.457 57.065 4914 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 5.77 % Allowed : 19.40 % Favored : 74.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.13), residues: 3846 helix: 1.56 (0.18), residues: 866 sheet: -1.21 (0.16), residues: 1002 loop : -1.58 (0.13), residues: 1978 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 451 HIS 0.005 0.001 HIS O 242 PHE 0.024 0.002 PHE B 48 TYR 0.011 0.001 TYR Q 486 ARG 0.004 0.000 ARG H 19 Details of bonding type rmsd link_NAG-ASN : bond 0.00551 ( 12) link_NAG-ASN : angle 1.88613 ( 36) link_BETA1-4 : bond 0.00387 ( 22) link_BETA1-4 : angle 2.23633 ( 66) link_ALPHA1-3 : bond 0.01136 ( 4) link_ALPHA1-3 : angle 1.50773 ( 12) hydrogen bonds : bond 0.04161 ( 1180) hydrogen bonds : angle 5.24023 ( 3216) link_BETA1-6 : bond 0.00601 ( 4) link_BETA1-6 : angle 1.78859 ( 12) SS BOND : bond 0.00344 ( 30) SS BOND : angle 1.03743 ( 60) covalent geometry : bond 0.00407 (30836) covalent geometry : angle 0.64315 (41806) *********************** 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 657 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 186 poor density : 471 time to evaluate : 3.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 GLU cc_start: 0.7520 (tm-30) cc_final: 0.6700 (tm-30) REVERT: A 130 VAL cc_start: 0.9349 (OUTLIER) cc_final: 0.9112 (p) REVERT: A 236 VAL cc_start: 0.9408 (OUTLIER) cc_final: 0.9187 (p) REVERT: A 285 LEU cc_start: 0.9541 (OUTLIER) cc_final: 0.9146 (mt) REVERT: B 30 GLU cc_start: 0.7329 (pt0) cc_final: 0.6924 (pt0) REVERT: B 70 VAL cc_start: 0.9134 (t) cc_final: 0.8745 (p) REVERT: C 473 MET cc_start: 0.7392 (mmp) cc_final: 0.6889 (mtt) REVERT: C 482 ILE cc_start: 0.9177 (mm) cc_final: 0.8839 (mt) REVERT: C 486 TYR cc_start: 0.8390 (t80) cc_final: 0.8170 (t80) REVERT: D 27 ARG cc_start: 0.8338 (ttp80) cc_final: 0.7918 (ttp-110) REVERT: D 74 MET cc_start: 0.8689 (tpp) cc_final: 0.8358 (mmm) REVERT: E 65 ILE cc_start: 0.9192 (OUTLIER) cc_final: 0.8808 (tp) REVERT: E 234 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.7895 (pp) REVERT: E 373 GLU cc_start: 0.6958 (OUTLIER) cc_final: 0.6225 (tp30) REVERT: E 410 MET cc_start: 0.8358 (ttm) cc_final: 0.8046 (ttm) REVERT: F 10 MET cc_start: 0.8536 (ppp) cc_final: 0.8227 (ppp) REVERT: H 62 ASP cc_start: 0.8172 (OUTLIER) cc_final: 0.7919 (t0) REVERT: H 107 TRP cc_start: 0.8471 (OUTLIER) cc_final: 0.7514 (p90) REVERT: L 24 LYS cc_start: 0.8775 (tptp) cc_final: 0.8298 (mtpp) REVERT: L 80 LYS cc_start: 0.8571 (mptt) cc_final: 0.8052 (mmtm) REVERT: O 13 GLU cc_start: 0.7518 (tm-30) cc_final: 0.6705 (tm-30) REVERT: O 205 MET cc_start: 0.8073 (ttm) cc_final: 0.7817 (mtp) REVERT: O 285 LEU cc_start: 0.9577 (OUTLIER) cc_final: 0.9210 (mt) REVERT: P 30 GLU cc_start: 0.7323 (pt0) cc_final: 0.6846 (pt0) REVERT: P 70 VAL cc_start: 0.9119 (t) cc_final: 0.8759 (p) REVERT: Q 473 MET cc_start: 0.7371 (mmp) cc_final: 0.6891 (mtt) REVERT: Q 482 ILE cc_start: 0.9174 (mm) cc_final: 0.8829 (mt) REVERT: Q 486 TYR cc_start: 0.8389 (t80) cc_final: 0.8173 (t80) REVERT: R 27 ARG cc_start: 0.8334 (ttp80) cc_final: 0.7906 (ttp-110) REVERT: R 74 MET cc_start: 0.8706 (tpp) cc_final: 0.8362 (mmm) REVERT: S 65 ILE cc_start: 0.9201 (OUTLIER) cc_final: 0.8810 (tp) REVERT: S 193 GLU cc_start: 0.7659 (mp0) cc_final: 0.7379 (mp0) REVERT: S 234 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.7902 (pp) REVERT: S 410 MET cc_start: 0.8344 (ttm) cc_final: 0.8058 (ttm) REVERT: U 107 TRP cc_start: 0.8478 (OUTLIER) cc_final: 0.7520 (p90) REVERT: V 24 LYS cc_start: 0.8966 (tptp) cc_final: 0.8436 (mtpp) REVERT: V 80 LYS cc_start: 0.8534 (mptt) cc_final: 0.8051 (mmtm) outliers start: 186 outliers final: 151 residues processed: 609 average time/residue: 0.4308 time to fit residues: 435.2469 Evaluate side-chains 613 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 450 time to evaluate : 3.892 ------------------------------------------------------------------------------- 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 233 GLU Chi-restraints excluded: chain A residue 236 VAL 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 376 ILE Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 399 MET Chi-restraints excluded: chain A residue 466 LEU 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 B residue 67 LEU Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 183 CYS Chi-restraints excluded: chain C residue 187 THR 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 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 66 LEU Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain E residue 27 HIS Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 65 ILE 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 206 VAL 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 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 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 30 THR 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 H residue 116 THR 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 163 THR Chi-restraints excluded: chain O residue 194 MET 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 376 ILE Chi-restraints excluded: chain O residue 385 LEU Chi-restraints excluded: chain O residue 399 MET Chi-restraints excluded: chain O residue 466 LEU Chi-restraints excluded: chain O residue 473 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 P residue 67 LEU Chi-restraints excluded: chain Q residue 10 ASP Chi-restraints excluded: chain Q residue 41 LEU Chi-restraints excluded: chain Q residue 183 CYS Chi-restraints excluded: chain Q residue 187 THR 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 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 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 62 GLU Chi-restraints excluded: chain S residue 65 ILE 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 206 VAL 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 263 THR Chi-restraints excluded: chain S residue 266 THR Chi-restraints excluded: chain S residue 356 VAL Chi-restraints excluded: chain S residue 416 THR 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 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 30 THR Chi-restraints excluded: chain U residue 56 ASN 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 U residue 116 THR 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 88 ASP 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 99 optimal weight: 6.9990 chunk 230 optimal weight: 5.9990 chunk 328 optimal weight: 6.9990 chunk 358 optimal weight: 6.9990 chunk 236 optimal weight: 5.9990 chunk 195 optimal weight: 3.9990 chunk 65 optimal weight: 8.9990 chunk 343 optimal weight: 10.0000 chunk 242 optimal weight: 7.9990 chunk 7 optimal weight: 0.9990 chunk 286 optimal weight: 20.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 492 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 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.089632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.077437 restraints weight = 72419.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.079562 restraints weight = 37124.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.080941 restraints weight = 23360.725| |-----------------------------------------------------------------------------| r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.3773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 30908 Z= 0.172 Angle : 0.645 10.214 41992 Z= 0.326 Chirality : 0.045 0.182 4938 Planarity : 0.004 0.043 5192 Dihedral : 7.260 58.108 4914 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 5.56 % Allowed : 19.34 % Favored : 75.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.13), residues: 3846 helix: 1.61 (0.18), residues: 866 sheet: -1.16 (0.16), residues: 1002 loop : -1.53 (0.13), residues: 1978 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 451 HIS 0.005 0.001 HIS O 242 PHE 0.022 0.002 PHE S 475 TYR 0.013 0.001 TYR Q 486 ARG 0.005 0.000 ARG L 109 Details of bonding type rmsd link_NAG-ASN : bond 0.00530 ( 12) link_NAG-ASN : angle 1.84872 ( 36) link_BETA1-4 : bond 0.00379 ( 22) link_BETA1-4 : angle 2.20688 ( 66) link_ALPHA1-3 : bond 0.01103 ( 4) link_ALPHA1-3 : angle 1.63682 ( 12) hydrogen bonds : bond 0.04068 ( 1180) hydrogen bonds : angle 5.18665 ( 3216) link_BETA1-6 : bond 0.00552 ( 4) link_BETA1-6 : angle 1.73690 ( 12) SS BOND : bond 0.00347 ( 30) SS BOND : angle 1.03729 ( 60) covalent geometry : bond 0.00403 (30836) covalent geometry : angle 0.63525 (41806) *********************** 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 639 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 179 poor density : 460 time to evaluate : 3.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 GLU cc_start: 0.7526 (tm-30) cc_final: 0.6703 (tm-30) REVERT: A 130 VAL cc_start: 0.9346 (OUTLIER) cc_final: 0.9111 (p) REVERT: A 236 VAL cc_start: 0.9387 (OUTLIER) cc_final: 0.9174 (p) REVERT: A 242 HIS cc_start: 0.8315 (OUTLIER) cc_final: 0.7648 (p-80) REVERT: A 285 LEU cc_start: 0.9541 (OUTLIER) cc_final: 0.9146 (mt) REVERT: B 30 GLU cc_start: 0.7319 (pt0) cc_final: 0.6904 (pt0) REVERT: B 70 VAL cc_start: 0.9174 (t) cc_final: 0.8790 (p) REVERT: C 473 MET cc_start: 0.7375 (mmp) cc_final: 0.6896 (mtt) REVERT: C 482 ILE cc_start: 0.9175 (mm) cc_final: 0.8835 (mt) REVERT: D 27 ARG cc_start: 0.8370 (ttp80) cc_final: 0.7930 (ttp-110) REVERT: D 68 MET cc_start: 0.8419 (mmm) cc_final: 0.7844 (mmt) REVERT: D 74 MET cc_start: 0.8674 (tpp) cc_final: 0.8383 (mmm) REVERT: E 65 ILE cc_start: 0.9166 (OUTLIER) cc_final: 0.8770 (tp) REVERT: E 234 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.7640 (pp) REVERT: E 373 GLU cc_start: 0.6983 (OUTLIER) cc_final: 0.6238 (tp30) REVERT: E 410 MET cc_start: 0.8334 (ttm) cc_final: 0.8033 (ttm) REVERT: F 10 MET cc_start: 0.8561 (ppp) cc_final: 0.8147 (ppp) REVERT: H 107 TRP cc_start: 0.8472 (OUTLIER) cc_final: 0.7451 (p90) REVERT: L 24 LYS cc_start: 0.8844 (tptp) cc_final: 0.8372 (mtpp) REVERT: L 80 LYS cc_start: 0.8622 (mptt) cc_final: 0.8101 (mmtm) REVERT: O 13 GLU cc_start: 0.7527 (tm-30) cc_final: 0.6698 (tm-30) REVERT: O 205 MET cc_start: 0.8063 (ttm) cc_final: 0.7799 (mtp) REVERT: O 285 LEU cc_start: 0.9549 (OUTLIER) cc_final: 0.9160 (mt) REVERT: P 30 GLU cc_start: 0.7343 (pt0) cc_final: 0.6872 (pt0) REVERT: P 70 VAL cc_start: 0.9176 (t) cc_final: 0.8803 (p) REVERT: Q 473 MET cc_start: 0.7358 (mmp) cc_final: 0.6994 (mtt) REVERT: Q 482 ILE cc_start: 0.9148 (mm) cc_final: 0.8832 (mt) REVERT: R 27 ARG cc_start: 0.8362 (ttp80) cc_final: 0.7920 (ttp-110) REVERT: R 68 MET cc_start: 0.8429 (mmm) cc_final: 0.7854 (mmt) REVERT: R 74 MET cc_start: 0.8688 (tpp) cc_final: 0.8386 (mmm) REVERT: S 65 ILE cc_start: 0.9180 (OUTLIER) cc_final: 0.8781 (tp) REVERT: S 193 GLU cc_start: 0.7610 (mp0) cc_final: 0.7343 (mp0) REVERT: S 234 LEU cc_start: 0.8240 (OUTLIER) cc_final: 0.7661 (pp) REVERT: S 410 MET cc_start: 0.8355 (ttm) cc_final: 0.8023 (ttm) REVERT: U 107 TRP cc_start: 0.8496 (OUTLIER) cc_final: 0.7459 (p90) REVERT: V 24 LYS cc_start: 0.8835 (tptp) cc_final: 0.8258 (mtpp) REVERT: V 80 LYS cc_start: 0.8578 (mptt) cc_final: 0.8100 (mmtm) outliers start: 179 outliers final: 151 residues processed: 596 average time/residue: 0.3954 time to fit residues: 388.2376 Evaluate side-chains 611 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 448 time to evaluate : 3.706 ------------------------------------------------------------------------------- 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 233 GLU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 242 HIS 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 376 ILE Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 399 MET Chi-restraints excluded: chain A residue 466 LEU 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 67 LEU Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 183 CYS Chi-restraints excluded: chain C residue 187 THR 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 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 C residue 485 LEU 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 31 VAL Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 65 ILE 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 206 VAL 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 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 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 30 THR Chi-restraints excluded: chain H residue 56 ASN 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 H residue 116 THR 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 122 LEU Chi-restraints excluded: chain O residue 163 THR Chi-restraints excluded: chain O residue 194 MET 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 376 ILE Chi-restraints excluded: chain O residue 385 LEU Chi-restraints excluded: chain O residue 399 MET Chi-restraints excluded: chain O residue 466 LEU 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 P residue 67 LEU Chi-restraints excluded: chain Q residue 10 ASP Chi-restraints excluded: chain Q residue 41 LEU Chi-restraints excluded: chain Q residue 183 CYS Chi-restraints excluded: chain Q residue 187 THR 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 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 Q residue 485 LEU Chi-restraints excluded: chain R residue 12 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 62 GLU Chi-restraints excluded: chain S residue 65 ILE 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 206 VAL 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 263 THR Chi-restraints excluded: chain S residue 266 THR Chi-restraints excluded: chain S residue 356 VAL Chi-restraints excluded: chain S residue 416 THR Chi-restraints excluded: chain S residue 426 VAL 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 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 30 THR Chi-restraints excluded: chain U residue 56 ASN 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 U residue 116 THR 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 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 116 optimal weight: 9.9990 chunk 306 optimal weight: 10.0000 chunk 74 optimal weight: 10.0000 chunk 10 optimal weight: 5.9990 chunk 303 optimal weight: 7.9990 chunk 354 optimal weight: 20.0000 chunk 71 optimal weight: 10.0000 chunk 78 optimal weight: 2.9990 chunk 277 optimal weight: 10.0000 chunk 86 optimal weight: 7.9990 chunk 42 optimal weight: 8.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- 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 = 0.3276 r_free = 0.3276 target = 0.088891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.076704 restraints weight = 72869.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.078819 restraints weight = 37295.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.080197 restraints weight = 23460.882| |-----------------------------------------------------------------------------| r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.3846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.108 30908 Z= 0.217 Angle : 0.677 9.755 41992 Z= 0.343 Chirality : 0.046 0.173 4938 Planarity : 0.004 0.042 5192 Dihedral : 7.299 59.787 4914 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 5.31 % Allowed : 19.86 % Favored : 74.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.13), residues: 3846 helix: 1.58 (0.18), residues: 866 sheet: -1.21 (0.16), residues: 1002 loop : -1.56 (0.13), residues: 1978 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 418 HIS 0.006 0.001 HIS T 7 PHE 0.026 0.002 PHE P 48 TYR 0.012 0.002 TYR E 176 ARG 0.005 0.001 ARG P 27 Details of bonding type rmsd link_NAG-ASN : bond 0.00650 ( 12) link_NAG-ASN : angle 1.94391 ( 36) link_BETA1-4 : bond 0.00361 ( 22) link_BETA1-4 : angle 2.23111 ( 66) link_ALPHA1-3 : bond 0.01077 ( 4) link_ALPHA1-3 : angle 1.80903 ( 12) hydrogen bonds : bond 0.04276 ( 1180) hydrogen bonds : angle 5.24696 ( 3216) link_BETA1-6 : bond 0.00475 ( 4) link_BETA1-6 : angle 1.84234 ( 12) SS BOND : bond 0.00389 ( 30) SS BOND : angle 1.15583 ( 60) covalent geometry : bond 0.00511 (30836) covalent geometry : angle 0.66781 (41806) ********************** 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 627 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 171 poor density : 456 time to evaluate : 3.433 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 GLU cc_start: 0.7511 (tm-30) cc_final: 0.6693 (tm-30) REVERT: A 130 VAL cc_start: 0.9349 (OUTLIER) cc_final: 0.9114 (p) REVERT: A 236 VAL cc_start: 0.9420 (OUTLIER) cc_final: 0.9206 (p) REVERT: A 242 HIS cc_start: 0.8232 (OUTLIER) cc_final: 0.7601 (p-80) REVERT: A 285 LEU cc_start: 0.9536 (OUTLIER) cc_final: 0.9130 (mt) REVERT: B 30 GLU cc_start: 0.7350 (pt0) cc_final: 0.6940 (pt0) REVERT: B 70 VAL cc_start: 0.9190 (t) cc_final: 0.8814 (p) REVERT: C 473 MET cc_start: 0.7388 (mmp) cc_final: 0.6891 (mtt) REVERT: C 482 ILE cc_start: 0.9173 (mm) cc_final: 0.8844 (mt) REVERT: D 27 ARG cc_start: 0.8322 (ttp80) cc_final: 0.7898 (ttp-110) REVERT: D 74 MET cc_start: 0.8703 (tpp) cc_final: 0.8402 (mmm) REVERT: E 65 ILE cc_start: 0.9179 (OUTLIER) cc_final: 0.8788 (tp) REVERT: E 193 GLU cc_start: 0.7698 (mp0) cc_final: 0.7163 (mp0) REVERT: E 234 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.7927 (pp) REVERT: E 373 GLU cc_start: 0.6958 (OUTLIER) cc_final: 0.6210 (tp30) REVERT: E 410 MET cc_start: 0.8418 (ttm) cc_final: 0.8103 (ttm) REVERT: F 10 MET cc_start: 0.8662 (ppp) cc_final: 0.8241 (ppp) REVERT: H 107 TRP cc_start: 0.8511 (OUTLIER) cc_final: 0.7566 (p90) REVERT: L 24 LYS cc_start: 0.8859 (tptp) cc_final: 0.8395 (mtpp) REVERT: L 80 LYS cc_start: 0.8603 (mptt) cc_final: 0.8085 (mmtm) REVERT: O 13 GLU cc_start: 0.7513 (tm-30) cc_final: 0.6692 (tm-30) REVERT: O 242 HIS cc_start: 0.8304 (OUTLIER) cc_final: 0.7675 (p-80) REVERT: O 285 LEU cc_start: 0.9545 (OUTLIER) cc_final: 0.9141 (mt) REVERT: P 27 ARG cc_start: 0.7233 (ptt-90) cc_final: 0.6996 (ptt-90) REVERT: P 30 GLU cc_start: 0.7398 (pt0) cc_final: 0.6963 (pt0) REVERT: P 70 VAL cc_start: 0.9183 (t) cc_final: 0.8814 (p) REVERT: Q 473 MET cc_start: 0.7374 (mmp) cc_final: 0.6911 (mtt) REVERT: Q 482 ILE cc_start: 0.9170 (mm) cc_final: 0.8835 (mt) REVERT: R 27 ARG cc_start: 0.8311 (ttp80) cc_final: 0.7883 (ttp-110) REVERT: R 74 MET cc_start: 0.8722 (tpp) cc_final: 0.8407 (mmm) REVERT: S 65 ILE cc_start: 0.9207 (OUTLIER) cc_final: 0.8816 (tp) REVERT: S 193 GLU cc_start: 0.7605 (mp0) cc_final: 0.7328 (mp0) REVERT: S 234 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.7912 (pp) REVERT: S 410 MET cc_start: 0.8413 (ttm) cc_final: 0.8102 (ttm) REVERT: U 107 TRP cc_start: 0.8538 (OUTLIER) cc_final: 0.7586 (p90) REVERT: V 24 LYS cc_start: 0.8948 (tptp) cc_final: 0.8392 (mtpp) REVERT: V 80 LYS cc_start: 0.8563 (mptt) cc_final: 0.8085 (mmtm) REVERT: V 83 ARG cc_start: 0.7974 (mtm110) cc_final: 0.7229 (mpp80) outliers start: 171 outliers final: 152 residues processed: 588 average time/residue: 0.4134 time to fit residues: 400.9063 Evaluate side-chains 613 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 165 poor density : 448 time to evaluate : 4.086 ------------------------------------------------------------------------------- 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 233 GLU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 242 HIS 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 376 ILE Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 399 MET Chi-restraints excluded: chain A residue 466 LEU 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 67 LEU Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 183 CYS Chi-restraints excluded: chain C residue 187 THR 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 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 C residue 485 LEU Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain E residue 27 HIS Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 65 ILE 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 206 VAL 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 263 THR Chi-restraints excluded: chain E residue 266 THR Chi-restraints excluded: chain E residue 317 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 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 30 THR Chi-restraints excluded: chain H residue 56 ASN 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 H residue 116 THR 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 122 LEU Chi-restraints excluded: chain O residue 163 THR Chi-restraints excluded: chain O residue 194 MET Chi-restraints excluded: chain O residue 195 ILE Chi-restraints excluded: chain O residue 233 GLU Chi-restraints excluded: chain O residue 242 HIS 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 376 ILE Chi-restraints excluded: chain O residue 385 LEU Chi-restraints excluded: chain O residue 399 MET Chi-restraints excluded: chain O residue 466 LEU 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 P residue 67 LEU Chi-restraints excluded: chain Q residue 10 ASP Chi-restraints excluded: chain Q residue 41 LEU Chi-restraints excluded: chain Q residue 183 CYS Chi-restraints excluded: chain Q residue 187 THR 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 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 Q residue 485 LEU Chi-restraints excluded: chain R residue 12 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 62 GLU Chi-restraints excluded: chain S residue 65 ILE 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 206 VAL 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 356 VAL Chi-restraints excluded: chain S residue 416 THR Chi-restraints excluded: chain S residue 426 VAL 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 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 30 THR Chi-restraints excluded: chain U residue 56 ASN 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 U residue 116 THR 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 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 98 optimal weight: 5.9990 chunk 228 optimal weight: 0.3980 chunk 362 optimal weight: 4.9990 chunk 368 optimal weight: 8.9990 chunk 35 optimal weight: 6.9990 chunk 224 optimal weight: 5.9990 chunk 138 optimal weight: 20.0000 chunk 30 optimal weight: 9.9990 chunk 378 optimal weight: 10.0000 chunk 219 optimal weight: 7.9990 chunk 199 optimal weight: 0.3980 overall best weight: 3.5586 ------------------------------------------------------------------------------- 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 = 0.3302 r_free = 0.3302 target = 0.090289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.078096 restraints weight = 72500.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.080276 restraints weight = 36434.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.081713 restraints weight = 22603.170| |-----------------------------------------------------------------------------| r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.3870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 30908 Z= 0.146 Angle : 0.634 10.295 41992 Z= 0.320 Chirality : 0.044 0.179 4938 Planarity : 0.004 0.040 5192 Dihedral : 7.046 58.222 4914 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 5.18 % Allowed : 20.20 % Favored : 74.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.13), residues: 3846 helix: 1.67 (0.18), residues: 866 sheet: -1.18 (0.16), residues: 1038 loop : -1.44 (0.13), residues: 1942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 451 HIS 0.005 0.001 HIS O 242 PHE 0.023 0.001 PHE R 64 TYR 0.009 0.001 TYR C 324 ARG 0.005 0.000 ARG U 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00424 ( 12) link_NAG-ASN : angle 1.74088 ( 36) link_BETA1-4 : bond 0.00432 ( 22) link_BETA1-4 : angle 2.16914 ( 66) link_ALPHA1-3 : bond 0.01119 ( 4) link_ALPHA1-3 : angle 1.55707 ( 12) hydrogen bonds : bond 0.03915 ( 1180) hydrogen bonds : angle 5.10680 ( 3216) link_BETA1-6 : bond 0.00557 ( 4) link_BETA1-6 : angle 1.75070 ( 12) SS BOND : bond 0.00307 ( 30) SS BOND : angle 0.96071 ( 60) covalent geometry : bond 0.00339 (30836) covalent geometry : angle 0.62521 (41806) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10929.92 seconds wall clock time: 195 minutes 32.39 seconds (11732.39 seconds total)