Starting phenix.real_space_refine on Mon Aug 25 17:45:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jn1_36429/08_2025/8jn1_36429.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jn1_36429/08_2025/8jn1_36429.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 { model { file = "/net/cci-nas-00/data/ceres_data/8jn1_36429/08_2025/8jn1_36429.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jn1_36429/08_2025/8jn1_36429.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jn1_36429/08_2025/8jn1_36429.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jn1_36429/08_2025/8jn1_36429.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 204 5.16 5 C 19042 2.51 5 N 5062 2.21 5 O 5662 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29970 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 3760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3760 Classifications: {'peptide': 493} Link IDs: {'PTRANS': 14, 'TRANS': 478} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "B" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 587 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: 3760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3760 Classifications: {'peptide': 493} Link IDs: {'PTRANS': 14, 'TRANS': 478} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "D" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 587 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: 3760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3760 Classifications: {'peptide': 493} Link IDs: {'PTRANS': 14, 'TRANS': 478} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "F" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 587 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: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 957 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "L" Number of atoms: 797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 797 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 7, 'TRANS': 101} Chain: "G" 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: "I" 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: "J" 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: "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: 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: "N" 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: "O" Number of atoms: 3760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3760 Classifications: {'peptide': 493} Link IDs: {'PTRANS': 14, 'TRANS': 478} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "P" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 587 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: 3760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3760 Classifications: {'peptide': 493} Link IDs: {'PTRANS': 14, 'TRANS': 478} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "R" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 587 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: 3760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3760 Classifications: {'peptide': 493} Link IDs: {'PTRANS': 14, 'TRANS': 478} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "T" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 587 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: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 957 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "V" Number of atoms: 797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 797 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 7, 'TRANS': 101} Chain: "W" 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: "X" 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: "Y" 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: "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: 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: "1" 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 Time building chain proxies: 5.61, per 1000 atoms: 0.19 Number of scatterers: 29970 At special positions: 0 Unit cell: (160.578, 238.434, 111.918, 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 204 16.00 O 5662 8.00 N 5062 7.00 C 19042 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=38, 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=2.03 Simple disulfide: pdb=" SG CYS A 74 " - pdb=" SG CYS A 105 " distance=2.03 Simple disulfide: pdb=" SG CYS A 92 " - pdb=" SG CYS A 116 " distance=2.04 Simple disulfide: pdb=" SG CYS A 183 " - pdb=" SG CYS A 283 " distance=2.03 Simple disulfide: pdb=" SG CYS A 300 " - pdb=" SG CYS A 331 " 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=2.05 Simple disulfide: pdb=" SG CYS C 183 " - pdb=" SG CYS C 283 " distance=2.03 Simple disulfide: pdb=" SG CYS C 300 " - pdb=" SG CYS C 331 " distance=2.02 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=2.02 Simple disulfide: pdb=" SG CYS E 74 " - pdb=" SG CYS E 105 " 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 22 " - pdb=" SG CYS L 89 " 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=2.03 Simple disulfide: pdb=" SG CYS O 74 " - pdb=" SG CYS O 105 " distance=2.03 Simple disulfide: pdb=" SG CYS O 92 " - pdb=" SG CYS O 116 " distance=2.04 Simple disulfide: pdb=" SG CYS O 183 " - pdb=" SG CYS O 283 " distance=2.03 Simple disulfide: pdb=" SG CYS O 300 " - pdb=" SG CYS O 331 " 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=2.05 Simple disulfide: pdb=" SG CYS Q 183 " - pdb=" SG CYS Q 283 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 300 " - pdb=" SG CYS Q 331 " distance=2.02 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=2.02 Simple disulfide: pdb=" SG CYS S 74 " - pdb=" SG CYS S 105 " 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 22 " - pdb=" SG CYS V 89 " 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 BETA1-4 " NAG 0 1 " - " NAG 0 2 " " NAG 0 2 " - " BMA 0 3 " " NAG 1 1 " - " NAG 1 2 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " NAG-ASN " NAG 0 1 " - " ASN S 67 " " NAG 1 1 " - " ASN S 153 " " NAG G 1 " - " ASN A 67 " " NAG I 1 " - " ASN A 153 " " NAG J 1 " - " ASN C 67 " " NAG K 1 " - " ASN C 153 " " NAG M 1 " - " ASN E 67 " " NAG N 1 " - " ASN E 153 " " NAG W 1 " - " ASN O 67 " " NAG X 1 " - " ASN O 153 " " NAG Y 1 " - " ASN Q 67 " " NAG Z 1 " - " ASN Q 153 " Time building additional restraints: 2.18 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 1.2 microseconds 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6948 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 72 sheets defined 26.7% alpha, 26.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.14 Creating SS restraints... Processing helix chain 'A' and resid 184 through 188 removed outlier: 3.592A pdb=" N THR A 187 " --> pdb=" O SER A 184 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLY A 188 " --> pdb=" O PRO A 185 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 184 through 188' Processing helix chain 'A' and resid 190 through 194 Processing helix chain 'A' and resid 207 through 212 removed outlier: 3.694A pdb=" N PHE A 211 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE A 212 " --> pdb=" O ARG A 208 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 207 through 212' Processing helix chain 'A' and resid 231 through 235 removed outlier: 3.697A pdb=" N LEU A 234 " --> pdb=" O LYS A 231 " (cutoff:3.500A) 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 Processing helix chain 'A' and resid 426 through 446 Processing helix chain 'A' and resid 450 through 467 removed outlier: 3.891A pdb=" N ILE A 455 " --> pdb=" O TRP A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 491 Processing helix chain 'B' and resid 20 through 25 Processing helix chain 'B' and resid 26 through 39 Processing helix chain 'B' and resid 40 through 52 removed outlier: 4.247A pdb=" N ILE B 44 " --> pdb=" O PRO B 40 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU B 45 " --> pdb=" O GLY B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 71 Processing helix chain 'C' and resid 190 through 192 No H-bonds generated for 'chain 'C' and resid 190 through 192' Processing helix chain 'C' and resid 208 through 214 Processing helix chain 'C' and resid 231 through 236 removed outlier: 3.905A pdb=" N LEU C 234 " --> pdb=" O LYS C 231 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU C 235 " --> pdb=" O LYS C 232 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL C 236 " --> pdb=" O GLU C 233 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 231 through 236' Processing helix chain 'C' and resid 254 through 262 Processing helix chain 'C' and resid 394 through 414 Processing helix chain 'C' and resid 415 through 420 removed outlier: 3.920A pdb=" N TRP C 418 " --> pdb=" O ASP C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 425 through 447 Processing helix chain 'C' and resid 450 through 467 Processing helix chain 'C' and resid 470 through 491 Processing helix chain 'D' and resid 20 through 39 removed outlier: 4.113A pdb=" N TRP D 26 " --> pdb=" O ALA D 22 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N GLN D 28 " --> pdb=" O GLY D 24 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N ILE D 29 " --> pdb=" O ALA D 25 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 52 removed outlier: 3.727A pdb=" N ILE D 44 " --> pdb=" O PRO D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 71 Processing helix chain 'E' and resid 82 through 86 Processing helix chain 'E' and resid 131 through 135 removed outlier: 3.552A pdb=" N LEU E 135 " --> pdb=" O HIS E 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 185 through 188 Processing helix chain 'E' and resid 208 through 213 Processing helix chain 'E' and resid 231 through 234 removed outlier: 3.531A pdb=" N LEU E 234 " --> pdb=" O LYS 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 414 through 420 removed outlier: 3.874A pdb=" N TRP E 418 " --> pdb=" O ASP E 415 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASP E 419 " --> pdb=" O THR E 416 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N PHE E 420 " --> pdb=" O ALA E 417 " (cutoff:3.500A) Processing helix chain 'E' and resid 425 through 446 removed outlier: 3.507A pdb=" N LEU E 445 " --> pdb=" O ALA E 441 " (cutoff:3.500A) Processing helix chain 'E' and resid 450 through 467 removed outlier: 3.741A pdb=" N ILE E 455 " --> pdb=" O TRP E 451 " (cutoff:3.500A) Processing helix chain 'E' and resid 470 through 491 removed outlier: 4.165A pdb=" N SER E 476 " --> pdb=" O SER E 472 " (cutoff:3.500A) Processing helix chain 'F' and resid 20 through 39 removed outlier: 4.329A pdb=" N TRP F 26 " --> pdb=" O ALA F 22 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N GLN F 28 " --> pdb=" O GLY F 24 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N ILE F 29 " --> pdb=" O ALA F 25 " (cutoff:3.500A) Processing helix chain 'F' and resid 40 through 52 removed outlier: 3.869A pdb=" N ILE F 44 " --> pdb=" O PRO F 40 " (cutoff:3.500A) Processing helix chain 'F' and resid 56 through 75 Proline residue: F 72 - end of helix Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'L' and resid 80 through 84 removed outlier: 3.629A pdb=" N GLU L 84 " --> pdb=" O SER L 81 " (cutoff:3.500A) Processing helix chain 'O' and resid 184 through 188 removed outlier: 3.592A pdb=" N THR O 187 " --> pdb=" O SER O 184 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLY O 188 " --> pdb=" O PRO O 185 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 184 through 188' Processing helix chain 'O' and resid 190 through 194 Processing helix chain 'O' and resid 207 through 212 removed outlier: 3.694A pdb=" N PHE O 211 " --> pdb=" O HIS O 207 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE O 212 " --> pdb=" O ARG O 208 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 207 through 212' Processing helix chain 'O' and resid 231 through 235 removed outlier: 3.697A pdb=" N LEU O 234 " --> pdb=" O LYS O 231 " (cutoff:3.500A) 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 Processing helix chain 'O' and resid 426 through 446 Processing helix chain 'O' and resid 450 through 467 removed outlier: 3.891A pdb=" N ILE O 455 " --> pdb=" O TRP O 451 " (cutoff:3.500A) Processing helix chain 'O' and resid 470 through 491 Processing helix chain 'P' and resid 20 through 25 Processing helix chain 'P' and resid 26 through 39 Processing helix chain 'P' and resid 40 through 52 removed outlier: 4.247A pdb=" N ILE P 44 " --> pdb=" O PRO P 40 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU P 45 " --> pdb=" O GLY P 41 " (cutoff:3.500A) Processing helix chain 'P' and resid 56 through 71 Processing helix chain 'Q' and resid 190 through 192 No H-bonds generated for 'chain 'Q' and resid 190 through 192' Processing helix chain 'Q' and resid 208 through 214 Processing helix chain 'Q' and resid 231 through 236 removed outlier: 3.905A pdb=" N LEU Q 234 " --> pdb=" O LYS Q 231 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU Q 235 " --> pdb=" O LYS Q 232 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL Q 236 " --> pdb=" O GLU Q 233 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 231 through 236' Processing helix chain 'Q' and resid 254 through 262 Processing helix chain 'Q' and resid 394 through 414 Processing helix chain 'Q' and resid 415 through 420 removed outlier: 3.920A pdb=" N TRP Q 418 " --> pdb=" O ASP Q 415 " (cutoff:3.500A) Processing helix chain 'Q' and resid 425 through 447 Processing helix chain 'Q' and resid 450 through 467 Processing helix chain 'Q' and resid 470 through 491 Processing helix chain 'R' and resid 20 through 39 removed outlier: 4.113A pdb=" N TRP R 26 " --> pdb=" O ALA R 22 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N GLN R 28 " --> pdb=" O GLY R 24 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N ILE R 29 " --> pdb=" O ALA R 25 " (cutoff:3.500A) Processing helix chain 'R' and resid 40 through 52 removed outlier: 3.727A pdb=" N ILE R 44 " --> pdb=" O PRO R 40 " (cutoff:3.500A) Processing helix chain 'R' and resid 56 through 71 Processing helix chain 'S' and resid 82 through 86 Processing helix chain 'S' and resid 131 through 135 removed outlier: 3.552A pdb=" N LEU S 135 " --> pdb=" O HIS S 132 " (cutoff:3.500A) Processing helix chain 'S' and resid 185 through 188 Processing helix chain 'S' and resid 208 through 213 Processing helix chain 'S' and resid 231 through 234 removed outlier: 3.531A pdb=" N LEU S 234 " --> pdb=" O LYS 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 414 through 420 removed outlier: 3.874A pdb=" N TRP S 418 " --> pdb=" O ASP S 415 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASP S 419 " --> pdb=" O THR S 416 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N PHE S 420 " --> pdb=" O ALA S 417 " (cutoff:3.500A) Processing helix chain 'S' and resid 425 through 446 removed outlier: 3.507A pdb=" N LEU S 445 " --> pdb=" O ALA S 441 " (cutoff:3.500A) Processing helix chain 'S' and resid 450 through 467 removed outlier: 3.741A pdb=" N ILE S 455 " --> pdb=" O TRP S 451 " (cutoff:3.500A) Processing helix chain 'S' and resid 470 through 491 removed outlier: 4.165A pdb=" N SER S 476 " --> pdb=" O SER S 472 " (cutoff:3.500A) Processing helix chain 'T' and resid 20 through 39 removed outlier: 4.329A pdb=" N TRP T 26 " --> pdb=" O ALA T 22 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N GLN T 28 " --> pdb=" O GLY T 24 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N ILE T 29 " --> pdb=" O ALA T 25 " (cutoff:3.500A) Processing helix chain 'T' and resid 40 through 52 removed outlier: 3.869A pdb=" N ILE T 44 " --> pdb=" O PRO T 40 " (cutoff:3.500A) Processing helix chain 'T' and resid 56 through 75 Proline residue: T 72 - end of helix Processing helix chain 'U' and resid 28 through 32 Processing helix chain 'V' and resid 80 through 84 removed outlier: 3.629A pdb=" N GLU V 84 " --> pdb=" O SER V 81 " (cutoff:3.500A) Processing sheet with id=1, first strand: chain 'A' and resid 11 through 12 removed outlier: 5.404A pdb=" N LEU A 45 " --> pdb=" O ILE A 140 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ILE A 140 " --> pdb=" O LEU A 45 " (cutoff:3.500A) Processing sheet with id=2, first strand: chain 'A' and resid 20 through 22 removed outlier: 3.897A pdb=" N GLY A 177 " --> pdb=" O LEU A 173 " (cutoff:3.500A) Processing sheet with id=3, first strand: chain 'A' and resid 25 through 26 Processing sheet with id=4, first strand: chain 'A' and resid 53 through 57 removed outlier: 7.451A pdb=" N GLY A 127 " --> pdb=" O LEU A 56 " (cutoff:3.500A) Processing sheet with id=5, first strand: chain 'A' and resid 64 through 66 Processing sheet with id=6, first strand: chain 'A' and resid 64 through 66 removed outlier: 3.530A pdb=" N GLY A 109 " --> pdb=" O ARG A 99 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N THR A 115 " --> pdb=" O LYS A 93 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N LYS A 93 " --> pdb=" O THR A 115 " (cutoff:3.500A) Processing sheet with id=7, first strand: chain 'A' and resid 203 through 204 removed outlier: 4.273A pdb=" N ALA A 203 " --> pdb=" O ILE A 268 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE A 268 " --> pdb=" O ALA A 203 " (cutoff:3.500A) No H-bonds generated for sheet with id=7 Processing sheet with id=8, first strand: chain 'A' and resid 237 through 239 Processing sheet with id=9, first strand: chain 'A' and resid 304 through 312 removed outlier: 7.525A pdb=" N LYS A 321 " --> pdb=" O LYS A 307 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N GLU A 309 " --> pdb=" O LEU A 319 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N LEU A 319 " --> pdb=" O GLU A 309 " (cutoff:3.500A) Processing sheet with id=10, first strand: chain 'A' and resid 373 through 377 Processing sheet with id=11, first strand: chain 'C' and resid 9 through 12 removed outlier: 3.965A pdb=" N THR C 32 " --> pdb=" O ASP C 10 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N THR C 142 " --> pdb=" O ASP C 42 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N THR C 138 " --> pdb=" O GLN C 46 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N THR C 48 " --> pdb=" O LYS C 136 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N LYS C 136 " --> pdb=" O THR C 48 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL C 158 " --> pdb=" O ILE C 141 " (cutoff:3.500A) Processing sheet with id=12, first strand: chain 'C' and resid 9 through 12 removed outlier: 3.965A pdb=" N THR C 32 " --> pdb=" O ASP C 10 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N THR C 274 " --> pdb=" O ALA C 50 " (cutoff:3.500A) Processing sheet with id=13, first strand: chain 'C' and resid 20 through 26 removed outlier: 3.944A pdb=" N LYS C 282 " --> pdb=" O SER C 184 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N ASP C 288 " --> pdb=" O THR C 178 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N THR C 178 " --> pdb=" O ASP C 288 " (cutoff:3.500A) Processing sheet with id=14, first strand: chain 'C' and resid 218 through 219 removed outlier: 5.574A pdb=" N THR C 55 " --> pdb=" O VAL C 129 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N VAL C 129 " --> pdb=" O THR C 55 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N ARG C 57 " --> pdb=" O GLY C 127 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLY C 127 " --> pdb=" O ARG C 57 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLU C 126 " --> pdb=" O THR C 198 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ALA C 203 " --> pdb=" O ILE C 268 " (cutoff:3.500A) Processing sheet with id=15, first strand: chain 'C' and resid 68 through 72 Processing sheet with id=16, first strand: chain 'C' and resid 68 through 72 removed outlier: 3.548A pdb=" N GLY C 109 " --> pdb=" O ARG C 99 " (cutoff:3.500A) Processing sheet with id=17, first strand: chain 'C' and resid 237 through 240 Processing sheet with id=18, first strand: chain 'C' and resid 304 through 306 removed outlier: 3.773A pdb=" N SER C 311 " --> pdb=" O LEU C 319 " (cutoff:3.500A) Processing sheet with id=19, first strand: chain 'C' and resid 304 through 306 Processing sheet with id=20, first strand: chain 'C' and resid 336 through 339 Processing sheet with id=21, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.564A pdb=" N ASP E 10 " --> pdb=" O THR E 32 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N MET E 34 " --> pdb=" O ASP E 10 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N VAL E 12 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N THR E 138 " --> pdb=" O GLN E 46 " (cutoff:3.500A) Processing sheet with id=22, first strand: chain 'E' and resid 20 through 26 removed outlier: 4.562A pdb=" N LYS E 282 " --> pdb=" O SER E 184 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLY E 177 " --> pdb=" O LEU E 173 " (cutoff:3.500A) Processing sheet with id=23, first strand: chain 'E' and resid 54 through 72 removed outlier: 5.647A pdb=" N THR E 55 " --> pdb=" O VAL E 129 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N VAL E 129 " --> pdb=" O THR E 55 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ARG E 57 " --> pdb=" O GLY E 127 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N GLU E 123 " --> pdb=" O ILE E 61 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N GLY E 63 " --> pdb=" O CYS E 121 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N CYS E 121 " --> pdb=" O GLY E 63 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N ILE E 65 " --> pdb=" O PHE E 119 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N PHE E 119 " --> pdb=" O ILE E 65 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N ASN E 67 " --> pdb=" O ALA E 117 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N ALA E 117 " --> pdb=" O ASN E 67 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N THR E 69 " --> pdb=" O THR E 115 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N THR E 115 " --> pdb=" O THR E 69 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ASP E 71 " --> pdb=" O LEU E 113 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N LEU E 113 " --> pdb=" O ASP E 71 " (cutoff:3.500A) Processing sheet with id=24, first strand: chain 'E' and resid 90 through 91 removed outlier: 3.503A pdb=" N GLU E 126 " --> pdb=" O THR E 198 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N THR E 266 " --> pdb=" O MET E 205 " (cutoff:3.500A) Processing sheet with id=25, first strand: chain 'E' and resid 236 through 241 removed outlier: 4.034A pdb=" N LYS E 245 " --> pdb=" O ALA E 241 " (cutoff:3.500A) Processing sheet with id=26, first strand: chain 'E' and resid 304 through 312 removed outlier: 7.339A pdb=" N LYS E 321 " --> pdb=" O LYS E 307 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N GLU E 309 " --> pdb=" O LEU E 319 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N LEU E 319 " --> pdb=" O GLU E 309 " (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 'H' and resid 3 through 6 removed outlier: 3.680A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N SER H 25 " --> pdb=" O GLN H 3 " (cutoff:3.500A) Processing sheet with id=30, first strand: chain 'H' and resid 10 through 12 Processing sheet with id=31, first strand: chain 'H' and resid 18 through 20 removed outlier: 3.627A pdb=" N VAL H 18 " --> pdb=" O LEU H 83 " (cutoff:3.500A) Processing sheet with id=32, first strand: chain 'H' and resid 33 through 34 Processing sheet with id=33, first strand: chain 'H' and resid 49 through 51 Processing sheet with id=34, first strand: chain 'L' and resid 20 through 23 removed outlier: 3.781A pdb=" N ILE L 20 " --> pdb=" O LEU L 74 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N SER L 71 " --> pdb=" O SER L 68 " (cutoff:3.500A) Processing sheet with id=35, first strand: chain 'L' and resid 46 through 47 Processing sheet with id=36, first strand: chain 'L' and resid 46 through 47 Processing sheet with id=37, first strand: chain 'O' and resid 11 through 12 removed outlier: 5.404A pdb=" N LEU O 45 " --> pdb=" O ILE O 140 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ILE O 140 " --> pdb=" O LEU O 45 " (cutoff:3.500A) Processing sheet with id=38, first strand: chain 'O' and resid 20 through 22 removed outlier: 3.897A pdb=" N GLY O 177 " --> pdb=" O LEU O 173 " (cutoff:3.500A) Processing sheet with id=39, first strand: chain 'O' and resid 25 through 26 Processing sheet with id=40, first strand: chain 'O' and resid 53 through 57 removed outlier: 7.451A pdb=" N GLY O 127 " --> pdb=" O LEU O 56 " (cutoff:3.500A) Processing sheet with id=41, first strand: chain 'O' and resid 64 through 66 Processing sheet with id=42, first strand: chain 'O' and resid 64 through 66 removed outlier: 3.530A pdb=" N GLY O 109 " --> pdb=" O ARG O 99 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N THR O 115 " --> pdb=" O LYS O 93 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N LYS O 93 " --> pdb=" O THR O 115 " (cutoff:3.500A) Processing sheet with id=43, first strand: chain 'O' and resid 203 through 204 removed outlier: 4.273A pdb=" N ALA O 203 " --> pdb=" O ILE O 268 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE O 268 " --> pdb=" O ALA O 203 " (cutoff:3.500A) No H-bonds generated for sheet with id=43 Processing sheet with id=44, first strand: chain 'O' and resid 237 through 239 Processing sheet with id=45, first strand: chain 'O' and resid 304 through 312 removed outlier: 7.525A pdb=" N LYS O 321 " --> pdb=" O LYS O 307 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N GLU O 309 " --> pdb=" O LEU O 319 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N LEU O 319 " --> pdb=" O GLU O 309 " (cutoff:3.500A) Processing sheet with id=46, first strand: chain 'O' and resid 373 through 377 Processing sheet with id=47, first strand: chain 'Q' and resid 9 through 12 removed outlier: 3.965A pdb=" N THR Q 32 " --> pdb=" O ASP Q 10 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N THR Q 142 " --> pdb=" O ASP Q 42 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N THR Q 138 " --> pdb=" O GLN Q 46 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N THR Q 48 " --> pdb=" O LYS Q 136 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N LYS Q 136 " --> pdb=" O THR Q 48 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL Q 158 " --> pdb=" O ILE Q 141 " (cutoff:3.500A) Processing sheet with id=48, first strand: chain 'Q' and resid 9 through 12 removed outlier: 3.965A pdb=" N THR Q 32 " --> pdb=" O ASP Q 10 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N THR Q 274 " --> pdb=" O ALA Q 50 " (cutoff:3.500A) Processing sheet with id=49, first strand: chain 'Q' and resid 20 through 26 removed outlier: 3.944A pdb=" N LYS Q 282 " --> pdb=" O SER Q 184 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N ASP Q 288 " --> pdb=" O THR Q 178 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N THR Q 178 " --> pdb=" O ASP Q 288 " (cutoff:3.500A) Processing sheet with id=50, first strand: chain 'Q' and resid 218 through 219 removed outlier: 5.574A pdb=" N THR Q 55 " --> pdb=" O VAL Q 129 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N VAL Q 129 " --> pdb=" O THR Q 55 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N ARG Q 57 " --> pdb=" O GLY Q 127 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLY Q 127 " --> pdb=" O ARG Q 57 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLU Q 126 " --> pdb=" O THR Q 198 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ALA Q 203 " --> pdb=" O ILE Q 268 " (cutoff:3.500A) Processing sheet with id=51, first strand: chain 'Q' and resid 68 through 72 Processing sheet with id=52, first strand: chain 'Q' and resid 68 through 72 removed outlier: 3.548A pdb=" N GLY Q 109 " --> pdb=" O ARG Q 99 " (cutoff:3.500A) Processing sheet with id=53, first strand: chain 'Q' and resid 237 through 240 Processing sheet with id=54, first strand: chain 'Q' and resid 304 through 306 removed outlier: 3.773A pdb=" N SER Q 311 " --> pdb=" O LEU Q 319 " (cutoff:3.500A) Processing sheet with id=55, first strand: chain 'Q' and resid 304 through 306 Processing sheet with id=56, first strand: chain 'Q' and resid 336 through 339 Processing sheet with id=57, first strand: chain 'S' and resid 10 through 13 removed outlier: 6.564A pdb=" N ASP S 10 " --> pdb=" O THR S 32 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N MET S 34 " --> pdb=" O ASP S 10 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N VAL S 12 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N THR S 138 " --> pdb=" O GLN S 46 " (cutoff:3.500A) Processing sheet with id=58, first strand: chain 'S' and resid 20 through 26 removed outlier: 4.562A pdb=" N LYS S 282 " --> pdb=" O SER S 184 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLY S 177 " --> pdb=" O LEU S 173 " (cutoff:3.500A) Processing sheet with id=59, first strand: chain 'S' and resid 54 through 72 removed outlier: 5.647A pdb=" N THR S 55 " --> pdb=" O VAL S 129 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N VAL S 129 " --> pdb=" O THR S 55 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ARG S 57 " --> pdb=" O GLY S 127 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N GLU S 123 " --> pdb=" O ILE S 61 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N GLY S 63 " --> pdb=" O CYS S 121 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N CYS S 121 " --> pdb=" O GLY S 63 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N ILE S 65 " --> pdb=" O PHE S 119 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N PHE S 119 " --> pdb=" O ILE S 65 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N ASN S 67 " --> pdb=" O ALA S 117 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N ALA S 117 " --> pdb=" O ASN S 67 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N THR S 69 " --> pdb=" O THR S 115 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N THR S 115 " --> pdb=" O THR S 69 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ASP S 71 " --> pdb=" O LEU S 113 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N LEU S 113 " --> pdb=" O ASP S 71 " (cutoff:3.500A) Processing sheet with id=60, first strand: chain 'S' and resid 90 through 91 removed outlier: 3.503A pdb=" N GLU S 126 " --> pdb=" O THR S 198 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N THR S 266 " --> pdb=" O MET S 205 " (cutoff:3.500A) Processing sheet with id=61, first strand: chain 'S' and resid 236 through 241 removed outlier: 4.034A pdb=" N LYS S 245 " --> pdb=" O ALA S 241 " (cutoff:3.500A) Processing sheet with id=62, first strand: chain 'S' and resid 304 through 312 removed outlier: 7.339A pdb=" N LYS S 321 " --> pdb=" O LYS S 307 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N GLU S 309 " --> pdb=" O LEU S 319 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N LEU S 319 " --> pdb=" O GLU S 309 " (cutoff:3.500A) Processing sheet with id=63, first strand: chain 'S' and resid 331 through 332 Processing sheet with id=64, first strand: chain 'S' and resid 336 through 338 Processing sheet with id=65, first strand: chain 'U' and resid 3 through 6 removed outlier: 3.680A pdb=" N GLN U 3 " --> pdb=" O SER U 25 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N SER U 25 " --> pdb=" O GLN U 3 " (cutoff:3.500A) Processing sheet with id=66, first strand: chain 'U' and resid 10 through 12 Processing sheet with id=67, first strand: chain 'U' and resid 18 through 20 removed outlier: 3.627A pdb=" N VAL U 18 " --> pdb=" O LEU U 83 " (cutoff:3.500A) Processing sheet with id=68, first strand: chain 'U' and resid 33 through 34 Processing sheet with id=69, first strand: chain 'U' and resid 49 through 51 Processing sheet with id=70, first strand: chain 'V' and resid 20 through 23 removed outlier: 3.781A pdb=" N ILE V 20 " --> pdb=" O LEU V 74 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N SER V 71 " --> pdb=" O SER V 68 " (cutoff:3.500A) Processing sheet with id=71, first strand: chain 'V' and resid 46 through 47 Processing sheet with id=72, first strand: chain 'V' and resid 46 through 47 1238 hydrogen bonds defined for protein. 3354 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: 4.58 Time building geometry restraints manager: 2.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 9592 1.35 - 1.48: 7436 1.48 - 1.60: 13222 1.60 - 1.73: 0 1.73 - 1.85: 322 Bond restraints: 30572 Sorted by residual: bond pdb=" C1 NAG N 2 " pdb=" O5 NAG N 2 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.04e+00 bond pdb=" C1 NAG 1 2 " pdb=" O5 NAG 1 2 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.04e+00 bond pdb=" N MET O 199 " pdb=" CA MET O 199 " ideal model delta sigma weight residual 1.457 1.476 -0.018 1.29e-02 6.01e+03 2.02e+00 bond pdb=" N MET A 199 " pdb=" CA MET A 199 " ideal model delta sigma weight residual 1.457 1.476 -0.018 1.29e-02 6.01e+03 2.02e+00 bond pdb=" C ASN Q 353 " pdb=" N PRO Q 354 " ideal model delta sigma weight residual 1.335 1.323 0.012 8.70e-03 1.32e+04 1.91e+00 ... (remaining 30567 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.90: 40434 1.90 - 3.80: 840 3.80 - 5.70: 114 5.70 - 7.60: 20 7.60 - 9.50: 10 Bond angle restraints: 41418 Sorted by residual: angle pdb=" C LYS S 358 " pdb=" N LYS S 359 " pdb=" CA LYS S 359 " ideal model delta sigma weight residual 121.54 129.40 -7.86 1.91e+00 2.74e-01 1.69e+01 angle pdb=" C LYS E 358 " pdb=" N LYS E 359 " pdb=" CA LYS E 359 " ideal model delta sigma weight residual 121.54 129.40 -7.86 1.91e+00 2.74e-01 1.69e+01 angle pdb=" N ILE A 61 " pdb=" CA ILE A 61 " pdb=" CB ILE A 61 " ideal model delta sigma weight residual 111.90 106.80 5.10 1.37e+00 5.33e-01 1.39e+01 angle pdb=" N ILE O 61 " pdb=" CA ILE O 61 " pdb=" CB ILE O 61 " ideal model delta sigma weight residual 111.90 106.80 5.10 1.37e+00 5.33e-01 1.39e+01 angle pdb=" CA GLY S 109 " pdb=" C GLY S 109 " pdb=" N LYS S 110 " ideal model delta sigma weight residual 114.23 117.23 -3.00 8.80e-01 1.29e+00 1.16e+01 ... (remaining 41413 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.63: 17292 21.63 - 43.25: 972 43.25 - 64.88: 136 64.88 - 86.50: 72 86.50 - 108.13: 20 Dihedral angle restraints: 18492 sinusoidal: 7608 harmonic: 10884 Sorted by residual: dihedral pdb=" CB CYS O 60 " pdb=" SG CYS O 60 " pdb=" SG CYS O 121 " pdb=" CB CYS O 121 " ideal model delta sinusoidal sigma weight residual -86.00 2.69 -88.69 1 1.00e+01 1.00e-02 9.38e+01 dihedral pdb=" CB CYS A 60 " pdb=" SG CYS A 60 " pdb=" SG CYS A 121 " pdb=" CB CYS A 121 " ideal model delta sinusoidal sigma weight residual -86.00 2.69 -88.69 1 1.00e+01 1.00e-02 9.38e+01 dihedral pdb=" CB CYS A 300 " pdb=" SG CYS A 300 " pdb=" SG CYS A 331 " pdb=" CB CYS A 331 " ideal model delta sinusoidal sigma weight residual -86.00 -163.80 77.80 1 1.00e+01 1.00e-02 7.57e+01 ... (remaining 18489 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 3988 0.057 - 0.114: 760 0.114 - 0.170: 86 0.170 - 0.227: 8 0.227 - 0.284: 6 Chirality restraints: 4848 Sorted by residual: chirality pdb=" C5 BMA Z 3 " pdb=" C4 BMA Z 3 " pdb=" C6 BMA Z 3 " pdb=" O5 BMA Z 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.28 2.00e-01 2.50e+01 2.02e+00 chirality pdb=" C5 BMA K 3 " pdb=" C4 BMA K 3 " pdb=" C6 BMA K 3 " pdb=" O5 BMA K 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.28 2.00e-01 2.50e+01 2.02e+00 chirality pdb=" C5 BMA M 3 " pdb=" C4 BMA M 3 " pdb=" C6 BMA M 3 " pdb=" O5 BMA M 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.89e+00 ... (remaining 4845 not shown) Planarity restraints: 5174 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 420 " -0.015 2.00e-02 2.50e+03 1.11e-02 2.17e+00 pdb=" CG PHE C 420 " 0.024 2.00e-02 2.50e+03 pdb=" CD1 PHE C 420 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 PHE C 420 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE C 420 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE C 420 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE C 420 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE Q 420 " 0.015 2.00e-02 2.50e+03 1.11e-02 2.17e+00 pdb=" CG PHE Q 420 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 PHE Q 420 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 PHE Q 420 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE Q 420 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE Q 420 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE Q 420 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR S 176 " 0.011 2.00e-02 2.50e+03 1.02e-02 2.08e+00 pdb=" CG TYR S 176 " -0.022 2.00e-02 2.50e+03 pdb=" CD1 TYR S 176 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 TYR S 176 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR S 176 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR S 176 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR S 176 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR S 176 " 0.005 2.00e-02 2.50e+03 ... (remaining 5171 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 1204 2.71 - 3.26: 29952 3.26 - 3.81: 48087 3.81 - 4.35: 58204 4.35 - 4.90: 102739 Nonbonded interactions: 240186 Sorted by model distance: nonbonded pdb=" OG SER B 73 " pdb=" OG SER P 73 " model vdw 2.168 3.040 nonbonded pdb=" OH TYR A 324 " pdb=" OD1 ASP A 328 " model vdw 2.202 3.040 nonbonded pdb=" OH TYR O 324 " pdb=" OD1 ASP O 328 " model vdw 2.202 3.040 nonbonded pdb=" ND2 ASN O 302 " pdb=" O LYS O 325 " model vdw 2.209 3.120 nonbonded pdb=" ND2 ASN A 302 " pdb=" O LYS A 325 " model vdw 2.209 3.120 ... (remaining 240181 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 'K' selection = chain 'M' selection = chain 'Z' } ncs_group { reference = chain '1' selection = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'N' selection = chain 'W' selection = chain 'X' selection = chain 'Y' } 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 'H' selection = chain 'U' } ncs_group { reference = chain 'L' selection = chain 'V' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.580 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: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 22.600 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 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 0.044 30638 Z= 0.194 Angle : 0.704 9.502 41578 Z= 0.384 Chirality : 0.046 0.284 4848 Planarity : 0.003 0.036 5162 Dihedral : 14.360 108.125 11430 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.24 (0.13), residues: 3838 helix: 1.34 (0.18), residues: 870 sheet: -1.51 (0.14), residues: 1226 loop : -1.35 (0.14), residues: 1742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG Q 73 TYR 0.022 0.002 TYR E 176 PHE 0.024 0.001 PHE Q 420 TRP 0.018 0.002 TRP O 451 HIS 0.009 0.001 HIS S 144 Details of bonding type rmsd covalent geometry : bond 0.00423 (30572) covalent geometry : angle 0.69575 (41418) SS BOND : bond 0.00706 ( 38) SS BOND : angle 1.77541 ( 76) hydrogen bonds : bond 0.21284 ( 1190) hydrogen bonds : angle 8.73351 ( 3354) link_BETA1-4 : bond 0.00459 ( 16) link_BETA1-4 : angle 2.02890 ( 48) link_NAG-ASN : bond 0.00441 ( 12) link_NAG-ASN : angle 1.88520 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 744 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 744 time to evaluate : 1.085 Fit side-chains REVERT: A 132 HIS cc_start: 0.8337 (t-90) cc_final: 0.7747 (t-170) REVERT: A 163 THR cc_start: 0.8611 (p) cc_final: 0.8370 (m) REVERT: A 324 TYR cc_start: 0.8890 (t80) cc_final: 0.8635 (t80) REVERT: A 438 PHE cc_start: 0.8236 (m-80) cc_final: 0.7952 (m-10) REVERT: A 442 TYR cc_start: 0.9228 (t80) cc_final: 0.8787 (t80) REVERT: B 10 MET cc_start: 0.7944 (mmm) cc_final: 0.7628 (mmp) REVERT: B 17 GLN cc_start: 0.8747 (tt0) cc_final: 0.8478 (tt0) REVERT: C 90 TYR cc_start: 0.8782 (m-80) cc_final: 0.8411 (m-80) REVERT: C 473 MET cc_start: 0.7268 (tpp) cc_final: 0.7020 (tpp) REVERT: D 52 TYR cc_start: 0.7901 (m-80) cc_final: 0.7328 (m-80) REVERT: E 49 GLU cc_start: 0.7652 (mt-10) cc_final: 0.7333 (tp30) REVERT: E 98 ASP cc_start: 0.7787 (m-30) cc_final: 0.7554 (m-30) REVERT: E 170 GLU cc_start: 0.8001 (tt0) cc_final: 0.7717 (mp0) REVERT: E 258 MET cc_start: 0.8727 (tpt) cc_final: 0.8426 (tpt) REVERT: E 368 GLU cc_start: 0.7541 (tm-30) cc_final: 0.7285 (tm-30) REVERT: E 400 PHE cc_start: 0.7898 (t80) cc_final: 0.7561 (t80) REVERT: F 10 MET cc_start: 0.8439 (mmp) cc_final: 0.7996 (mmp) REVERT: F 14 THR cc_start: 0.9056 (t) cc_final: 0.8762 (p) REVERT: F 68 MET cc_start: 0.8790 (mmm) cc_final: 0.8273 (mmm) REVERT: H 10 GLU cc_start: 0.7977 (tt0) cc_final: 0.7721 (tt0) REVERT: H 12 LYS cc_start: 0.8338 (mttp) cc_final: 0.8093 (mttm) REVERT: L 49 MET cc_start: 0.6518 (mmt) cc_final: 0.5871 (mmt) REVERT: L 71 SER cc_start: 0.8863 (m) cc_final: 0.8566 (p) REVERT: L 107 LEU cc_start: 0.5967 (tp) cc_final: 0.5699 (tp) REVERT: O 132 HIS cc_start: 0.8332 (t-90) cc_final: 0.7745 (t-170) REVERT: O 163 THR cc_start: 0.8611 (p) cc_final: 0.8368 (m) REVERT: O 324 TYR cc_start: 0.8886 (t80) cc_final: 0.8630 (t80) REVERT: O 438 PHE cc_start: 0.8231 (m-80) cc_final: 0.7945 (m-10) REVERT: O 442 TYR cc_start: 0.9228 (t80) cc_final: 0.8788 (t80) REVERT: P 10 MET cc_start: 0.7927 (mmm) cc_final: 0.7619 (mmp) REVERT: P 17 GLN cc_start: 0.8745 (tt0) cc_final: 0.8472 (tt0) REVERT: Q 90 TYR cc_start: 0.8785 (m-80) cc_final: 0.8416 (m-80) REVERT: Q 473 MET cc_start: 0.7257 (tpp) cc_final: 0.7012 (tpp) REVERT: R 52 TYR cc_start: 0.7898 (m-80) cc_final: 0.7322 (m-80) REVERT: S 49 GLU cc_start: 0.7649 (mt-10) cc_final: 0.7325 (tp30) REVERT: S 98 ASP cc_start: 0.7780 (m-30) cc_final: 0.7555 (m-30) REVERT: S 170 GLU cc_start: 0.8007 (tt0) cc_final: 0.7718 (mp0) REVERT: S 258 MET cc_start: 0.8745 (tpt) cc_final: 0.8428 (tpt) REVERT: S 368 GLU cc_start: 0.7552 (tm-30) cc_final: 0.7294 (tm-30) REVERT: S 400 PHE cc_start: 0.7900 (t80) cc_final: 0.7566 (t80) REVERT: T 10 MET cc_start: 0.8444 (mmp) cc_final: 0.7991 (mmp) REVERT: T 14 THR cc_start: 0.9055 (t) cc_final: 0.8767 (p) REVERT: T 68 MET cc_start: 0.8800 (mmm) cc_final: 0.8270 (mmm) REVERT: U 10 GLU cc_start: 0.7979 (tt0) cc_final: 0.7726 (tt0) REVERT: U 12 LYS cc_start: 0.8345 (mttp) cc_final: 0.8098 (mttm) REVERT: V 49 MET cc_start: 0.6510 (mmt) cc_final: 0.5852 (mmt) REVERT: V 71 SER cc_start: 0.8844 (m) cc_final: 0.8561 (p) outliers start: 0 outliers final: 0 residues processed: 744 average time/residue: 0.1684 time to fit residues: 197.3659 Evaluate side-chains 493 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 493 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 197 optimal weight: 8.9990 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 5.9990 chunk 298 optimal weight: 9.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 ASN A 375 ASN B 51 HIS C 8 ASN C 132 HIS ** C 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 52 GLN ** E 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 246 GLN ** F 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 GLN O 134 ASN O 375 ASN P 51 HIS Q 8 ASN Q 132 HIS ** Q 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 52 GLN S 246 GLN ** T 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 6 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.110164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.097263 restraints weight = 43011.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.098603 restraints weight = 28191.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.099636 restraints weight = 22486.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.100089 restraints weight = 17616.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.100534 restraints weight = 14785.163| |-----------------------------------------------------------------------------| r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.1531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 30638 Z= 0.198 Angle : 0.689 14.230 41578 Z= 0.354 Chirality : 0.047 0.293 4848 Planarity : 0.004 0.047 5162 Dihedral : 8.256 65.578 4632 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.06 % Allowed : 11.19 % Favored : 86.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.07 (0.13), residues: 3838 helix: 1.64 (0.18), residues: 858 sheet: -1.55 (0.15), residues: 1070 loop : -1.27 (0.13), residues: 1910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG Q 9 TYR 0.017 0.002 TYR B 52 PHE 0.030 0.002 PHE C 420 TRP 0.020 0.002 TRP A 451 HIS 0.008 0.001 HIS E 144 Details of bonding type rmsd covalent geometry : bond 0.00470 (30572) covalent geometry : angle 0.67832 (41418) SS BOND : bond 0.00868 ( 38) SS BOND : angle 2.08038 ( 76) hydrogen bonds : bond 0.04588 ( 1190) hydrogen bonds : angle 6.22349 ( 3354) link_BETA1-4 : bond 0.00463 ( 16) link_BETA1-4 : angle 2.02725 ( 48) link_NAG-ASN : bond 0.00348 ( 12) link_NAG-ASN : angle 1.94948 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 615 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 549 time to evaluate : 0.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 HIS cc_start: 0.8369 (t-90) cc_final: 0.7708 (t-170) REVERT: A 287 MET cc_start: 0.9177 (OUTLIER) cc_final: 0.8817 (mtp) REVERT: A 324 TYR cc_start: 0.8952 (t80) cc_final: 0.8616 (t80) REVERT: A 438 PHE cc_start: 0.8261 (m-80) cc_final: 0.8011 (m-10) REVERT: A 442 TYR cc_start: 0.9187 (t80) cc_final: 0.8860 (t80) REVERT: B 10 MET cc_start: 0.8061 (mmm) cc_final: 0.7634 (mmp) REVERT: B 17 GLN cc_start: 0.8736 (tt0) cc_final: 0.8468 (tt0) REVERT: D 59 GLN cc_start: 0.7414 (mt0) cc_final: 0.6862 (mt0) REVERT: E 49 GLU cc_start: 0.7622 (mt-10) cc_final: 0.7366 (tp30) REVERT: E 98 ASP cc_start: 0.7877 (m-30) cc_final: 0.7664 (m-30) REVERT: E 400 PHE cc_start: 0.7977 (t80) cc_final: 0.7579 (t80) REVERT: F 10 MET cc_start: 0.8384 (mmp) cc_final: 0.8142 (mmp) REVERT: F 20 MET cc_start: 0.9044 (mtm) cc_final: 0.8663 (mtm) REVERT: F 59 GLN cc_start: 0.8027 (mt0) cc_final: 0.7518 (mt0) REVERT: H 10 GLU cc_start: 0.8252 (tt0) cc_final: 0.7966 (mt-10) REVERT: L 49 MET cc_start: 0.6477 (mmt) cc_final: 0.5922 (mmt) REVERT: L 71 SER cc_start: 0.8699 (m) cc_final: 0.8416 (p) REVERT: L 107 LEU cc_start: 0.6082 (tp) cc_final: 0.5841 (tp) REVERT: O 132 HIS cc_start: 0.8369 (t-90) cc_final: 0.7716 (t-170) REVERT: O 287 MET cc_start: 0.9172 (OUTLIER) cc_final: 0.8818 (mtp) REVERT: O 324 TYR cc_start: 0.8944 (t80) cc_final: 0.8607 (t80) REVERT: O 438 PHE cc_start: 0.8252 (m-80) cc_final: 0.8006 (m-10) REVERT: O 442 TYR cc_start: 0.9188 (t80) cc_final: 0.8866 (t80) REVERT: P 10 MET cc_start: 0.8044 (mmm) cc_final: 0.7635 (mmp) REVERT: P 17 GLN cc_start: 0.8740 (tt0) cc_final: 0.8475 (tt0) REVERT: R 59 GLN cc_start: 0.7415 (mt0) cc_final: 0.6864 (mt0) REVERT: S 49 GLU cc_start: 0.7622 (mt-10) cc_final: 0.7356 (tp30) REVERT: S 98 ASP cc_start: 0.7873 (m-30) cc_final: 0.7672 (m-30) REVERT: S 400 PHE cc_start: 0.7973 (t80) cc_final: 0.7575 (t80) REVERT: T 10 MET cc_start: 0.8388 (mmp) cc_final: 0.8137 (mmp) REVERT: T 20 MET cc_start: 0.9030 (mtm) cc_final: 0.8664 (mtm) REVERT: T 59 GLN cc_start: 0.8024 (mt0) cc_final: 0.7513 (mt0) REVERT: U 10 GLU cc_start: 0.8253 (tt0) cc_final: 0.7973 (mt-10) REVERT: V 49 MET cc_start: 0.6468 (mmt) cc_final: 0.5910 (mmt) REVERT: V 71 SER cc_start: 0.8703 (m) cc_final: 0.8419 (p) outliers start: 66 outliers final: 44 residues processed: 589 average time/residue: 0.1481 time to fit residues: 143.7411 Evaluate side-chains 540 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 494 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 183 CYS Chi-restraints excluded: chain A residue 258 MET Chi-restraints excluded: chain A residue 269 GLN Chi-restraints excluded: chain A residue 283 CYS Chi-restraints excluded: chain A residue 287 MET Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain C residue 2 ARG Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 401 GLU Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 270 THR Chi-restraints excluded: chain E residue 311 SER Chi-restraints excluded: chain E residue 464 ILE Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 182 GLU Chi-restraints excluded: chain O residue 183 CYS Chi-restraints excluded: chain O residue 258 MET Chi-restraints excluded: chain O residue 269 GLN Chi-restraints excluded: chain O residue 283 CYS Chi-restraints excluded: chain O residue 287 MET Chi-restraints excluded: chain O residue 319 LEU Chi-restraints excluded: chain O residue 336 SER Chi-restraints excluded: chain O residue 491 VAL Chi-restraints excluded: chain Q residue 2 ARG Chi-restraints excluded: chain Q residue 43 ILE Chi-restraints excluded: chain Q residue 65 ILE Chi-restraints excluded: chain Q residue 70 THR Chi-restraints excluded: chain Q residue 151 VAL Chi-restraints excluded: chain Q residue 262 LEU Chi-restraints excluded: chain Q residue 337 THR Chi-restraints excluded: chain Q residue 401 GLU Chi-restraints excluded: chain S residue 33 THR Chi-restraints excluded: chain S residue 270 THR Chi-restraints excluded: chain S residue 311 SER Chi-restraints excluded: chain S residue 464 ILE Chi-restraints excluded: chain U residue 28 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 192 optimal weight: 7.9990 chunk 139 optimal weight: 0.0370 chunk 286 optimal weight: 5.9990 chunk 67 optimal weight: 7.9990 chunk 19 optimal weight: 2.9990 chunk 196 optimal weight: 0.7980 chunk 141 optimal weight: 9.9990 chunk 69 optimal weight: 6.9990 chunk 153 optimal weight: 9.9990 chunk 170 optimal weight: 10.0000 chunk 301 optimal weight: 10.0000 overall best weight: 3.3664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 ASN A 314 GLN A 364 ASN ** C 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 134 ASN O 314 GLN O 364 ASN ** Q 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 59 GLN ** S 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 28 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.109516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.095669 restraints weight = 43097.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.097789 restraints weight = 26368.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.099206 restraints weight = 18496.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.100142 restraints weight = 14304.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.100775 restraints weight = 11870.970| |-----------------------------------------------------------------------------| r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 30638 Z= 0.187 Angle : 0.642 13.112 41578 Z= 0.328 Chirality : 0.045 0.279 4848 Planarity : 0.004 0.036 5162 Dihedral : 6.699 54.905 4632 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.50 % Allowed : 14.53 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.01 (0.13), residues: 3838 helix: 1.57 (0.18), residues: 876 sheet: -1.41 (0.15), residues: 1070 loop : -1.26 (0.13), residues: 1892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG U 100 TYR 0.014 0.002 TYR H 32 PHE 0.026 0.002 PHE C 420 TRP 0.017 0.001 TRP O 451 HIS 0.009 0.001 HIS E 149 Details of bonding type rmsd covalent geometry : bond 0.00442 (30572) covalent geometry : angle 0.63388 (41418) SS BOND : bond 0.00684 ( 38) SS BOND : angle 1.50921 ( 76) hydrogen bonds : bond 0.04164 ( 1190) hydrogen bonds : angle 5.68468 ( 3354) link_BETA1-4 : bond 0.00411 ( 16) link_BETA1-4 : angle 1.91822 ( 48) link_NAG-ASN : bond 0.00321 ( 12) link_NAG-ASN : angle 1.93383 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 634 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 522 time to evaluate : 0.997 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: A 132 HIS cc_start: 0.8348 (t-90) cc_final: 0.7732 (t-170) REVERT: A 324 TYR cc_start: 0.8903 (t80) cc_final: 0.8617 (t80) REVERT: A 438 PHE cc_start: 0.8244 (m-80) cc_final: 0.7953 (m-10) REVERT: A 442 TYR cc_start: 0.9188 (t80) cc_final: 0.8873 (t80) REVERT: B 10 MET cc_start: 0.8040 (mmm) cc_final: 0.7627 (mmp) REVERT: B 17 GLN cc_start: 0.8784 (tt0) cc_final: 0.8507 (tt0) REVERT: C 41 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8199 (pp) REVERT: C 181 LEU cc_start: 0.8051 (OUTLIER) cc_final: 0.7713 (pp) REVERT: C 485 LEU cc_start: 0.9077 (mm) cc_final: 0.8873 (mm) REVERT: D 52 TYR cc_start: 0.8072 (m-80) cc_final: 0.7608 (m-80) REVERT: D 59 GLN cc_start: 0.7409 (mt0) cc_final: 0.7177 (mt0) REVERT: E 49 GLU cc_start: 0.7674 (mt-10) cc_final: 0.7406 (tp30) REVERT: E 91 VAL cc_start: 0.8953 (p) cc_final: 0.8746 (p) REVERT: E 297 TYR cc_start: 0.8015 (m-80) cc_final: 0.7647 (m-80) REVERT: E 400 PHE cc_start: 0.8020 (t80) cc_final: 0.7577 (t80) REVERT: F 10 MET cc_start: 0.8370 (mmp) cc_final: 0.8164 (mmp) REVERT: F 68 MET cc_start: 0.8634 (mmm) cc_final: 0.8237 (mmm) REVERT: H 10 GLU cc_start: 0.8113 (tt0) cc_final: 0.7799 (mt-10) REVERT: H 63 ARG cc_start: 0.8523 (ttt90) cc_final: 0.7940 (tmm-80) REVERT: L 49 MET cc_start: 0.6326 (mmt) cc_final: 0.5939 (mmt) REVERT: L 71 SER cc_start: 0.8738 (m) cc_final: 0.8499 (p) REVERT: L 107 LEU cc_start: 0.6204 (tp) cc_final: 0.5885 (tp) REVERT: O 132 HIS cc_start: 0.8341 (t-90) cc_final: 0.7730 (t-170) REVERT: O 324 TYR cc_start: 0.8894 (t80) cc_final: 0.8608 (t80) REVERT: O 438 PHE cc_start: 0.8240 (m-80) cc_final: 0.7951 (m-10) REVERT: O 442 TYR cc_start: 0.9191 (t80) cc_final: 0.8876 (t80) REVERT: P 10 MET cc_start: 0.8021 (mmm) cc_final: 0.7625 (mmp) REVERT: P 17 GLN cc_start: 0.8784 (tt0) cc_final: 0.8506 (tt0) REVERT: Q 41 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8204 (pp) REVERT: Q 181 LEU cc_start: 0.8054 (OUTLIER) cc_final: 0.7723 (pp) REVERT: R 52 TYR cc_start: 0.8067 (m-80) cc_final: 0.7599 (m-80) REVERT: R 59 GLN cc_start: 0.7505 (mt0) cc_final: 0.7228 (mt0) REVERT: S 49 GLU cc_start: 0.7684 (mt-10) cc_final: 0.7401 (tp30) REVERT: S 297 TYR cc_start: 0.8014 (m-80) cc_final: 0.7648 (m-80) REVERT: S 400 PHE cc_start: 0.8018 (t80) cc_final: 0.7576 (t80) REVERT: T 10 MET cc_start: 0.8374 (mmp) cc_final: 0.8153 (mmp) REVERT: T 68 MET cc_start: 0.8656 (mmm) cc_final: 0.8247 (mmm) REVERT: U 10 GLU cc_start: 0.8114 (tt0) cc_final: 0.7817 (mt-10) REVERT: U 63 ARG cc_start: 0.8524 (ttt90) cc_final: 0.7939 (tmm-80) REVERT: V 49 MET cc_start: 0.6145 (mmt) cc_final: 0.5781 (mmt) REVERT: V 71 SER cc_start: 0.8740 (m) cc_final: 0.8501 (p) outliers start: 112 outliers final: 74 residues processed: 598 average time/residue: 0.1760 time to fit residues: 173.4516 Evaluate side-chains 572 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 494 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 134 ASN Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 183 CYS Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 258 MET Chi-restraints excluded: chain A residue 269 GLN Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain B residue 20 MET Chi-restraints excluded: chain C residue 2 ARG Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 295 MET Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 401 GLU Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 270 THR Chi-restraints excluded: chain E residue 311 SER Chi-restraints excluded: chain E residue 464 ILE Chi-restraints excluded: chain E residue 487 LEU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 102 PHE Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 48 THR Chi-restraints excluded: chain O residue 115 THR Chi-restraints excluded: chain O residue 124 LEU Chi-restraints excluded: chain O residue 134 ASN Chi-restraints excluded: chain O residue 163 THR Chi-restraints excluded: chain O residue 182 GLU Chi-restraints excluded: chain O residue 183 CYS Chi-restraints excluded: chain O residue 251 LEU Chi-restraints excluded: chain O residue 258 MET Chi-restraints excluded: chain O residue 269 GLN Chi-restraints excluded: chain O residue 319 LEU Chi-restraints excluded: chain O residue 336 SER Chi-restraints excluded: chain O residue 355 VAL Chi-restraints excluded: chain O residue 491 VAL Chi-restraints excluded: chain P residue 20 MET Chi-restraints excluded: chain Q residue 2 ARG Chi-restraints excluded: chain Q residue 41 LEU Chi-restraints excluded: chain Q residue 43 ILE Chi-restraints excluded: chain Q residue 65 ILE Chi-restraints excluded: chain Q residue 70 THR Chi-restraints excluded: chain Q residue 92 CYS Chi-restraints excluded: chain Q residue 151 VAL Chi-restraints excluded: chain Q residue 181 LEU Chi-restraints excluded: chain Q residue 197 LEU Chi-restraints excluded: chain Q residue 262 LEU Chi-restraints excluded: chain Q residue 281 LEU Chi-restraints excluded: chain Q residue 295 MET Chi-restraints excluded: chain Q residue 319 LEU Chi-restraints excluded: chain Q residue 337 THR Chi-restraints excluded: chain Q residue 401 GLU Chi-restraints excluded: chain S residue 33 THR Chi-restraints excluded: chain S residue 51 THR Chi-restraints excluded: chain S residue 270 THR Chi-restraints excluded: chain S residue 311 SER Chi-restraints excluded: chain S residue 464 ILE Chi-restraints excluded: chain S residue 487 LEU Chi-restraints excluded: chain U residue 28 THR Chi-restraints excluded: chain U residue 102 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 308 optimal weight: 5.9990 chunk 187 optimal weight: 40.0000 chunk 85 optimal weight: 9.9990 chunk 232 optimal weight: 8.9990 chunk 293 optimal weight: 5.9990 chunk 129 optimal weight: 7.9990 chunk 338 optimal weight: 4.9990 chunk 305 optimal weight: 1.9990 chunk 171 optimal weight: 10.0000 chunk 236 optimal weight: 6.9990 chunk 233 optimal weight: 1.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 ASN A 364 ASN ** C 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 28 GLN F 39 HIS O 134 ASN O 364 ASN ** Q 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 39 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.108082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.094282 restraints weight = 43192.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.096363 restraints weight = 26516.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.097764 restraints weight = 18627.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.098708 restraints weight = 14426.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.099379 restraints weight = 11975.855| |-----------------------------------------------------------------------------| r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 30638 Z= 0.216 Angle : 0.652 13.126 41578 Z= 0.334 Chirality : 0.046 0.274 4848 Planarity : 0.004 0.046 5162 Dihedral : 6.436 54.773 4632 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 4.25 % Allowed : 16.28 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.01 (0.13), residues: 3838 helix: 1.54 (0.18), residues: 876 sheet: -1.36 (0.15), residues: 1070 loop : -1.27 (0.13), residues: 1892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 15 TYR 0.013 0.002 TYR A 297 PHE 0.026 0.002 PHE C 420 TRP 0.015 0.002 TRP A 451 HIS 0.006 0.001 HIS E 149 Details of bonding type rmsd covalent geometry : bond 0.00519 (30572) covalent geometry : angle 0.64515 (41418) SS BOND : bond 0.00723 ( 38) SS BOND : angle 1.50419 ( 76) hydrogen bonds : bond 0.04062 ( 1190) hydrogen bonds : angle 5.53732 ( 3354) link_BETA1-4 : bond 0.00345 ( 16) link_BETA1-4 : angle 1.74791 ( 48) link_NAG-ASN : bond 0.00352 ( 12) link_NAG-ASN : angle 1.94266 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 646 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 510 time to evaluate : 1.054 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: A 324 TYR cc_start: 0.8872 (t80) cc_final: 0.8610 (t80) REVERT: A 438 PHE cc_start: 0.8241 (m-80) cc_final: 0.8009 (m-10) REVERT: A 442 TYR cc_start: 0.9186 (t80) cc_final: 0.8824 (t80) REVERT: B 10 MET cc_start: 0.8074 (mmm) cc_final: 0.7584 (mmp) REVERT: B 17 GLN cc_start: 0.8711 (tt0) cc_final: 0.8454 (tt0) REVERT: C 41 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8219 (pp) REVERT: C 181 LEU cc_start: 0.8149 (OUTLIER) cc_final: 0.7807 (pp) REVERT: C 485 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8775 (mm) REVERT: D 52 TYR cc_start: 0.8005 (m-80) cc_final: 0.7564 (m-80) REVERT: D 59 GLN cc_start: 0.7651 (mt0) cc_final: 0.7289 (mt0) REVERT: E 49 GLU cc_start: 0.7773 (mt-10) cc_final: 0.7311 (tp30) REVERT: E 91 VAL cc_start: 0.9006 (p) cc_final: 0.8756 (p) REVERT: E 297 TYR cc_start: 0.7958 (m-80) cc_final: 0.7608 (m-80) REVERT: E 400 PHE cc_start: 0.7936 (t80) cc_final: 0.7446 (t80) REVERT: F 20 MET cc_start: 0.9085 (mtm) cc_final: 0.8725 (mtm) REVERT: F 68 MET cc_start: 0.8684 (mmm) cc_final: 0.8285 (mmm) REVERT: H 10 GLU cc_start: 0.8076 (tt0) cc_final: 0.7755 (mt-10) REVERT: H 100 ARG cc_start: 0.7790 (mmm-85) cc_final: 0.7350 (mmm-85) REVERT: L 49 MET cc_start: 0.6319 (mmt) cc_final: 0.5646 (mmt) REVERT: L 71 SER cc_start: 0.8522 (m) cc_final: 0.8255 (p) REVERT: O 324 TYR cc_start: 0.8864 (t80) cc_final: 0.8599 (t80) REVERT: O 438 PHE cc_start: 0.8238 (m-80) cc_final: 0.8006 (m-10) REVERT: O 442 TYR cc_start: 0.9184 (t80) cc_final: 0.8822 (t80) REVERT: P 10 MET cc_start: 0.8056 (mmm) cc_final: 0.7585 (mmp) REVERT: P 17 GLN cc_start: 0.8711 (tt0) cc_final: 0.8450 (tt0) REVERT: Q 41 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8223 (pp) REVERT: Q 181 LEU cc_start: 0.8150 (OUTLIER) cc_final: 0.7815 (pp) REVERT: R 52 TYR cc_start: 0.8000 (m-80) cc_final: 0.7563 (m-80) REVERT: R 59 GLN cc_start: 0.7797 (mt0) cc_final: 0.7083 (mt0) REVERT: S 49 GLU cc_start: 0.7778 (mt-10) cc_final: 0.7304 (tp30) REVERT: S 297 TYR cc_start: 0.7960 (m-80) cc_final: 0.7615 (m-80) REVERT: S 400 PHE cc_start: 0.7933 (t80) cc_final: 0.7441 (t80) REVERT: T 20 MET cc_start: 0.9071 (mtm) cc_final: 0.8726 (mtm) REVERT: T 59 GLN cc_start: 0.8018 (mt0) cc_final: 0.7474 (mt0) REVERT: T 68 MET cc_start: 0.8704 (mmm) cc_final: 0.8296 (mmm) REVERT: U 10 GLU cc_start: 0.8075 (tt0) cc_final: 0.7772 (mt-10) REVERT: U 100 ARG cc_start: 0.7784 (mmm-85) cc_final: 0.7347 (mmm-85) REVERT: V 49 MET cc_start: 0.6324 (mmt) cc_final: 0.5642 (mmt) REVERT: V 71 SER cc_start: 0.8522 (m) cc_final: 0.8260 (p) outliers start: 136 outliers final: 98 residues processed: 607 average time/residue: 0.1563 time to fit residues: 158.3919 Evaluate side-chains 587 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 484 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 134 ASN Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 183 CYS Chi-restraints excluded: chain A residue 244 LYS Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 258 MET Chi-restraints excluded: chain A residue 269 GLN Chi-restraints excluded: chain A residue 283 CYS Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain B residue 20 MET Chi-restraints excluded: chain C residue 2 ARG Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 295 MET Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 401 GLU Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 34 MET Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 205 MET Chi-restraints excluded: chain E residue 268 ILE Chi-restraints excluded: chain E residue 270 THR Chi-restraints excluded: chain E residue 311 SER Chi-restraints excluded: chain E residue 336 SER Chi-restraints excluded: chain E residue 464 ILE Chi-restraints excluded: chain E residue 487 LEU Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 102 PHE Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 48 THR Chi-restraints excluded: chain O residue 115 THR Chi-restraints excluded: chain O residue 124 LEU Chi-restraints excluded: chain O residue 134 ASN Chi-restraints excluded: chain O residue 163 THR Chi-restraints excluded: chain O residue 183 CYS Chi-restraints excluded: chain O residue 244 LYS Chi-restraints excluded: chain O residue 251 LEU Chi-restraints excluded: chain O residue 258 MET Chi-restraints excluded: chain O residue 269 GLN Chi-restraints excluded: chain O residue 283 CYS Chi-restraints excluded: chain O residue 319 LEU Chi-restraints excluded: chain O residue 336 SER Chi-restraints excluded: chain O residue 485 LEU Chi-restraints excluded: chain O residue 491 VAL Chi-restraints excluded: chain P residue 20 MET Chi-restraints excluded: chain Q residue 2 ARG Chi-restraints excluded: chain Q residue 19 THR Chi-restraints excluded: chain Q residue 41 LEU Chi-restraints excluded: chain Q residue 43 ILE Chi-restraints excluded: chain Q residue 65 ILE Chi-restraints excluded: chain Q residue 70 THR Chi-restraints excluded: chain Q residue 92 CYS Chi-restraints excluded: chain Q residue 181 LEU Chi-restraints excluded: chain Q residue 197 LEU Chi-restraints excluded: chain Q residue 262 LEU Chi-restraints excluded: chain Q residue 266 THR Chi-restraints excluded: chain Q residue 281 LEU Chi-restraints excluded: chain Q residue 285 LEU Chi-restraints excluded: chain Q residue 295 MET Chi-restraints excluded: chain Q residue 319 LEU Chi-restraints excluded: chain Q residue 337 THR Chi-restraints excluded: chain Q residue 401 GLU Chi-restraints excluded: chain S residue 33 THR Chi-restraints excluded: chain S residue 34 MET Chi-restraints excluded: chain S residue 51 THR Chi-restraints excluded: chain S residue 130 VAL Chi-restraints excluded: chain S residue 205 MET Chi-restraints excluded: chain S residue 268 ILE Chi-restraints excluded: chain S residue 270 THR Chi-restraints excluded: chain S residue 311 SER Chi-restraints excluded: chain S residue 336 SER Chi-restraints excluded: chain S residue 464 ILE Chi-restraints excluded: chain S residue 487 LEU Chi-restraints excluded: chain T residue 2 VAL Chi-restraints excluded: chain T residue 70 VAL Chi-restraints excluded: chain U residue 28 THR Chi-restraints excluded: chain U residue 78 VAL Chi-restraints excluded: chain U residue 102 PHE Chi-restraints excluded: chain U residue 116 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 290 optimal weight: 5.9990 chunk 171 optimal weight: 9.9990 chunk 49 optimal weight: 10.0000 chunk 180 optimal weight: 8.9990 chunk 159 optimal weight: 7.9990 chunk 302 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 291 optimal weight: 7.9990 chunk 145 optimal weight: 10.0000 chunk 361 optimal weight: 9.9990 chunk 224 optimal weight: 10.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 ASN ** C 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 134 ASN ** Q 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 375 ASN ** R 59 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 = 0.3097 r_free = 0.3097 target = 0.104602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.092279 restraints weight = 43551.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.093150 restraints weight = 30368.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.094448 restraints weight = 24063.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.094712 restraints weight = 19145.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.094788 restraints weight = 16554.619| |-----------------------------------------------------------------------------| r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.2410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.063 30638 Z= 0.332 Angle : 0.753 12.875 41578 Z= 0.386 Chirality : 0.050 0.317 4848 Planarity : 0.004 0.040 5162 Dihedral : 6.651 55.432 4632 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 5.50 % Allowed : 17.88 % Favored : 76.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.31 (0.13), residues: 3838 helix: 1.22 (0.17), residues: 876 sheet: -1.43 (0.15), residues: 1126 loop : -1.49 (0.13), residues: 1836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 15 TYR 0.020 0.002 TYR U 27 PHE 0.028 0.002 PHE C 420 TRP 0.019 0.002 TRP U 50 HIS 0.008 0.001 HIS S 144 Details of bonding type rmsd covalent geometry : bond 0.00798 (30572) covalent geometry : angle 0.74532 (41418) SS BOND : bond 0.00974 ( 38) SS BOND : angle 1.81495 ( 76) hydrogen bonds : bond 0.04358 ( 1190) hydrogen bonds : angle 5.67086 ( 3354) link_BETA1-4 : bond 0.00413 ( 16) link_BETA1-4 : angle 1.66321 ( 48) link_NAG-ASN : bond 0.00547 ( 12) link_NAG-ASN : angle 2.21951 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 682 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 176 poor density : 506 time to evaluate : 1.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 324 TYR cc_start: 0.8831 (t80) cc_final: 0.8579 (t80) REVERT: A 438 PHE cc_start: 0.8319 (m-80) cc_final: 0.8094 (m-10) REVERT: A 442 TYR cc_start: 0.9082 (t80) cc_final: 0.8701 (t80) REVERT: B 10 MET cc_start: 0.8241 (mmm) cc_final: 0.7778 (mmp) REVERT: C 41 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8404 (pp) REVERT: C 181 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8322 (pp) REVERT: C 485 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8826 (mm) REVERT: D 59 GLN cc_start: 0.7981 (mt0) cc_final: 0.7565 (mt0) REVERT: E 49 GLU cc_start: 0.7934 (mt-10) cc_final: 0.7444 (tp30) REVERT: E 282 LYS cc_start: 0.8553 (ttpt) cc_final: 0.8010 (ttpp) REVERT: E 400 PHE cc_start: 0.7853 (t80) cc_final: 0.7379 (t80) REVERT: F 20 MET cc_start: 0.9090 (mtm) cc_final: 0.8805 (mtm) REVERT: H 10 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7850 (mt-10) REVERT: H 106 TYR cc_start: 0.8579 (OUTLIER) cc_final: 0.8083 (m-80) REVERT: L 4 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8103 (pp) REVERT: L 48 LEU cc_start: 0.8147 (tt) cc_final: 0.7828 (tp) REVERT: L 49 MET cc_start: 0.6309 (mmt) cc_final: 0.5923 (mmt) REVERT: L 55 ARG cc_start: 0.8332 (mtm110) cc_final: 0.7959 (mtm110) REVERT: L 71 SER cc_start: 0.8560 (m) cc_final: 0.8272 (p) REVERT: O 324 TYR cc_start: 0.8827 (t80) cc_final: 0.8572 (t80) REVERT: O 438 PHE cc_start: 0.8314 (m-80) cc_final: 0.8088 (m-10) REVERT: O 442 TYR cc_start: 0.9082 (t80) cc_final: 0.8702 (t80) REVERT: P 10 MET cc_start: 0.8228 (mmm) cc_final: 0.7784 (mmp) REVERT: Q 41 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8408 (pp) REVERT: Q 181 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.8323 (pp) REVERT: Q 375 ASN cc_start: 0.8290 (OUTLIER) cc_final: 0.7578 (t0) REVERT: Q 485 LEU cc_start: 0.9072 (mm) cc_final: 0.8804 (mm) REVERT: R 59 GLN cc_start: 0.7929 (mt0) cc_final: 0.7657 (mt0) REVERT: S 49 GLU cc_start: 0.7934 (mt-10) cc_final: 0.7441 (tp30) REVERT: S 282 LYS cc_start: 0.8551 (ttpt) cc_final: 0.8006 (ttpp) REVERT: S 400 PHE cc_start: 0.7850 (t80) cc_final: 0.7376 (t80) REVERT: T 20 MET cc_start: 0.9077 (mtm) cc_final: 0.8809 (mtm) REVERT: U 10 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7858 (mt-10) REVERT: U 106 TYR cc_start: 0.8589 (OUTLIER) cc_final: 0.8089 (m-80) REVERT: V 4 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8110 (pp) REVERT: V 48 LEU cc_start: 0.8132 (tt) cc_final: 0.7821 (tp) REVERT: V 49 MET cc_start: 0.6308 (mmt) cc_final: 0.5909 (mmt) REVERT: V 55 ARG cc_start: 0.8329 (mtm110) cc_final: 0.7952 (mtm110) REVERT: V 71 SER cc_start: 0.8558 (m) cc_final: 0.8278 (p) outliers start: 176 outliers final: 129 residues processed: 626 average time/residue: 0.1721 time to fit residues: 177.6787 Evaluate side-chains 606 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 465 time to evaluate : 1.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 183 CYS Chi-restraints excluded: chain A residue 244 LYS Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 258 MET Chi-restraints excluded: chain A residue 269 GLN Chi-restraints excluded: chain A residue 283 CYS Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 371 PHE Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 20 MET Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 295 MET Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 394 SER Chi-restraints excluded: chain C residue 401 GLU Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 34 MET Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 121 CYS Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 144 HIS Chi-restraints excluded: chain E residue 205 MET Chi-restraints excluded: chain E residue 268 ILE Chi-restraints excluded: chain E residue 270 THR Chi-restraints excluded: chain E residue 311 SER Chi-restraints excluded: chain E residue 336 SER Chi-restraints excluded: chain E residue 355 VAL Chi-restraints excluded: chain E residue 361 GLU Chi-restraints excluded: chain E residue 380 ILE Chi-restraints excluded: chain E residue 464 ILE Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 70 MET Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 106 TYR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 48 THR Chi-restraints excluded: chain O residue 66 THR Chi-restraints excluded: chain O residue 115 THR Chi-restraints excluded: chain O residue 124 LEU Chi-restraints excluded: chain O residue 163 THR Chi-restraints excluded: chain O residue 182 GLU Chi-restraints excluded: chain O residue 183 CYS Chi-restraints excluded: chain O residue 244 LYS Chi-restraints excluded: chain O residue 251 LEU Chi-restraints excluded: chain O residue 258 MET Chi-restraints excluded: chain O residue 269 GLN Chi-restraints excluded: chain O residue 283 CYS Chi-restraints excluded: chain O residue 319 LEU Chi-restraints excluded: chain O residue 336 SER Chi-restraints excluded: chain O residue 355 VAL Chi-restraints excluded: chain O residue 363 VAL Chi-restraints excluded: chain O residue 371 PHE Chi-restraints excluded: chain O residue 485 LEU Chi-restraints excluded: chain O residue 491 VAL Chi-restraints excluded: chain P residue 8 VAL Chi-restraints excluded: chain P residue 20 MET Chi-restraints excluded: chain Q residue 19 THR Chi-restraints excluded: chain Q residue 41 LEU Chi-restraints excluded: chain Q residue 43 ILE Chi-restraints excluded: chain Q residue 53 LEU Chi-restraints excluded: chain Q residue 65 ILE Chi-restraints excluded: chain Q residue 70 THR Chi-restraints excluded: chain Q residue 92 CYS Chi-restraints excluded: chain Q residue 126 GLU Chi-restraints excluded: chain Q residue 139 VAL Chi-restraints excluded: chain Q residue 158 VAL Chi-restraints excluded: chain Q residue 181 LEU Chi-restraints excluded: chain Q residue 197 LEU Chi-restraints excluded: chain Q residue 262 LEU Chi-restraints excluded: chain Q residue 266 THR Chi-restraints excluded: chain Q residue 281 LEU Chi-restraints excluded: chain Q residue 285 LEU Chi-restraints excluded: chain Q residue 295 MET Chi-restraints excluded: chain Q residue 319 LEU Chi-restraints excluded: chain Q residue 337 THR Chi-restraints excluded: chain Q residue 375 ASN Chi-restraints excluded: chain Q residue 394 SER Chi-restraints excluded: chain Q residue 401 GLU Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain S residue 33 THR Chi-restraints excluded: chain S residue 34 MET Chi-restraints excluded: chain S residue 51 THR Chi-restraints excluded: chain S residue 121 CYS Chi-restraints excluded: chain S residue 130 VAL Chi-restraints excluded: chain S residue 144 HIS Chi-restraints excluded: chain S residue 205 MET Chi-restraints excluded: chain S residue 268 ILE Chi-restraints excluded: chain S residue 311 SER Chi-restraints excluded: chain S residue 336 SER Chi-restraints excluded: chain S residue 355 VAL Chi-restraints excluded: chain S residue 361 GLU Chi-restraints excluded: chain S residue 380 ILE Chi-restraints excluded: chain S residue 464 ILE Chi-restraints excluded: chain T residue 2 VAL Chi-restraints excluded: chain T residue 70 VAL Chi-restraints excluded: chain U residue 10 GLU Chi-restraints excluded: chain U residue 28 THR Chi-restraints excluded: chain U residue 69 THR Chi-restraints excluded: chain U residue 70 MET Chi-restraints excluded: chain U residue 90 ASP Chi-restraints excluded: chain U residue 93 VAL Chi-restraints excluded: chain U residue 106 TYR Chi-restraints excluded: chain U residue 116 THR Chi-restraints excluded: chain V residue 4 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 156 optimal weight: 1.9990 chunk 159 optimal weight: 7.9990 chunk 41 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 chunk 76 optimal weight: 0.9990 chunk 137 optimal weight: 0.9980 chunk 306 optimal weight: 3.9990 chunk 368 optimal weight: 6.9990 chunk 153 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 ASN A 364 ASN ** C 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 GLN E 134 ASN ** L 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 132 HIS O 134 ASN O 364 ASN ** Q 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 134 ASN ** V 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.110542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.096900 restraints weight = 42895.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.098990 restraints weight = 26203.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.100408 restraints weight = 18325.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.101245 restraints weight = 14117.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.101992 restraints weight = 11793.181| |-----------------------------------------------------------------------------| r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 30638 Z= 0.126 Angle : 0.602 13.523 41578 Z= 0.307 Chirality : 0.044 0.297 4848 Planarity : 0.004 0.040 5162 Dihedral : 6.098 54.640 4632 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 3.75 % Allowed : 20.69 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.05 (0.13), residues: 3838 helix: 1.63 (0.18), residues: 876 sheet: -1.48 (0.15), residues: 1164 loop : -1.28 (0.14), residues: 1798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 100 TYR 0.015 0.001 TYR U 27 PHE 0.019 0.001 PHE C 420 TRP 0.014 0.001 TRP U 50 HIS 0.007 0.001 HIS S 144 Details of bonding type rmsd covalent geometry : bond 0.00282 (30572) covalent geometry : angle 0.59501 (41418) SS BOND : bond 0.00600 ( 38) SS BOND : angle 1.54118 ( 76) hydrogen bonds : bond 0.03736 ( 1190) hydrogen bonds : angle 5.29730 ( 3354) link_BETA1-4 : bond 0.00405 ( 16) link_BETA1-4 : angle 1.62612 ( 48) link_NAG-ASN : bond 0.00263 ( 12) link_NAG-ASN : angle 1.62106 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 670 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 550 time to evaluate : 1.135 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: A 324 TYR cc_start: 0.8832 (t80) cc_final: 0.8526 (t80) REVERT: A 438 PHE cc_start: 0.8238 (m-80) cc_final: 0.8019 (m-10) REVERT: A 442 TYR cc_start: 0.9147 (t80) cc_final: 0.8832 (t80) REVERT: B 10 MET cc_start: 0.7935 (mmm) cc_final: 0.7626 (mmp) REVERT: B 17 GLN cc_start: 0.8793 (tt0) cc_final: 0.8590 (tt0) REVERT: C 1 MET cc_start: 0.9105 (tpp) cc_final: 0.8888 (tpp) REVERT: C 13 GLU cc_start: 0.8069 (tm-30) cc_final: 0.7778 (tm-30) REVERT: C 41 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8117 (pp) REVERT: C 181 LEU cc_start: 0.8288 (OUTLIER) cc_final: 0.8038 (pp) REVERT: C 312 GLU cc_start: 0.7119 (tt0) cc_final: 0.6889 (tt0) REVERT: C 485 LEU cc_start: 0.9121 (OUTLIER) cc_final: 0.8817 (mm) REVERT: D 52 TYR cc_start: 0.7982 (m-80) cc_final: 0.7643 (m-80) REVERT: D 59 GLN cc_start: 0.7905 (mt0) cc_final: 0.7556 (mt0) REVERT: E 49 GLU cc_start: 0.7701 (mt-10) cc_final: 0.7137 (tp30) REVERT: E 91 VAL cc_start: 0.8951 (p) cc_final: 0.8676 (p) REVERT: E 282 LYS cc_start: 0.8225 (ttpt) cc_final: 0.7831 (ttpp) REVERT: E 297 TYR cc_start: 0.8066 (m-80) cc_final: 0.7853 (m-80) REVERT: E 400 PHE cc_start: 0.7897 (t80) cc_final: 0.7429 (t80) REVERT: F 20 MET cc_start: 0.9064 (mtm) cc_final: 0.8735 (mtm) REVERT: H 10 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.7670 (mt-10) REVERT: H 100 ARG cc_start: 0.7805 (mmm-85) cc_final: 0.7355 (mmm-85) REVERT: H 106 TYR cc_start: 0.8436 (OUTLIER) cc_final: 0.7948 (m-80) REVERT: L 4 LEU cc_start: 0.8306 (OUTLIER) cc_final: 0.7803 (pp) REVERT: L 48 LEU cc_start: 0.8021 (tt) cc_final: 0.7781 (tp) REVERT: L 49 MET cc_start: 0.6138 (mmt) cc_final: 0.5746 (mmt) REVERT: L 55 ARG cc_start: 0.8305 (mtm110) cc_final: 0.7909 (mtm110) REVERT: L 71 SER cc_start: 0.8572 (m) cc_final: 0.8263 (p) REVERT: O 132 HIS cc_start: 0.8158 (t70) cc_final: 0.7939 (t-170) REVERT: O 324 TYR cc_start: 0.8828 (t80) cc_final: 0.8522 (t80) REVERT: O 438 PHE cc_start: 0.8236 (m-80) cc_final: 0.8020 (m-10) REVERT: O 442 TYR cc_start: 0.9147 (t80) cc_final: 0.8832 (t80) REVERT: P 10 MET cc_start: 0.7921 (mmm) cc_final: 0.7625 (mmp) REVERT: P 17 GLN cc_start: 0.8796 (tt0) cc_final: 0.8593 (tt0) REVERT: Q 1 MET cc_start: 0.9122 (tpp) cc_final: 0.8907 (tpp) REVERT: Q 13 GLU cc_start: 0.8059 (tm-30) cc_final: 0.7774 (tm-30) REVERT: Q 41 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8119 (pp) REVERT: Q 181 LEU cc_start: 0.8296 (OUTLIER) cc_final: 0.8043 (pp) REVERT: Q 312 GLU cc_start: 0.7119 (tt0) cc_final: 0.6878 (tt0) REVERT: Q 485 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8834 (mm) REVERT: R 52 TYR cc_start: 0.7976 (m-80) cc_final: 0.7642 (m-80) REVERT: R 59 GLN cc_start: 0.7871 (mt0) cc_final: 0.7582 (mt0) REVERT: S 49 GLU cc_start: 0.7694 (mt-10) cc_final: 0.7119 (tp30) REVERT: S 282 LYS cc_start: 0.8223 (ttpt) cc_final: 0.7826 (ttpp) REVERT: S 297 TYR cc_start: 0.8065 (m-80) cc_final: 0.7859 (m-80) REVERT: S 400 PHE cc_start: 0.7894 (t80) cc_final: 0.7430 (t80) REVERT: T 20 MET cc_start: 0.9040 (mtm) cc_final: 0.8737 (mtm) REVERT: U 10 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7683 (mt-10) REVERT: U 100 ARG cc_start: 0.7798 (mmm-85) cc_final: 0.7355 (mmm-85) REVERT: U 106 TYR cc_start: 0.8439 (OUTLIER) cc_final: 0.7951 (m-80) REVERT: V 4 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.7807 (pp) REVERT: V 48 LEU cc_start: 0.8033 (tt) cc_final: 0.7794 (tp) REVERT: V 49 MET cc_start: 0.6138 (mmt) cc_final: 0.5737 (mmt) REVERT: V 55 ARG cc_start: 0.8298 (mtm110) cc_final: 0.7908 (mtm110) REVERT: V 71 SER cc_start: 0.8567 (m) cc_final: 0.8270 (p) outliers start: 120 outliers final: 75 residues processed: 632 average time/residue: 0.1777 time to fit residues: 187.2235 Evaluate side-chains 595 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 508 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 134 ASN Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 183 CYS Chi-restraints excluded: chain A residue 244 LYS Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 371 PHE Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain B residue 20 MET Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 401 GLU Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain E residue 34 MET Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 121 CYS Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 205 MET Chi-restraints excluded: chain E residue 268 ILE Chi-restraints excluded: chain E residue 311 SER Chi-restraints excluded: chain E residue 336 SER Chi-restraints excluded: chain E residue 487 LEU Chi-restraints excluded: chain F residue 21 SER Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 70 MET Chi-restraints excluded: chain H residue 106 TYR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 20 ILE Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 48 THR Chi-restraints excluded: chain O residue 134 ASN Chi-restraints excluded: chain O residue 163 THR Chi-restraints excluded: chain O residue 179 LEU Chi-restraints excluded: chain O residue 182 GLU Chi-restraints excluded: chain O residue 183 CYS Chi-restraints excluded: chain O residue 244 LYS Chi-restraints excluded: chain O residue 355 VAL Chi-restraints excluded: chain O residue 371 PHE Chi-restraints excluded: chain O residue 485 LEU Chi-restraints excluded: chain O residue 491 VAL Chi-restraints excluded: chain P residue 20 MET Chi-restraints excluded: chain Q residue 19 THR Chi-restraints excluded: chain Q residue 41 LEU Chi-restraints excluded: chain Q residue 43 ILE Chi-restraints excluded: chain Q residue 65 ILE Chi-restraints excluded: chain Q residue 70 THR Chi-restraints excluded: chain Q residue 92 CYS Chi-restraints excluded: chain Q residue 181 LEU Chi-restraints excluded: chain Q residue 197 LEU Chi-restraints excluded: chain Q residue 266 THR Chi-restraints excluded: chain Q residue 281 LEU Chi-restraints excluded: chain Q residue 285 LEU Chi-restraints excluded: chain Q residue 337 THR Chi-restraints excluded: chain Q residue 401 GLU Chi-restraints excluded: chain Q residue 485 LEU Chi-restraints excluded: chain S residue 34 MET Chi-restraints excluded: chain S residue 51 THR Chi-restraints excluded: chain S residue 121 CYS Chi-restraints excluded: chain S residue 130 VAL Chi-restraints excluded: chain S residue 205 MET Chi-restraints excluded: chain S residue 268 ILE Chi-restraints excluded: chain S residue 270 THR Chi-restraints excluded: chain S residue 311 SER Chi-restraints excluded: chain S residue 336 SER Chi-restraints excluded: chain S residue 487 LEU Chi-restraints excluded: chain T residue 21 SER Chi-restraints excluded: chain U residue 10 GLU Chi-restraints excluded: chain U residue 70 MET Chi-restraints excluded: chain U residue 106 TYR Chi-restraints excluded: chain U residue 116 THR Chi-restraints excluded: chain V residue 4 LEU Chi-restraints excluded: chain V residue 20 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 56 optimal weight: 9.9990 chunk 289 optimal weight: 10.0000 chunk 72 optimal weight: 8.9990 chunk 257 optimal weight: 9.9990 chunk 41 optimal weight: 0.8980 chunk 342 optimal weight: 6.9990 chunk 12 optimal weight: 7.9990 chunk 77 optimal weight: 4.9990 chunk 298 optimal weight: 10.0000 chunk 84 optimal weight: 10.0000 chunk 160 optimal weight: 6.9990 overall best weight: 5.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 144 HIS ** C 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 144 HIS ** Q 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 52 ASN ** 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 = 0.3117 r_free = 0.3117 target = 0.105974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.091488 restraints weight = 43482.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.093686 restraints weight = 26069.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.095222 restraints weight = 18103.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.096234 restraints weight = 13818.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.096966 restraints weight = 11366.458| |-----------------------------------------------------------------------------| r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.2619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.074 30638 Z= 0.271 Angle : 0.696 12.881 41578 Z= 0.358 Chirality : 0.048 0.268 4848 Planarity : 0.004 0.075 5162 Dihedral : 6.332 55.470 4632 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 4.97 % Allowed : 20.41 % Favored : 74.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.22 (0.13), residues: 3838 helix: 1.42 (0.18), residues: 876 sheet: -1.55 (0.14), residues: 1252 loop : -1.33 (0.14), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG U 85 TYR 0.020 0.002 TYR U 27 PHE 0.032 0.002 PHE O 191 TRP 0.018 0.002 TRP H 50 HIS 0.012 0.001 HIS S 144 Details of bonding type rmsd covalent geometry : bond 0.00651 (30572) covalent geometry : angle 0.68939 (41418) SS BOND : bond 0.00814 ( 38) SS BOND : angle 1.67472 ( 76) hydrogen bonds : bond 0.04039 ( 1190) hydrogen bonds : angle 5.43639 ( 3354) link_BETA1-4 : bond 0.00420 ( 16) link_BETA1-4 : angle 1.59574 ( 48) link_NAG-ASN : bond 0.00492 ( 12) link_NAG-ASN : angle 1.97406 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 661 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 502 time to evaluate : 1.219 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: A 251 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8773 (mp) REVERT: A 324 TYR cc_start: 0.8759 (t80) cc_final: 0.8503 (t80) REVERT: A 438 PHE cc_start: 0.8298 (m-80) cc_final: 0.8055 (m-10) REVERT: A 442 TYR cc_start: 0.9156 (t80) cc_final: 0.8789 (t80) REVERT: B 10 MET cc_start: 0.8174 (mmm) cc_final: 0.7737 (mmp) REVERT: C 13 GLU cc_start: 0.8185 (tm-30) cc_final: 0.7847 (tm-30) REVERT: C 41 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8241 (pp) REVERT: C 181 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8253 (pp) REVERT: C 309 GLU cc_start: 0.6626 (tt0) cc_final: 0.6385 (tt0) REVERT: C 485 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8814 (mm) REVERT: D 59 GLN cc_start: 0.7966 (mt0) cc_final: 0.7548 (mt0) REVERT: E 49 GLU cc_start: 0.8018 (mt-10) cc_final: 0.7429 (tp30) REVERT: E 91 VAL cc_start: 0.9058 (p) cc_final: 0.8766 (p) REVERT: E 170 GLU cc_start: 0.6684 (mp0) cc_final: 0.6294 (mp0) REVERT: E 282 LYS cc_start: 0.8492 (ttpt) cc_final: 0.7885 (ttpp) REVERT: E 400 PHE cc_start: 0.7919 (t80) cc_final: 0.7427 (t80) REVERT: F 20 MET cc_start: 0.9125 (mtm) cc_final: 0.8853 (mtm) REVERT: H 10 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7719 (mt-10) REVERT: H 100 ARG cc_start: 0.7760 (mmm-85) cc_final: 0.7389 (mmm-85) REVERT: H 102 PHE cc_start: 0.8701 (p90) cc_final: 0.8375 (p90) REVERT: H 106 TYR cc_start: 0.8611 (OUTLIER) cc_final: 0.7989 (m-80) REVERT: L 4 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.7887 (pp) REVERT: L 48 LEU cc_start: 0.8092 (tt) cc_final: 0.7859 (tp) REVERT: L 49 MET cc_start: 0.6058 (mmt) cc_final: 0.5655 (mmt) REVERT: L 55 ARG cc_start: 0.8337 (mtm110) cc_final: 0.7906 (mtm110) REVERT: L 71 SER cc_start: 0.8596 (m) cc_final: 0.8282 (p) REVERT: O 251 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8773 (mp) REVERT: O 324 TYR cc_start: 0.8756 (t80) cc_final: 0.8493 (t80) REVERT: O 438 PHE cc_start: 0.8294 (m-80) cc_final: 0.8050 (m-10) REVERT: O 442 TYR cc_start: 0.9155 (t80) cc_final: 0.8790 (t80) REVERT: P 10 MET cc_start: 0.8158 (mmm) cc_final: 0.7741 (mmp) REVERT: Q 13 GLU cc_start: 0.8175 (tm-30) cc_final: 0.7846 (tm-30) REVERT: Q 41 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8246 (pp) REVERT: Q 181 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8258 (pp) REVERT: Q 309 GLU cc_start: 0.6631 (tt0) cc_final: 0.6385 (tt0) REVERT: Q 485 LEU cc_start: 0.9121 (OUTLIER) cc_final: 0.8834 (mm) REVERT: R 30 GLU cc_start: 0.7665 (mm-30) cc_final: 0.7406 (mm-30) REVERT: R 52 TYR cc_start: 0.8003 (m-80) cc_final: 0.7693 (m-80) REVERT: R 59 GLN cc_start: 0.7939 (mt0) cc_final: 0.7659 (mt0) REVERT: S 49 GLU cc_start: 0.8017 (mt-10) cc_final: 0.7425 (tp30) REVERT: S 170 GLU cc_start: 0.6681 (mp0) cc_final: 0.6289 (mp0) REVERT: S 282 LYS cc_start: 0.8489 (ttpt) cc_final: 0.7883 (ttpp) REVERT: S 400 PHE cc_start: 0.7919 (t80) cc_final: 0.7427 (t80) REVERT: T 20 MET cc_start: 0.9105 (mtm) cc_final: 0.8854 (mtm) REVERT: U 10 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7728 (mt-10) REVERT: U 100 ARG cc_start: 0.7759 (mmm-85) cc_final: 0.7393 (mmm-85) REVERT: U 102 PHE cc_start: 0.8699 (p90) cc_final: 0.8373 (p90) REVERT: U 106 TYR cc_start: 0.8615 (OUTLIER) cc_final: 0.7992 (m-80) REVERT: V 4 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.7901 (pp) REVERT: V 48 LEU cc_start: 0.8098 (tt) cc_final: 0.7865 (tp) REVERT: V 49 MET cc_start: 0.6058 (mmt) cc_final: 0.5648 (mmt) REVERT: V 55 ARG cc_start: 0.8332 (mtm110) cc_final: 0.7904 (mtm110) REVERT: V 71 SER cc_start: 0.8593 (m) cc_final: 0.8283 (p) outliers start: 159 outliers final: 115 residues processed: 607 average time/residue: 0.1802 time to fit residues: 182.9651 Evaluate side-chains 615 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 486 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 183 CYS Chi-restraints excluded: chain A residue 244 LYS Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 371 PHE Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 20 MET Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 42 ASP Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 205 MET Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 295 MET Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 401 GLU Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain E residue 34 MET Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 121 CYS Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 205 MET Chi-restraints excluded: chain E residue 268 ILE Chi-restraints excluded: chain E residue 270 THR Chi-restraints excluded: chain E residue 310 VAL Chi-restraints excluded: chain E residue 311 SER Chi-restraints excluded: chain E residue 336 SER Chi-restraints excluded: chain E residue 464 ILE Chi-restraints excluded: chain E residue 487 LEU Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 21 SER Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 70 MET Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 106 TYR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 20 ILE Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 48 THR Chi-restraints excluded: chain O residue 115 THR Chi-restraints excluded: chain O residue 124 LEU Chi-restraints excluded: chain O residue 163 THR Chi-restraints excluded: chain O residue 179 LEU Chi-restraints excluded: chain O residue 182 GLU Chi-restraints excluded: chain O residue 183 CYS Chi-restraints excluded: chain O residue 244 LYS Chi-restraints excluded: chain O residue 251 LEU Chi-restraints excluded: chain O residue 319 LEU Chi-restraints excluded: chain O residue 336 SER Chi-restraints excluded: chain O residue 355 VAL Chi-restraints excluded: chain O residue 371 PHE Chi-restraints excluded: chain O residue 485 LEU Chi-restraints excluded: chain O residue 491 VAL Chi-restraints excluded: chain P residue 8 VAL Chi-restraints excluded: chain P residue 20 MET Chi-restraints excluded: chain Q residue 19 THR Chi-restraints excluded: chain Q residue 41 LEU Chi-restraints excluded: chain Q residue 42 ASP Chi-restraints excluded: chain Q residue 43 ILE Chi-restraints excluded: chain Q residue 65 ILE Chi-restraints excluded: chain Q residue 70 THR Chi-restraints excluded: chain Q residue 92 CYS Chi-restraints excluded: chain Q residue 126 GLU Chi-restraints excluded: chain Q residue 139 VAL Chi-restraints excluded: chain Q residue 181 LEU Chi-restraints excluded: chain Q residue 197 LEU Chi-restraints excluded: chain Q residue 205 MET Chi-restraints excluded: chain Q residue 262 LEU Chi-restraints excluded: chain Q residue 266 THR Chi-restraints excluded: chain Q residue 281 LEU Chi-restraints excluded: chain Q residue 285 LEU Chi-restraints excluded: chain Q residue 295 MET Chi-restraints excluded: chain Q residue 319 LEU Chi-restraints excluded: chain Q residue 337 THR Chi-restraints excluded: chain Q residue 401 GLU Chi-restraints excluded: chain Q residue 485 LEU Chi-restraints excluded: chain R residue 33 GLU Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain S residue 34 MET Chi-restraints excluded: chain S residue 51 THR Chi-restraints excluded: chain S residue 121 CYS Chi-restraints excluded: chain S residue 130 VAL Chi-restraints excluded: chain S residue 205 MET Chi-restraints excluded: chain S residue 268 ILE Chi-restraints excluded: chain S residue 270 THR Chi-restraints excluded: chain S residue 310 VAL Chi-restraints excluded: chain S residue 311 SER Chi-restraints excluded: chain S residue 336 SER Chi-restraints excluded: chain S residue 464 ILE Chi-restraints excluded: chain S residue 487 LEU Chi-restraints excluded: chain T residue 2 VAL Chi-restraints excluded: chain T residue 21 SER Chi-restraints excluded: chain T residue 70 VAL Chi-restraints excluded: chain U residue 10 GLU Chi-restraints excluded: chain U residue 69 THR Chi-restraints excluded: chain U residue 70 MET Chi-restraints excluded: chain U residue 93 VAL Chi-restraints excluded: chain U residue 106 TYR Chi-restraints excluded: chain U residue 116 THR Chi-restraints excluded: chain V residue 4 LEU Chi-restraints excluded: chain V residue 20 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 5 optimal weight: 7.9990 chunk 321 optimal weight: 4.9990 chunk 127 optimal weight: 5.9990 chunk 157 optimal weight: 3.9990 chunk 88 optimal weight: 0.9980 chunk 52 optimal weight: 8.9990 chunk 59 optimal weight: 1.9990 chunk 182 optimal weight: 0.9980 chunk 170 optimal weight: 10.0000 chunk 306 optimal weight: 1.9990 chunk 241 optimal weight: 10.0000 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 HIS ** C 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 59 GLN ** V 52 ASN ** 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 = 0.3165 r_free = 0.3165 target = 0.109492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.095985 restraints weight = 43135.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.098433 restraints weight = 27799.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.099866 restraints weight = 17033.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.100222 restraints weight = 13038.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.100172 restraints weight = 11351.016| |-----------------------------------------------------------------------------| r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.2697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 30638 Z= 0.141 Angle : 0.601 13.329 41578 Z= 0.307 Chirality : 0.044 0.269 4848 Planarity : 0.004 0.064 5162 Dihedral : 6.018 54.928 4632 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 4.31 % Allowed : 21.38 % Favored : 74.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.06 (0.13), residues: 3838 helix: 1.62 (0.18), residues: 882 sheet: -1.47 (0.15), residues: 1136 loop : -1.31 (0.13), residues: 1820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 85 TYR 0.019 0.002 TYR H 27 PHE 0.018 0.001 PHE Q 420 TRP 0.015 0.001 TRP U 50 HIS 0.004 0.001 HIS S 149 Details of bonding type rmsd covalent geometry : bond 0.00328 (30572) covalent geometry : angle 0.59592 (41418) SS BOND : bond 0.00632 ( 38) SS BOND : angle 1.25137 ( 76) hydrogen bonds : bond 0.03705 ( 1190) hydrogen bonds : angle 5.17564 ( 3354) link_BETA1-4 : bond 0.00399 ( 16) link_BETA1-4 : angle 1.58121 ( 48) link_NAG-ASN : bond 0.00305 ( 12) link_NAG-ASN : angle 1.62310 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 662 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 524 time to evaluate : 1.161 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: A 324 TYR cc_start: 0.8795 (t80) cc_final: 0.8483 (t80) REVERT: A 438 PHE cc_start: 0.8237 (m-80) cc_final: 0.8014 (m-10) REVERT: A 442 TYR cc_start: 0.9153 (t80) cc_final: 0.8783 (t80) REVERT: B 10 MET cc_start: 0.8019 (mmm) cc_final: 0.7670 (mmp) REVERT: C 13 GLU cc_start: 0.8014 (tm-30) cc_final: 0.7621 (tm-30) REVERT: C 41 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8146 (pp) REVERT: C 181 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.8065 (pp) REVERT: C 312 GLU cc_start: 0.7101 (tt0) cc_final: 0.6855 (tt0) REVERT: C 485 LEU cc_start: 0.9123 (OUTLIER) cc_final: 0.8812 (mm) REVERT: D 30 GLU cc_start: 0.7586 (mm-30) cc_final: 0.7276 (mm-30) REVERT: D 52 TYR cc_start: 0.8092 (m-80) cc_final: 0.7826 (m-80) REVERT: D 59 GLN cc_start: 0.7947 (mt0) cc_final: 0.7591 (mt0) REVERT: E 91 VAL cc_start: 0.8966 (p) cc_final: 0.8679 (p) REVERT: E 282 LYS cc_start: 0.8388 (ttpt) cc_final: 0.7930 (ttpp) REVERT: E 297 TYR cc_start: 0.7947 (m-80) cc_final: 0.7625 (m-80) REVERT: E 400 PHE cc_start: 0.7906 (t80) cc_final: 0.7449 (t80) REVERT: F 20 MET cc_start: 0.9068 (mtm) cc_final: 0.8762 (mtm) REVERT: H 10 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.7710 (mt-10) REVERT: H 100 ARG cc_start: 0.7809 (mmm-85) cc_final: 0.7451 (mmm-85) REVERT: H 106 TYR cc_start: 0.8502 (OUTLIER) cc_final: 0.7962 (m-80) REVERT: L 4 LEU cc_start: 0.8366 (OUTLIER) cc_final: 0.7722 (pp) REVERT: L 37 TYR cc_start: 0.8378 (m-80) cc_final: 0.8114 (m-80) REVERT: L 48 LEU cc_start: 0.7983 (tt) cc_final: 0.7770 (tp) REVERT: L 49 MET cc_start: 0.6147 (mmt) cc_final: 0.5724 (mmt) REVERT: L 55 ARG cc_start: 0.8348 (mtm110) cc_final: 0.7913 (mtm110) REVERT: L 71 SER cc_start: 0.8577 (m) cc_final: 0.8298 (p) REVERT: O 324 TYR cc_start: 0.8788 (t80) cc_final: 0.8475 (t80) REVERT: O 438 PHE cc_start: 0.8231 (m-80) cc_final: 0.8008 (m-10) REVERT: O 442 TYR cc_start: 0.9150 (t80) cc_final: 0.8800 (t80) REVERT: P 10 MET cc_start: 0.8006 (mmm) cc_final: 0.7657 (mmp) REVERT: Q 13 GLU cc_start: 0.8008 (tm-30) cc_final: 0.7622 (tm-30) REVERT: Q 41 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8152 (pp) REVERT: Q 181 LEU cc_start: 0.8257 (OUTLIER) cc_final: 0.8009 (pp) REVERT: Q 312 GLU cc_start: 0.7100 (tt0) cc_final: 0.6847 (tt0) REVERT: Q 485 LEU cc_start: 0.9120 (OUTLIER) cc_final: 0.8831 (mm) REVERT: R 30 GLU cc_start: 0.7608 (mm-30) cc_final: 0.7276 (mm-30) REVERT: R 52 TYR cc_start: 0.7987 (m-80) cc_final: 0.7699 (m-80) REVERT: R 59 GLN cc_start: 0.7936 (mt0) cc_final: 0.7620 (mt0) REVERT: S 282 LYS cc_start: 0.8385 (ttpt) cc_final: 0.7927 (ttpp) REVERT: S 297 TYR cc_start: 0.7943 (m-80) cc_final: 0.7624 (m-80) REVERT: S 400 PHE cc_start: 0.7905 (t80) cc_final: 0.7445 (t80) REVERT: T 20 MET cc_start: 0.9050 (mtm) cc_final: 0.8771 (mtm) REVERT: U 10 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.7711 (mt-10) REVERT: U 100 ARG cc_start: 0.7802 (mmm-85) cc_final: 0.7454 (mmm-85) REVERT: U 106 TYR cc_start: 0.8458 (OUTLIER) cc_final: 0.7940 (m-80) REVERT: V 4 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.7727 (pp) REVERT: V 37 TYR cc_start: 0.8420 (m-80) cc_final: 0.8135 (m-80) REVERT: V 48 LEU cc_start: 0.7985 (tt) cc_final: 0.7773 (tp) REVERT: V 49 MET cc_start: 0.6131 (mmt) cc_final: 0.5701 (mmt) REVERT: V 55 ARG cc_start: 0.8341 (mtm110) cc_final: 0.7910 (mtm110) REVERT: V 71 SER cc_start: 0.8586 (m) cc_final: 0.8308 (p) outliers start: 138 outliers final: 104 residues processed: 616 average time/residue: 0.1796 time to fit residues: 183.8043 Evaluate side-chains 626 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 510 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 183 CYS Chi-restraints excluded: chain A residue 220 SER Chi-restraints excluded: chain A residue 244 LYS Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 371 PHE Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 20 MET Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 42 ASP Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 205 MET Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 295 MET Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 401 GLU Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain E residue 16 SER Chi-restraints excluded: chain E residue 34 MET Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 121 CYS Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 205 MET Chi-restraints excluded: chain E residue 268 ILE Chi-restraints excluded: chain E residue 270 THR Chi-restraints excluded: chain E residue 310 VAL Chi-restraints excluded: chain E residue 311 SER Chi-restraints excluded: chain E residue 336 SER Chi-restraints excluded: chain E residue 464 ILE Chi-restraints excluded: chain E residue 487 LEU Chi-restraints excluded: chain F residue 21 SER Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 70 MET Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 106 TYR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 48 THR Chi-restraints excluded: chain O residue 115 THR Chi-restraints excluded: chain O residue 124 LEU Chi-restraints excluded: chain O residue 163 THR Chi-restraints excluded: chain O residue 179 LEU Chi-restraints excluded: chain O residue 182 GLU Chi-restraints excluded: chain O residue 183 CYS Chi-restraints excluded: chain O residue 220 SER Chi-restraints excluded: chain O residue 244 LYS Chi-restraints excluded: chain O residue 336 SER Chi-restraints excluded: chain O residue 355 VAL Chi-restraints excluded: chain O residue 371 PHE Chi-restraints excluded: chain O residue 491 VAL Chi-restraints excluded: chain P residue 8 VAL Chi-restraints excluded: chain P residue 20 MET Chi-restraints excluded: chain Q residue 19 THR Chi-restraints excluded: chain Q residue 41 LEU Chi-restraints excluded: chain Q residue 42 ASP Chi-restraints excluded: chain Q residue 43 ILE Chi-restraints excluded: chain Q residue 65 ILE Chi-restraints excluded: chain Q residue 70 THR Chi-restraints excluded: chain Q residue 92 CYS Chi-restraints excluded: chain Q residue 126 GLU Chi-restraints excluded: chain Q residue 139 VAL Chi-restraints excluded: chain Q residue 181 LEU Chi-restraints excluded: chain Q residue 197 LEU Chi-restraints excluded: chain Q residue 205 MET Chi-restraints excluded: chain Q residue 262 LEU Chi-restraints excluded: chain Q residue 266 THR Chi-restraints excluded: chain Q residue 281 LEU Chi-restraints excluded: chain Q residue 285 LEU Chi-restraints excluded: chain Q residue 295 MET Chi-restraints excluded: chain Q residue 337 THR Chi-restraints excluded: chain Q residue 401 GLU Chi-restraints excluded: chain Q residue 485 LEU Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain S residue 16 SER Chi-restraints excluded: chain S residue 34 MET Chi-restraints excluded: chain S residue 51 THR Chi-restraints excluded: chain S residue 121 CYS Chi-restraints excluded: chain S residue 130 VAL Chi-restraints excluded: chain S residue 205 MET Chi-restraints excluded: chain S residue 268 ILE Chi-restraints excluded: chain S residue 270 THR Chi-restraints excluded: chain S residue 310 VAL Chi-restraints excluded: chain S residue 311 SER Chi-restraints excluded: chain S residue 336 SER Chi-restraints excluded: chain S residue 464 ILE Chi-restraints excluded: chain S residue 487 LEU Chi-restraints excluded: chain T residue 21 SER Chi-restraints excluded: chain T residue 70 VAL Chi-restraints excluded: chain U residue 10 GLU Chi-restraints excluded: chain U residue 70 MET Chi-restraints excluded: chain U residue 93 VAL Chi-restraints excluded: chain U residue 106 TYR Chi-restraints excluded: chain U residue 116 THR Chi-restraints excluded: chain V residue 4 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 55 optimal weight: 9.9990 chunk 359 optimal weight: 2.9990 chunk 61 optimal weight: 10.0000 chunk 42 optimal weight: 5.9990 chunk 69 optimal weight: 4.9990 chunk 285 optimal weight: 7.9990 chunk 338 optimal weight: 4.9990 chunk 243 optimal weight: 7.9990 chunk 347 optimal weight: 6.9990 chunk 150 optimal weight: 9.9990 chunk 265 optimal weight: 7.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 HIS A 134 ASN A 364 ASN ** C 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 375 ASN ** L 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 134 ASN O 364 ASN ** Q 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.105994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.091562 restraints weight = 43191.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.093785 restraints weight = 25824.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.095280 restraints weight = 17877.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.096320 restraints weight = 13651.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.097030 restraints weight = 11262.689| |-----------------------------------------------------------------------------| r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.2763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 30638 Z= 0.253 Angle : 0.687 13.098 41578 Z= 0.352 Chirality : 0.048 0.252 4848 Planarity : 0.004 0.065 5162 Dihedral : 6.258 55.565 4632 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 5.03 % Allowed : 20.97 % Favored : 74.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.22 (0.13), residues: 3838 helix: 1.41 (0.18), residues: 876 sheet: -1.44 (0.15), residues: 1112 loop : -1.46 (0.13), residues: 1850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 85 TYR 0.020 0.002 TYR H 27 PHE 0.025 0.002 PHE C 420 TRP 0.017 0.002 TRP H 50 HIS 0.006 0.001 HIS C 94 Details of bonding type rmsd covalent geometry : bond 0.00610 (30572) covalent geometry : angle 0.68074 (41418) SS BOND : bond 0.00787 ( 38) SS BOND : angle 1.54529 ( 76) hydrogen bonds : bond 0.03988 ( 1190) hydrogen bonds : angle 5.32915 ( 3354) link_BETA1-4 : bond 0.00407 ( 16) link_BETA1-4 : angle 1.56959 ( 48) link_NAG-ASN : bond 0.00468 ( 12) link_NAG-ASN : angle 1.91354 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 655 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 494 time to evaluate : 1.184 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: A 324 TYR cc_start: 0.8750 (t80) cc_final: 0.8447 (t80) REVERT: A 438 PHE cc_start: 0.8278 (m-80) cc_final: 0.8056 (m-10) REVERT: A 442 TYR cc_start: 0.9162 (t80) cc_final: 0.8782 (t80) REVERT: B 10 MET cc_start: 0.8123 (mmm) cc_final: 0.7756 (mmp) REVERT: C 13 GLU cc_start: 0.8099 (tm-30) cc_final: 0.7707 (tm-30) REVERT: C 41 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8297 (pp) REVERT: C 181 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8278 (pp) REVERT: C 415 ASP cc_start: 0.8261 (t0) cc_final: 0.7887 (t0) REVERT: C 485 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8808 (mm) REVERT: D 30 GLU cc_start: 0.7622 (mm-30) cc_final: 0.7325 (mm-30) REVERT: D 52 TYR cc_start: 0.8075 (m-80) cc_final: 0.7721 (m-80) REVERT: D 59 GLN cc_start: 0.7984 (mt0) cc_final: 0.7565 (mt0) REVERT: E 47 LYS cc_start: 0.8399 (ptmt) cc_final: 0.7997 (pttm) REVERT: E 91 VAL cc_start: 0.9057 (p) cc_final: 0.8759 (p) REVERT: E 282 LYS cc_start: 0.8490 (ttpt) cc_final: 0.7880 (ttpp) REVERT: E 297 TYR cc_start: 0.8009 (m-80) cc_final: 0.7714 (m-80) REVERT: E 359 LYS cc_start: 0.8349 (OUTLIER) cc_final: 0.7893 (tptt) REVERT: E 400 PHE cc_start: 0.7923 (t80) cc_final: 0.7441 (t80) REVERT: F 20 MET cc_start: 0.9120 (mtm) cc_final: 0.8847 (mtm) REVERT: H 10 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7709 (mt-10) REVERT: H 102 PHE cc_start: 0.8561 (p90) cc_final: 0.8332 (p90) REVERT: H 106 TYR cc_start: 0.8605 (OUTLIER) cc_final: 0.7987 (m-80) REVERT: L 4 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.7883 (pp) REVERT: L 48 LEU cc_start: 0.8046 (tt) cc_final: 0.7832 (tp) REVERT: L 49 MET cc_start: 0.6067 (mmt) cc_final: 0.5676 (mmt) REVERT: L 55 ARG cc_start: 0.8399 (mtm110) cc_final: 0.7905 (mtm110) REVERT: L 71 SER cc_start: 0.8584 (m) cc_final: 0.8267 (p) REVERT: O 324 TYR cc_start: 0.8744 (t80) cc_final: 0.8433 (t80) REVERT: O 438 PHE cc_start: 0.8279 (m-80) cc_final: 0.8054 (m-10) REVERT: O 442 TYR cc_start: 0.9176 (t80) cc_final: 0.8800 (t80) REVERT: P 10 MET cc_start: 0.8215 (mmm) cc_final: 0.7735 (mmp) REVERT: Q 13 GLU cc_start: 0.8085 (tm-30) cc_final: 0.7702 (tm-30) REVERT: Q 41 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8303 (pp) REVERT: Q 181 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.8280 (pp) REVERT: Q 312 GLU cc_start: 0.7380 (tt0) cc_final: 0.7128 (tt0) REVERT: Q 415 ASP cc_start: 0.8235 (t0) cc_final: 0.7897 (t0) REVERT: Q 485 LEU cc_start: 0.9118 (OUTLIER) cc_final: 0.8829 (mm) REVERT: R 30 GLU cc_start: 0.7631 (mm-30) cc_final: 0.7315 (mm-30) REVERT: R 52 TYR cc_start: 0.8003 (m-80) cc_final: 0.7761 (m-80) REVERT: R 59 GLN cc_start: 0.7998 (mt0) cc_final: 0.7589 (mt0) REVERT: S 282 LYS cc_start: 0.8491 (ttpt) cc_final: 0.7884 (ttpp) REVERT: S 297 TYR cc_start: 0.8007 (m-80) cc_final: 0.7720 (m-80) REVERT: S 359 LYS cc_start: 0.8354 (OUTLIER) cc_final: 0.7909 (tptt) REVERT: S 400 PHE cc_start: 0.7920 (t80) cc_final: 0.7431 (t80) REVERT: T 20 MET cc_start: 0.9101 (mtm) cc_final: 0.8836 (mtm) REVERT: U 10 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.7714 (mt-10) REVERT: U 102 PHE cc_start: 0.8563 (p90) cc_final: 0.8326 (p90) REVERT: U 106 TYR cc_start: 0.8612 (OUTLIER) cc_final: 0.7992 (m-80) REVERT: V 4 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.7908 (pp) REVERT: V 48 LEU cc_start: 0.8044 (tt) cc_final: 0.7830 (tp) REVERT: V 49 MET cc_start: 0.6058 (mmt) cc_final: 0.5657 (mmt) REVERT: V 55 ARG cc_start: 0.8393 (mtm110) cc_final: 0.7894 (mtm110) REVERT: V 71 SER cc_start: 0.8581 (m) cc_final: 0.8269 (p) outliers start: 161 outliers final: 129 residues processed: 609 average time/residue: 0.1783 time to fit residues: 180.9358 Evaluate side-chains 631 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 488 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 183 CYS Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 220 SER Chi-restraints excluded: chain A residue 244 LYS Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 371 PHE Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 20 MET Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 42 ASP Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 205 MET Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 295 MET Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 401 GLU Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain E residue 16 SER Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 34 MET Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 121 CYS Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 205 MET Chi-restraints excluded: chain E residue 268 ILE Chi-restraints excluded: chain E residue 270 THR Chi-restraints excluded: chain E residue 310 VAL Chi-restraints excluded: chain E residue 311 SER Chi-restraints excluded: chain E residue 336 SER Chi-restraints excluded: chain E residue 359 LYS Chi-restraints excluded: chain E residue 361 GLU Chi-restraints excluded: chain E residue 380 ILE Chi-restraints excluded: chain E residue 464 ILE Chi-restraints excluded: chain E residue 487 LEU Chi-restraints excluded: chain F residue 21 SER Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 70 MET Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 106 TYR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 20 ILE Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 48 THR Chi-restraints excluded: chain O residue 115 THR Chi-restraints excluded: chain O residue 124 LEU Chi-restraints excluded: chain O residue 125 ILE Chi-restraints excluded: chain O residue 163 THR Chi-restraints excluded: chain O residue 179 LEU Chi-restraints excluded: chain O residue 182 GLU Chi-restraints excluded: chain O residue 183 CYS Chi-restraints excluded: chain O residue 220 SER Chi-restraints excluded: chain O residue 244 LYS Chi-restraints excluded: chain O residue 319 LEU Chi-restraints excluded: chain O residue 336 SER Chi-restraints excluded: chain O residue 355 VAL Chi-restraints excluded: chain O residue 363 VAL Chi-restraints excluded: chain O residue 371 PHE Chi-restraints excluded: chain O residue 491 VAL Chi-restraints excluded: chain P residue 8 VAL Chi-restraints excluded: chain P residue 20 MET Chi-restraints excluded: chain Q residue 19 THR Chi-restraints excluded: chain Q residue 41 LEU Chi-restraints excluded: chain Q residue 42 ASP Chi-restraints excluded: chain Q residue 43 ILE Chi-restraints excluded: chain Q residue 65 ILE Chi-restraints excluded: chain Q residue 70 THR Chi-restraints excluded: chain Q residue 92 CYS Chi-restraints excluded: chain Q residue 126 GLU Chi-restraints excluded: chain Q residue 139 VAL Chi-restraints excluded: chain Q residue 181 LEU Chi-restraints excluded: chain Q residue 197 LEU Chi-restraints excluded: chain Q residue 205 MET Chi-restraints excluded: chain Q residue 262 LEU Chi-restraints excluded: chain Q residue 266 THR Chi-restraints excluded: chain Q residue 281 LEU Chi-restraints excluded: chain Q residue 285 LEU Chi-restraints excluded: chain Q residue 295 MET Chi-restraints excluded: chain Q residue 319 LEU Chi-restraints excluded: chain Q residue 337 THR Chi-restraints excluded: chain Q residue 394 SER Chi-restraints excluded: chain Q residue 401 GLU Chi-restraints excluded: chain Q residue 485 LEU Chi-restraints excluded: chain R residue 33 GLU Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain S residue 32 THR Chi-restraints excluded: chain S residue 34 MET Chi-restraints excluded: chain S residue 51 THR Chi-restraints excluded: chain S residue 121 CYS Chi-restraints excluded: chain S residue 130 VAL Chi-restraints excluded: chain S residue 145 THR Chi-restraints excluded: chain S residue 205 MET Chi-restraints excluded: chain S residue 268 ILE Chi-restraints excluded: chain S residue 270 THR Chi-restraints excluded: chain S residue 310 VAL Chi-restraints excluded: chain S residue 311 SER Chi-restraints excluded: chain S residue 336 SER Chi-restraints excluded: chain S residue 359 LYS Chi-restraints excluded: chain S residue 361 GLU Chi-restraints excluded: chain S residue 380 ILE Chi-restraints excluded: chain S residue 464 ILE Chi-restraints excluded: chain S residue 487 LEU Chi-restraints excluded: chain T residue 21 SER Chi-restraints excluded: chain T residue 70 VAL Chi-restraints excluded: chain U residue 10 GLU Chi-restraints excluded: chain U residue 28 THR Chi-restraints excluded: chain U residue 37 VAL Chi-restraints excluded: chain U residue 69 THR Chi-restraints excluded: chain U residue 70 MET Chi-restraints excluded: chain U residue 93 VAL Chi-restraints excluded: chain U residue 106 TYR Chi-restraints excluded: chain U residue 116 THR Chi-restraints excluded: chain V residue 4 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 72 optimal weight: 0.8980 chunk 128 optimal weight: 4.9990 chunk 119 optimal weight: 0.9990 chunk 148 optimal weight: 7.9990 chunk 291 optimal weight: 2.9990 chunk 149 optimal weight: 3.9990 chunk 294 optimal weight: 0.9990 chunk 139 optimal weight: 9.9990 chunk 200 optimal weight: 0.8980 chunk 257 optimal weight: 2.9990 chunk 333 optimal weight: 0.8980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 HIS ** C 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 314 GLN ** S 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 52 ASN ** 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 = 0.3194 r_free = 0.3194 target = 0.111676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.098872 restraints weight = 42477.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.100248 restraints weight = 27036.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.101822 restraints weight = 20203.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.102085 restraints weight = 15726.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.102189 restraints weight = 13307.202| |-----------------------------------------------------------------------------| r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.2868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 30638 Z= 0.119 Angle : 0.598 13.204 41578 Z= 0.303 Chirality : 0.043 0.190 4848 Planarity : 0.004 0.060 5162 Dihedral : 5.849 54.462 4632 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.84 % Allowed : 22.03 % Favored : 74.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.95 (0.13), residues: 3838 helix: 1.85 (0.18), residues: 870 sheet: -1.50 (0.15), residues: 1050 loop : -1.26 (0.13), residues: 1918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 85 TYR 0.018 0.002 TYR U 27 PHE 0.015 0.001 PHE F 42 TRP 0.017 0.001 TRP H 50 HIS 0.005 0.001 HIS Q 259 Details of bonding type rmsd covalent geometry : bond 0.00267 (30572) covalent geometry : angle 0.59344 (41418) SS BOND : bond 0.00448 ( 38) SS BOND : angle 1.15668 ( 76) hydrogen bonds : bond 0.03580 ( 1190) hydrogen bonds : angle 5.04130 ( 3354) link_BETA1-4 : bond 0.00379 ( 16) link_BETA1-4 : angle 1.59753 ( 48) link_NAG-ASN : bond 0.00273 ( 12) link_NAG-ASN : angle 1.48692 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 666 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 543 time to evaluate : 1.236 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: A 125 ILE cc_start: 0.8911 (OUTLIER) cc_final: 0.8633 (mt) REVERT: A 132 HIS cc_start: 0.8183 (OUTLIER) cc_final: 0.7866 (t-90) REVERT: A 324 TYR cc_start: 0.8758 (t80) cc_final: 0.8466 (t80) REVERT: A 438 PHE cc_start: 0.8201 (m-80) cc_final: 0.7993 (m-10) REVERT: A 442 TYR cc_start: 0.9142 (t80) cc_final: 0.8766 (t80) REVERT: A 478 ILE cc_start: 0.9121 (mt) cc_final: 0.8854 (mp) REVERT: C 13 GLU cc_start: 0.7981 (tm-30) cc_final: 0.7569 (tm-30) REVERT: C 41 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.7980 (pp) REVERT: C 181 LEU cc_start: 0.8154 (OUTLIER) cc_final: 0.7890 (pp) REVERT: C 312 GLU cc_start: 0.7110 (tt0) cc_final: 0.6871 (tt0) REVERT: C 415 ASP cc_start: 0.8078 (t0) cc_final: 0.7554 (m-30) REVERT: C 485 LEU cc_start: 0.9124 (OUTLIER) cc_final: 0.8828 (mm) REVERT: D 30 GLU cc_start: 0.7575 (mm-30) cc_final: 0.7181 (mm-30) REVERT: D 52 TYR cc_start: 0.8020 (m-80) cc_final: 0.7773 (m-80) REVERT: D 59 GLN cc_start: 0.7941 (mt0) cc_final: 0.7583 (mt0) REVERT: E 91 VAL cc_start: 0.8945 (p) cc_final: 0.8630 (p) REVERT: E 282 LYS cc_start: 0.8340 (ttpt) cc_final: 0.7891 (ttpp) REVERT: E 297 TYR cc_start: 0.7897 (m-80) cc_final: 0.7549 (m-80) REVERT: E 359 LYS cc_start: 0.8266 (OUTLIER) cc_final: 0.7846 (tptt) REVERT: E 400 PHE cc_start: 0.7868 (t80) cc_final: 0.7499 (t80) REVERT: F 20 MET cc_start: 0.8999 (mtm) cc_final: 0.8689 (mtm) REVERT: F 74 MET cc_start: 0.8776 (tpp) cc_final: 0.8392 (tpt) REVERT: H 10 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.7663 (mt-10) REVERT: H 63 ARG cc_start: 0.8792 (ttt90) cc_final: 0.8438 (tmm-80) REVERT: H 106 TYR cc_start: 0.8389 (OUTLIER) cc_final: 0.7954 (m-80) REVERT: L 4 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.7709 (pp) REVERT: L 48 LEU cc_start: 0.7949 (tt) cc_final: 0.7733 (tp) REVERT: L 49 MET cc_start: 0.6106 (mmt) cc_final: 0.5683 (mmt) REVERT: L 55 ARG cc_start: 0.8424 (mtm110) cc_final: 0.7951 (mtm110) REVERT: L 71 SER cc_start: 0.8504 (m) cc_final: 0.8264 (p) REVERT: O 125 ILE cc_start: 0.8923 (OUTLIER) cc_final: 0.8638 (mt) REVERT: O 324 TYR cc_start: 0.8752 (t80) cc_final: 0.8458 (t80) REVERT: O 438 PHE cc_start: 0.8201 (m-80) cc_final: 0.7982 (m-10) REVERT: O 442 TYR cc_start: 0.9153 (t80) cc_final: 0.8761 (t80) REVERT: P 10 MET cc_start: 0.7973 (mmm) cc_final: 0.7603 (mmp) REVERT: Q 13 GLU cc_start: 0.7976 (tm-30) cc_final: 0.7568 (tm-30) REVERT: Q 41 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.7987 (pp) REVERT: Q 181 LEU cc_start: 0.8151 (OUTLIER) cc_final: 0.7893 (pp) REVERT: Q 312 GLU cc_start: 0.7116 (tt0) cc_final: 0.6886 (tt0) REVERT: Q 415 ASP cc_start: 0.8112 (t0) cc_final: 0.7608 (m-30) REVERT: Q 485 LEU cc_start: 0.9110 (OUTLIER) cc_final: 0.8837 (mm) REVERT: R 30 GLU cc_start: 0.7595 (mm-30) cc_final: 0.7173 (mm-30) REVERT: R 52 TYR cc_start: 0.7897 (m-80) cc_final: 0.7670 (m-80) REVERT: R 59 GLN cc_start: 0.7967 (mt0) cc_final: 0.7608 (mt0) REVERT: S 47 LYS cc_start: 0.8193 (ptmt) cc_final: 0.7796 (pttm) REVERT: S 282 LYS cc_start: 0.8339 (ttpt) cc_final: 0.7893 (ttpp) REVERT: S 297 TYR cc_start: 0.7897 (m-80) cc_final: 0.7549 (m-80) REVERT: S 359 LYS cc_start: 0.8285 (OUTLIER) cc_final: 0.7860 (tptt) REVERT: S 400 PHE cc_start: 0.7860 (t80) cc_final: 0.7496 (t80) REVERT: T 20 MET cc_start: 0.8969 (mtm) cc_final: 0.8680 (mtm) REVERT: T 74 MET cc_start: 0.8747 (tpp) cc_final: 0.8386 (tpt) REVERT: U 10 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.7661 (mt-10) REVERT: U 47 TRP cc_start: 0.8929 (t60) cc_final: 0.8699 (t60) REVERT: U 63 ARG cc_start: 0.8800 (ttt90) cc_final: 0.8443 (tmm-80) REVERT: U 106 TYR cc_start: 0.8396 (OUTLIER) cc_final: 0.7960 (m-80) REVERT: V 4 LEU cc_start: 0.8355 (OUTLIER) cc_final: 0.7704 (pp) REVERT: V 49 MET cc_start: 0.6083 (mmt) cc_final: 0.5667 (mmt) REVERT: V 55 ARG cc_start: 0.8415 (mtm110) cc_final: 0.7935 (mtm110) REVERT: V 71 SER cc_start: 0.8509 (m) cc_final: 0.8261 (p) outliers start: 123 outliers final: 94 residues processed: 629 average time/residue: 0.1709 time to fit residues: 177.6719 Evaluate side-chains 608 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 497 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 132 HIS Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 183 CYS Chi-restraints excluded: chain A residue 220 SER Chi-restraints excluded: chain A residue 244 LYS Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain B residue 20 MET Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 42 ASP Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 205 MET Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 401 GLU Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain E residue 16 SER Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 34 MET Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 121 CYS Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 205 MET Chi-restraints excluded: chain E residue 213 ASP Chi-restraints excluded: chain E residue 268 ILE Chi-restraints excluded: chain E residue 310 VAL Chi-restraints excluded: chain E residue 359 LYS Chi-restraints excluded: chain E residue 361 GLU Chi-restraints excluded: chain E residue 487 LEU Chi-restraints excluded: chain F residue 21 SER Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 70 MET Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 106 TYR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 20 ILE Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 48 THR Chi-restraints excluded: chain O residue 115 THR Chi-restraints excluded: chain O residue 125 ILE Chi-restraints excluded: chain O residue 163 THR Chi-restraints excluded: chain O residue 182 GLU Chi-restraints excluded: chain O residue 183 CYS Chi-restraints excluded: chain O residue 220 SER Chi-restraints excluded: chain O residue 244 LYS Chi-restraints excluded: chain O residue 336 SER Chi-restraints excluded: chain O residue 355 VAL Chi-restraints excluded: chain O residue 491 VAL Chi-restraints excluded: chain Q residue 19 THR Chi-restraints excluded: chain Q residue 41 LEU Chi-restraints excluded: chain Q residue 42 ASP Chi-restraints excluded: chain Q residue 43 ILE Chi-restraints excluded: chain Q residue 65 ILE Chi-restraints excluded: chain Q residue 70 THR Chi-restraints excluded: chain Q residue 92 CYS Chi-restraints excluded: chain Q residue 126 GLU Chi-restraints excluded: chain Q residue 139 VAL Chi-restraints excluded: chain Q residue 181 LEU Chi-restraints excluded: chain Q residue 197 LEU Chi-restraints excluded: chain Q residue 205 MET Chi-restraints excluded: chain Q residue 262 LEU Chi-restraints excluded: chain Q residue 281 LEU Chi-restraints excluded: chain Q residue 285 LEU Chi-restraints excluded: chain Q residue 337 THR Chi-restraints excluded: chain Q residue 401 GLU Chi-restraints excluded: chain Q residue 485 LEU Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain S residue 16 SER Chi-restraints excluded: chain S residue 33 THR Chi-restraints excluded: chain S residue 34 MET Chi-restraints excluded: chain S residue 51 THR Chi-restraints excluded: chain S residue 121 CYS Chi-restraints excluded: chain S residue 130 VAL Chi-restraints excluded: chain S residue 205 MET Chi-restraints excluded: chain S residue 268 ILE Chi-restraints excluded: chain S residue 270 THR Chi-restraints excluded: chain S residue 310 VAL Chi-restraints excluded: chain S residue 359 LYS Chi-restraints excluded: chain S residue 361 GLU Chi-restraints excluded: chain S residue 487 LEU Chi-restraints excluded: chain T residue 21 SER Chi-restraints excluded: chain T residue 70 VAL Chi-restraints excluded: chain U residue 5 VAL Chi-restraints excluded: chain U residue 10 GLU Chi-restraints excluded: chain U residue 28 THR Chi-restraints excluded: chain U residue 70 MET Chi-restraints excluded: chain U residue 93 VAL Chi-restraints excluded: chain U residue 106 TYR Chi-restraints excluded: chain U residue 116 THR Chi-restraints excluded: chain V residue 4 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 27 optimal weight: 10.0000 chunk 346 optimal weight: 9.9990 chunk 149 optimal weight: 10.0000 chunk 244 optimal weight: 9.9990 chunk 258 optimal weight: 6.9990 chunk 189 optimal weight: 0.9990 chunk 108 optimal weight: 7.9990 chunk 363 optimal weight: 9.9990 chunk 208 optimal weight: 0.0770 chunk 196 optimal weight: 0.9990 chunk 167 optimal weight: 0.8980 overall best weight: 1.9944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 ASN A 132 HIS ** C 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 8 ASN O 364 ASN O 467 ASN ** Q 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.110580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.097376 restraints weight = 42973.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.098973 restraints weight = 26837.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.099626 restraints weight = 21414.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.100144 restraints weight = 16841.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.100486 restraints weight = 15008.820| |-----------------------------------------------------------------------------| r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 30638 Z= 0.142 Angle : 0.615 13.157 41578 Z= 0.312 Chirality : 0.044 0.185 4848 Planarity : 0.004 0.063 5162 Dihedral : 5.841 54.863 4632 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 3.94 % Allowed : 22.59 % Favored : 73.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.95 (0.13), residues: 3838 helix: 1.80 (0.18), residues: 864 sheet: -1.45 (0.15), residues: 1082 loop : -1.24 (0.13), residues: 1892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG H 85 TYR 0.029 0.002 TYR U 27 PHE 0.017 0.001 PHE C 420 TRP 0.017 0.001 TRP U 50 HIS 0.015 0.001 HIS A 132 Details of bonding type rmsd covalent geometry : bond 0.00333 (30572) covalent geometry : angle 0.60641 (41418) SS BOND : bond 0.00571 ( 38) SS BOND : angle 2.03080 ( 76) hydrogen bonds : bond 0.03590 ( 1190) hydrogen bonds : angle 5.00367 ( 3354) link_BETA1-4 : bond 0.00412 ( 16) link_BETA1-4 : angle 1.57894 ( 48) link_NAG-ASN : bond 0.00297 ( 12) link_NAG-ASN : angle 1.55759 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5067.20 seconds wall clock time: 88 minutes 45.44 seconds (5325.44 seconds total)