Starting phenix.real_space_refine on Tue May 27 17:01:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jn1_36429/05_2025/8jn1_36429.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jn1_36429/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8jn1_36429/05_2025/8jn1_36429.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jn1_36429/05_2025/8jn1_36429.map" model { file = "/net/cci-nas-00/data/ceres_data/8jn1_36429/05_2025/8jn1_36429.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jn1_36429/05_2025/8jn1_36429.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 17.78, per 1000 atoms: 0.59 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: 7.25 Conformation dependent library (CDL) restraints added in 3.6 seconds 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: 4.19 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: 12.58 Time building geometry restraints manager: 8.44 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: 0.00 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: 0.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.130 Check model and map are aligned: 0.220 Set scattering table: 0.280 Process input model: 66.750 Find NCS groups from input model: 1.080 Set up NCS constraints: 0.200 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: 0.010 Load rotamer database and sin/cos tables:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.810 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.13), residues: 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 TRP 0.018 0.002 TRP O 451 HIS 0.009 0.001 HIS S 144 PHE 0.024 0.001 PHE Q 420 TYR 0.022 0.002 TYR E 176 ARG 0.005 0.001 ARG Q 73 Details of bonding type rmsd link_NAG-ASN : bond 0.00441 ( 12) link_NAG-ASN : angle 1.88520 ( 36) link_BETA1-4 : bond 0.00459 ( 16) link_BETA1-4 : angle 2.02890 ( 48) hydrogen bonds : bond 0.21284 ( 1190) hydrogen bonds : angle 8.73351 ( 3354) SS BOND : bond 0.00706 ( 38) SS BOND : angle 1.77541 ( 76) covalent geometry : bond 0.00423 (30572) covalent geometry : angle 0.69575 (41418) *********************** 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 : 3.101 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: 0.4254 time to fit residues: 495.4168 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 : 3.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 320 optimal weight: 8.9990 chunk 288 optimal weight: 0.0770 chunk 159 optimal weight: 10.0000 chunk 98 optimal weight: 10.0000 chunk 194 optimal weight: 4.9990 chunk 153 optimal weight: 8.9990 chunk 297 optimal weight: 9.9990 chunk 115 optimal weight: 0.6980 chunk 181 optimal weight: 30.0000 chunk 221 optimal weight: 9.9990 chunk 345 optimal weight: 10.0000 overall best weight: 4.7544 ------------------------------------------------------------------------------- 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 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 246 GLN ** F 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 GLN O 134 ASN O 314 GLN 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 V 6 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.108085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.094801 restraints weight = 42975.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.097190 restraints weight = 28922.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.098185 restraints weight = 18163.408| |-----------------------------------------------------------------------------| r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.1649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 30638 Z= 0.245 Angle : 0.723 13.909 41578 Z= 0.370 Chirality : 0.048 0.296 4848 Planarity : 0.004 0.038 5162 Dihedral : 8.039 60.465 4632 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.19 % Allowed : 11.91 % Favored : 85.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.13), residues: 3838 helix: 1.48 (0.18), residues: 858 sheet: -1.57 (0.15), residues: 1070 loop : -1.34 (0.13), residues: 1910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 451 HIS 0.009 0.001 HIS E 144 PHE 0.033 0.002 PHE C 420 TYR 0.017 0.002 TYR B 52 ARG 0.006 0.001 ARG Q 9 Details of bonding type rmsd link_NAG-ASN : bond 0.00469 ( 12) link_NAG-ASN : angle 2.08646 ( 36) link_BETA1-4 : bond 0.00381 ( 16) link_BETA1-4 : angle 2.10802 ( 48) hydrogen bonds : bond 0.04774 ( 1190) hydrogen bonds : angle 6.21118 ( 3354) SS BOND : bond 0.00942 ( 38) SS BOND : angle 2.25779 ( 76) covalent geometry : bond 0.00587 (30572) covalent geometry : angle 0.71153 (41418) *********************** 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: 70 poor density : 545 time to evaluate : 3.467 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: 0.8382 (t-90) cc_final: 0.7778 (t-170) REVERT: A 287 MET cc_start: 0.9182 (OUTLIER) cc_final: 0.8893 (mtp) REVERT: A 324 TYR cc_start: 0.8958 (t80) cc_final: 0.8700 (t80) REVERT: A 438 PHE cc_start: 0.8289 (m-80) cc_final: 0.8085 (m-10) REVERT: A 442 TYR cc_start: 0.9188 (t80) cc_final: 0.8899 (t80) REVERT: B 10 MET cc_start: 0.8140 (mmm) cc_final: 0.7674 (mmp) REVERT: B 17 GLN cc_start: 0.8765 (tt0) cc_final: 0.8500 (tt0) REVERT: D 52 TYR cc_start: 0.7919 (m-80) cc_final: 0.7383 (m-80) REVERT: D 59 GLN cc_start: 0.7428 (mt0) cc_final: 0.6851 (mt0) REVERT: E 49 GLU cc_start: 0.7726 (mt-10) cc_final: 0.7414 (tp30) REVERT: E 318 ILE cc_start: 0.8743 (mm) cc_final: 0.8429 (pt) REVERT: E 400 PHE cc_start: 0.8028 (t80) cc_final: 0.7572 (t80) REVERT: F 10 MET cc_start: 0.8422 (mmp) cc_final: 0.8178 (mmp) REVERT: F 20 MET cc_start: 0.9028 (mtm) cc_final: 0.8658 (mtm) REVERT: F 59 GLN cc_start: 0.8082 (mt0) cc_final: 0.7540 (mt0) REVERT: H 10 GLU cc_start: 0.8295 (tt0) cc_final: 0.7999 (mt-10) REVERT: L 48 LEU cc_start: 0.7655 (tt) cc_final: 0.7447 (tt) REVERT: L 49 MET cc_start: 0.6250 (mmt) cc_final: 0.5683 (mmt) REVERT: L 71 SER cc_start: 0.8760 (m) cc_final: 0.8491 (p) REVERT: L 107 LEU cc_start: 0.6168 (tp) cc_final: 0.5882 (tp) REVERT: O 132 HIS cc_start: 0.8383 (t-90) cc_final: 0.7784 (t-170) REVERT: O 287 MET cc_start: 0.9170 (OUTLIER) cc_final: 0.8890 (mtp) REVERT: O 324 TYR cc_start: 0.8950 (t80) cc_final: 0.8693 (t80) REVERT: O 438 PHE cc_start: 0.8283 (m-80) cc_final: 0.8081 (m-10) REVERT: O 442 TYR cc_start: 0.9187 (t80) cc_final: 0.8906 (t80) REVERT: P 10 MET cc_start: 0.8122 (mmm) cc_final: 0.7676 (mmp) REVERT: P 17 GLN cc_start: 0.8770 (tt0) cc_final: 0.8498 (tt0) REVERT: R 52 TYR cc_start: 0.7913 (m-80) cc_final: 0.7373 (m-80) REVERT: R 59 GLN cc_start: 0.7433 (mt0) cc_final: 0.6854 (mt0) REVERT: S 49 GLU cc_start: 0.7723 (mt-10) cc_final: 0.7408 (tp30) REVERT: S 318 ILE cc_start: 0.8740 (mm) cc_final: 0.8429 (pt) REVERT: S 400 PHE cc_start: 0.8030 (t80) cc_final: 0.7575 (t80) REVERT: T 10 MET cc_start: 0.8421 (mmp) cc_final: 0.8166 (mmp) REVERT: T 59 GLN cc_start: 0.8076 (mt0) cc_final: 0.7536 (mt0) REVERT: U 10 GLU cc_start: 0.8297 (tt0) cc_final: 0.7999 (mt-10) REVERT: V 48 LEU cc_start: 0.7646 (tt) cc_final: 0.7427 (tt) REVERT: V 49 MET cc_start: 0.6239 (mmt) cc_final: 0.5670 (mmt) REVERT: V 71 SER cc_start: 0.8763 (m) cc_final: 0.8493 (p) outliers start: 70 outliers final: 46 residues processed: 589 average time/residue: 0.3825 time to fit residues: 368.2138 Evaluate side-chains 537 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 489 time to evaluate : 3.502 ------------------------------------------------------------------------------- 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 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 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 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 U residue 28 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 221 optimal weight: 0.9990 chunk 121 optimal weight: 4.9990 chunk 254 optimal weight: 8.9990 chunk 362 optimal weight: 8.9990 chunk 219 optimal weight: 10.0000 chunk 372 optimal weight: 6.9990 chunk 122 optimal weight: 0.9980 chunk 275 optimal weight: 10.0000 chunk 58 optimal weight: 6.9990 chunk 12 optimal weight: 9.9990 chunk 315 optimal weight: 5.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- 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** ** D 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 28 GLN 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** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.108132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.094249 restraints weight = 43030.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.096351 restraints weight = 26401.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.097767 restraints weight = 18539.324| |-----------------------------------------------------------------------------| r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 30638 Z= 0.209 Angle : 0.662 13.095 41578 Z= 0.339 Chirality : 0.046 0.281 4848 Planarity : 0.004 0.037 5162 Dihedral : 6.796 54.960 4632 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 3.72 % Allowed : 15.41 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.13), residues: 3838 helix: 1.48 (0.18), residues: 876 sheet: -1.48 (0.15), residues: 1066 loop : -1.33 (0.13), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 451 HIS 0.008 0.001 HIS E 149 PHE 0.027 0.002 PHE C 420 TYR 0.014 0.002 TYR U 32 ARG 0.006 0.001 ARG H 100 Details of bonding type rmsd link_NAG-ASN : bond 0.00347 ( 12) link_NAG-ASN : angle 1.98793 ( 36) link_BETA1-4 : bond 0.00436 ( 16) link_BETA1-4 : angle 1.92280 ( 48) hydrogen bonds : bond 0.04302 ( 1190) hydrogen bonds : angle 5.74686 ( 3354) SS BOND : bond 0.00715 ( 38) SS BOND : angle 1.60989 ( 76) covalent geometry : bond 0.00498 (30572) covalent geometry : angle 0.65373 (41418) *********************** 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: 119 poor density : 515 time to evaluate : 3.061 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 132 HIS cc_start: 0.8365 (t-90) cc_final: 0.7825 (t-170) REVERT: A 324 TYR cc_start: 0.8908 (t80) cc_final: 0.8582 (t80) REVERT: A 438 PHE cc_start: 0.8302 (m-80) cc_final: 0.8066 (m-10) REVERT: A 442 TYR cc_start: 0.9181 (t80) cc_final: 0.8855 (t80) REVERT: B 10 MET cc_start: 0.8091 (mmm) cc_final: 0.7649 (mmp) REVERT: B 17 GLN cc_start: 0.8825 (tt0) cc_final: 0.8569 (tt0) REVERT: C 41 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8204 (pp) REVERT: C 181 LEU cc_start: 0.8162 (OUTLIER) cc_final: 0.7829 (pp) REVERT: C 485 LEU cc_start: 0.9084 (mm) cc_final: 0.8873 (mm) REVERT: D 52 TYR cc_start: 0.8023 (m-80) cc_final: 0.7531 (m-80) REVERT: D 59 GLN cc_start: 0.7567 (mt0) cc_final: 0.7253 (mt0) REVERT: E 49 GLU cc_start: 0.7762 (mt-10) cc_final: 0.7475 (tp30) REVERT: E 205 MET cc_start: 0.7958 (OUTLIER) cc_final: 0.7736 (ttm) REVERT: E 400 PHE cc_start: 0.8029 (t80) cc_final: 0.7557 (t80) REVERT: F 10 MET cc_start: 0.8395 (mmp) cc_final: 0.8181 (mmp) REVERT: H 10 GLU cc_start: 0.8159 (tt0) cc_final: 0.7834 (mt-10) REVERT: H 81 MET cc_start: 0.6870 (OUTLIER) cc_final: 0.6668 (ttm) REVERT: L 49 MET cc_start: 0.6336 (mmt) cc_final: 0.5710 (mmt) REVERT: L 71 SER cc_start: 0.8602 (m) cc_final: 0.8297 (p) REVERT: L 107 LEU cc_start: 0.6535 (tp) cc_final: 0.6266 (tp) REVERT: O 132 HIS cc_start: 0.8362 (t-90) cc_final: 0.7725 (t-170) REVERT: O 324 TYR cc_start: 0.8901 (t80) cc_final: 0.8575 (t80) REVERT: O 438 PHE cc_start: 0.8294 (m-80) cc_final: 0.8057 (m-10) REVERT: O 442 TYR cc_start: 0.9184 (t80) cc_final: 0.8864 (t80) REVERT: P 10 MET cc_start: 0.8082 (mmm) cc_final: 0.7656 (mmp) REVERT: P 17 GLN cc_start: 0.8822 (tt0) cc_final: 0.8565 (tt0) REVERT: Q 41 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8203 (pp) REVERT: Q 181 LEU cc_start: 0.8162 (OUTLIER) cc_final: 0.7839 (pp) REVERT: R 52 TYR cc_start: 0.8017 (m-80) cc_final: 0.7520 (m-80) REVERT: R 59 GLN cc_start: 0.7565 (mt0) cc_final: 0.7250 (mt0) REVERT: S 49 GLU cc_start: 0.7764 (mt-10) cc_final: 0.7474 (tp30) REVERT: S 205 MET cc_start: 0.7950 (OUTLIER) cc_final: 0.7730 (ttm) REVERT: S 400 PHE cc_start: 0.8027 (t80) cc_final: 0.7557 (t80) REVERT: T 10 MET cc_start: 0.8396 (mmp) cc_final: 0.8175 (mmp) REVERT: T 20 MET cc_start: 0.9035 (mtm) cc_final: 0.8714 (mtm) REVERT: U 10 GLU cc_start: 0.8156 (tt0) cc_final: 0.7837 (mt-10) REVERT: U 81 MET cc_start: 0.6875 (OUTLIER) cc_final: 0.6663 (ttm) REVERT: V 49 MET cc_start: 0.6331 (mmt) cc_final: 0.5766 (mmt) REVERT: V 71 SER cc_start: 0.8598 (m) cc_final: 0.8288 (p) outliers start: 119 outliers final: 79 residues processed: 593 average time/residue: 0.3724 time to fit residues: 362.6289 Evaluate side-chains 579 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 492 time to evaluate : 3.645 ------------------------------------------------------------------------------- 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 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 491 VAL Chi-restraints excluded: chain B residue 8 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 262 LEU 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 E residue 33 THR Chi-restraints excluded: chain E residue 205 MET Chi-restraints excluded: chain E residue 270 THR Chi-restraints excluded: chain E residue 311 SER Chi-restraints excluded: chain E residue 343 LYS 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 H residue 28 THR Chi-restraints excluded: chain H residue 81 MET 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 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 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 491 VAL Chi-restraints excluded: chain P residue 8 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 262 LEU 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 205 MET Chi-restraints excluded: chain S residue 270 THR Chi-restraints excluded: chain S residue 311 SER Chi-restraints excluded: chain S residue 343 LYS 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 U residue 28 THR Chi-restraints excluded: chain U residue 81 MET Chi-restraints excluded: chain U residue 116 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 181 optimal weight: 20.0000 chunk 241 optimal weight: 9.9990 chunk 117 optimal weight: 2.9990 chunk 261 optimal weight: 9.9990 chunk 157 optimal weight: 6.9990 chunk 332 optimal weight: 10.0000 chunk 357 optimal weight: 1.9990 chunk 198 optimal weight: 1.9990 chunk 217 optimal weight: 5.9990 chunk 19 optimal weight: 0.9980 chunk 164 optimal weight: 9.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- 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 39 HIS O 134 ASN O 364 ASN ** Q 302 ASN ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.109249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.095424 restraints weight = 42910.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.097531 restraints weight = 26269.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.098951 restraints weight = 18410.982| |-----------------------------------------------------------------------------| r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 30638 Z= 0.167 Angle : 0.625 13.316 41578 Z= 0.319 Chirality : 0.045 0.267 4848 Planarity : 0.004 0.045 5162 Dihedral : 6.366 54.335 4632 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 4.09 % Allowed : 16.81 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.13), residues: 3838 helix: 1.62 (0.18), residues: 876 sheet: -1.40 (0.15), residues: 1070 loop : -1.28 (0.13), residues: 1892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP U 50 HIS 0.006 0.001 HIS S 144 PHE 0.024 0.002 PHE Q 420 TYR 0.013 0.001 TYR A 297 ARG 0.005 0.001 ARG U 100 Details of bonding type rmsd link_NAG-ASN : bond 0.00296 ( 12) link_NAG-ASN : angle 1.83686 ( 36) link_BETA1-4 : bond 0.00389 ( 16) link_BETA1-4 : angle 1.75082 ( 48) hydrogen bonds : bond 0.03963 ( 1190) hydrogen bonds : angle 5.50459 ( 3354) SS BOND : bond 0.00641 ( 38) SS BOND : angle 1.39939 ( 76) covalent geometry : bond 0.00395 (30572) covalent geometry : angle 0.61826 (41418) *********************** 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 657 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 526 time to evaluate : 3.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 324 TYR cc_start: 0.8881 (t80) cc_final: 0.8601 (t80) REVERT: A 438 PHE cc_start: 0.8284 (m-80) cc_final: 0.8045 (m-10) REVERT: A 442 TYR cc_start: 0.9173 (t80) cc_final: 0.8825 (t80) REVERT: B 10 MET cc_start: 0.8050 (mmm) cc_final: 0.7608 (mmp) REVERT: B 12 LEU cc_start: 0.8398 (mt) cc_final: 0.8159 (mp) REVERT: B 17 GLN cc_start: 0.8747 (tt0) cc_final: 0.8501 (tt0) REVERT: C 41 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8172 (pp) REVERT: C 181 LEU cc_start: 0.8120 (OUTLIER) cc_final: 0.7787 (pp) REVERT: C 485 LEU cc_start: 0.9120 (OUTLIER) cc_final: 0.8840 (mm) REVERT: D 52 TYR cc_start: 0.7974 (m-80) cc_final: 0.7533 (m-80) REVERT: D 59 GLN cc_start: 0.7647 (mt0) cc_final: 0.7304 (mt0) REVERT: E 49 GLU cc_start: 0.7742 (mt-10) cc_final: 0.7358 (tp30) REVERT: E 282 LYS cc_start: 0.8510 (ttpt) cc_final: 0.8018 (ttpp) REVERT: E 297 TYR cc_start: 0.7988 (m-80) cc_final: 0.7633 (m-80) REVERT: E 400 PHE cc_start: 0.8021 (t80) cc_final: 0.7469 (t80) REVERT: F 20 MET cc_start: 0.9050 (mtm) cc_final: 0.8681 (mtm) REVERT: H 10 GLU cc_start: 0.8089 (tt0) cc_final: 0.7764 (mt-10) REVERT: L 48 LEU cc_start: 0.7439 (tt) cc_final: 0.7074 (tt) REVERT: L 49 MET cc_start: 0.6069 (mmt) cc_final: 0.5716 (mmt) REVERT: L 71 SER cc_start: 0.8533 (m) cc_final: 0.8254 (p) REVERT: L 107 LEU cc_start: 0.6515 (tp) cc_final: 0.6305 (tp) REVERT: O 324 TYR cc_start: 0.8869 (t80) cc_final: 0.8591 (t80) REVERT: O 438 PHE cc_start: 0.8274 (m-80) cc_final: 0.8040 (m-10) REVERT: O 442 TYR cc_start: 0.9179 (t80) cc_final: 0.8809 (t80) REVERT: P 10 MET cc_start: 0.8026 (mmm) cc_final: 0.7608 (mmp) REVERT: P 17 GLN cc_start: 0.8739 (tt0) cc_final: 0.8484 (tt0) REVERT: Q 41 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8184 (pp) REVERT: Q 181 LEU cc_start: 0.8122 (OUTLIER) cc_final: 0.7799 (pp) REVERT: R 52 TYR cc_start: 0.7974 (m-80) cc_final: 0.7530 (m-80) REVERT: R 59 GLN cc_start: 0.7646 (mt0) cc_final: 0.7301 (mt0) REVERT: S 49 GLU cc_start: 0.7743 (mt-10) cc_final: 0.7350 (tp30) REVERT: S 282 LYS cc_start: 0.8508 (ttpt) cc_final: 0.8007 (ttpp) REVERT: S 297 TYR cc_start: 0.7985 (m-80) cc_final: 0.7634 (m-80) REVERT: S 400 PHE cc_start: 0.8021 (t80) cc_final: 0.7472 (t80) REVERT: T 20 MET cc_start: 0.8995 (mtm) cc_final: 0.8673 (mtm) REVERT: U 10 GLU cc_start: 0.8093 (tt0) cc_final: 0.7778 (mt-10) REVERT: V 48 LEU cc_start: 0.7438 (tt) cc_final: 0.7073 (tt) REVERT: V 49 MET cc_start: 0.6059 (mmt) cc_final: 0.5719 (mmt) REVERT: V 71 SER cc_start: 0.8529 (m) cc_final: 0.8247 (p) outliers start: 131 outliers final: 90 residues processed: 620 average time/residue: 0.3773 time to fit residues: 386.5568 Evaluate side-chains 590 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 495 time to evaluate : 3.365 ------------------------------------------------------------------------------- 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 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 363 VAL 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 139 VAL Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 181 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 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 51 THR Chi-restraints excluded: chain E residue 121 CYS Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 268 ILE Chi-restraints excluded: chain E residue 270 THR Chi-restraints excluded: chain E residue 276 ILE Chi-restraints excluded: chain E residue 311 SER Chi-restraints excluded: chain E residue 343 LYS 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 28 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 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 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 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 139 VAL Chi-restraints excluded: chain Q residue 151 VAL Chi-restraints excluded: chain Q residue 181 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 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 51 THR Chi-restraints excluded: chain S residue 121 CYS Chi-restraints excluded: chain S residue 130 VAL Chi-restraints excluded: chain S residue 268 ILE Chi-restraints excluded: chain S residue 270 THR Chi-restraints excluded: chain S residue 276 ILE Chi-restraints excluded: chain S residue 311 SER Chi-restraints excluded: chain S residue 343 LYS 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 28 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 36 optimal weight: 4.9990 chunk 299 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 174 optimal weight: 0.7980 chunk 106 optimal weight: 8.9990 chunk 35 optimal weight: 0.9990 chunk 102 optimal weight: 10.0000 chunk 248 optimal weight: 0.0470 chunk 20 optimal weight: 4.9990 chunk 371 optimal weight: 2.9990 chunk 350 optimal weight: 10.0000 overall best weight: 0.7684 ------------------------------------------------------------------------------- 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 E 207 HIS O 134 ASN ** Q 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 134 ASN S 207 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.112925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.099679 restraints weight = 42261.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.102303 restraints weight = 28039.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.103467 restraints weight = 16943.762| |-----------------------------------------------------------------------------| r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.2344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 30638 Z= 0.111 Angle : 0.577 13.458 41578 Z= 0.294 Chirality : 0.043 0.322 4848 Planarity : 0.003 0.046 5162 Dihedral : 5.935 54.186 4632 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.94 % Allowed : 18.50 % Favored : 77.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.13), residues: 3838 helix: 1.83 (0.18), residues: 882 sheet: -1.25 (0.16), residues: 1038 loop : -1.24 (0.13), residues: 1918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 50 HIS 0.006 0.001 HIS S 144 PHE 0.017 0.001 PHE C 420 TYR 0.019 0.001 TYR H 27 ARG 0.005 0.000 ARG U 100 Details of bonding type rmsd link_NAG-ASN : bond 0.00209 ( 12) link_NAG-ASN : angle 1.56759 ( 36) link_BETA1-4 : bond 0.00382 ( 16) link_BETA1-4 : angle 1.69451 ( 48) hydrogen bonds : bond 0.03672 ( 1190) hydrogen bonds : angle 5.22794 ( 3354) SS BOND : bond 0.00449 ( 38) SS BOND : angle 1.04745 ( 76) covalent geometry : bond 0.00244 (30572) covalent geometry : angle 0.57199 (41418) *********************** 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 673 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 547 time to evaluate : 3.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 324 TYR cc_start: 0.8818 (t80) cc_final: 0.8556 (t80) REVERT: A 327 GLU cc_start: 0.7805 (mp0) cc_final: 0.7513 (mp0) REVERT: A 438 PHE cc_start: 0.8230 (m-80) cc_final: 0.7998 (m-10) REVERT: A 442 TYR cc_start: 0.9165 (t80) cc_final: 0.8767 (t80) REVERT: B 10 MET cc_start: 0.7866 (mmm) cc_final: 0.7555 (mmp) REVERT: B 17 GLN cc_start: 0.8795 (tt0) cc_final: 0.8571 (tt0) REVERT: C 13 GLU cc_start: 0.8023 (tm-30) cc_final: 0.7652 (tm-30) REVERT: C 41 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8065 (pp) REVERT: C 181 LEU cc_start: 0.7953 (OUTLIER) cc_final: 0.7602 (pp) REVERT: C 485 LEU cc_start: 0.9119 (OUTLIER) cc_final: 0.8832 (mm) REVERT: D 52 TYR cc_start: 0.7891 (m-80) cc_final: 0.7549 (m-80) REVERT: D 59 GLN cc_start: 0.7641 (mt0) cc_final: 0.6898 (mt0) REVERT: E 49 GLU cc_start: 0.7313 (mt-10) cc_final: 0.6729 (tp30) REVERT: E 95 THR cc_start: 0.9352 (t) cc_final: 0.8987 (m) REVERT: E 282 LYS cc_start: 0.8234 (ttpt) cc_final: 0.7784 (ttpp) REVERT: E 297 TYR cc_start: 0.7865 (m-80) cc_final: 0.7544 (m-80) REVERT: E 400 PHE cc_start: 0.7868 (t80) cc_final: 0.7488 (t80) REVERT: F 20 MET cc_start: 0.8944 (mtm) cc_final: 0.8572 (mtm) REVERT: F 59 GLN cc_start: 0.7922 (mt0) cc_final: 0.7412 (mt0) REVERT: H 10 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7722 (mt-10) REVERT: H 106 TYR cc_start: 0.8410 (OUTLIER) cc_final: 0.7941 (m-80) REVERT: L 4 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.7685 (pp) REVERT: L 48 LEU cc_start: 0.7737 (tt) cc_final: 0.7424 (tt) REVERT: L 49 MET cc_start: 0.6067 (mmt) cc_final: 0.5713 (mmt) REVERT: L 107 LEU cc_start: 0.6129 (tp) cc_final: 0.5865 (tp) REVERT: O 324 TYR cc_start: 0.8806 (t80) cc_final: 0.8543 (t80) REVERT: O 327 GLU cc_start: 0.7790 (mp0) cc_final: 0.7499 (mp0) REVERT: O 438 PHE cc_start: 0.8228 (m-80) cc_final: 0.7994 (m-10) REVERT: O 442 TYR cc_start: 0.9144 (t80) cc_final: 0.8765 (t80) REVERT: P 10 MET cc_start: 0.7843 (mmm) cc_final: 0.7559 (mmp) REVERT: P 17 GLN cc_start: 0.8794 (tt0) cc_final: 0.8569 (tt0) REVERT: Q 13 GLU cc_start: 0.8032 (tm-30) cc_final: 0.7669 (tm-30) REVERT: Q 41 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8052 (pp) REVERT: Q 181 LEU cc_start: 0.7960 (OUTLIER) cc_final: 0.7605 (pp) REVERT: Q 485 LEU cc_start: 0.9046 (mm) cc_final: 0.8804 (mm) REVERT: R 52 TYR cc_start: 0.7888 (m-80) cc_final: 0.7540 (m-80) REVERT: R 59 GLN cc_start: 0.7643 (mt0) cc_final: 0.6902 (mt0) REVERT: S 49 GLU cc_start: 0.7317 (mt-10) cc_final: 0.6723 (tp30) REVERT: S 95 THR cc_start: 0.9361 (t) cc_final: 0.9007 (m) REVERT: S 282 LYS cc_start: 0.8227 (ttpt) cc_final: 0.7775 (ttpp) REVERT: S 297 TYR cc_start: 0.7861 (m-80) cc_final: 0.7542 (m-80) REVERT: S 400 PHE cc_start: 0.7869 (t80) cc_final: 0.7488 (t80) REVERT: T 20 MET cc_start: 0.8859 (mtm) cc_final: 0.8550 (mtm) REVERT: T 59 GLN cc_start: 0.7913 (mt0) cc_final: 0.7401 (mt0) REVERT: U 10 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7725 (mt-10) REVERT: U 106 TYR cc_start: 0.8414 (OUTLIER) cc_final: 0.7949 (m-80) REVERT: V 4 LEU cc_start: 0.8332 (OUTLIER) cc_final: 0.7680 (pp) REVERT: V 49 MET cc_start: 0.6081 (mmt) cc_final: 0.5722 (mmt) outliers start: 126 outliers final: 63 residues processed: 624 average time/residue: 0.3698 time to fit residues: 380.5439 Evaluate side-chains 580 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 506 time to evaluate : 3.033 ------------------------------------------------------------------------------- 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 183 CYS Chi-restraints excluded: chain A residue 269 GLN Chi-restraints excluded: chain A residue 491 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 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 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 16 SER Chi-restraints excluded: chain E residue 34 MET Chi-restraints excluded: chain E residue 55 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 311 SER Chi-restraints excluded: chain E residue 464 ILE Chi-restraints excluded: chain E residue 487 LEU Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain H residue 10 GLU 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 183 CYS Chi-restraints excluded: chain O residue 491 VAL Chi-restraints excluded: chain P residue 20 MET Chi-restraints excluded: chain P residue 49 LEU 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 151 VAL 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 S residue 16 SER Chi-restraints excluded: chain S residue 34 MET Chi-restraints excluded: chain S residue 55 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 311 SER Chi-restraints excluded: chain S residue 464 ILE Chi-restraints excluded: chain S residue 487 LEU Chi-restraints excluded: chain T residue 70 VAL Chi-restraints excluded: chain U residue 10 GLU 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 187 optimal weight: 5.9990 chunk 214 optimal weight: 6.9990 chunk 98 optimal weight: 10.0000 chunk 95 optimal weight: 20.0000 chunk 47 optimal weight: 10.0000 chunk 377 optimal weight: 20.0000 chunk 138 optimal weight: 4.9990 chunk 49 optimal weight: 9.9990 chunk 305 optimal weight: 7.9990 chunk 325 optimal weight: 3.9990 chunk 152 optimal weight: 5.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 364 ASN ** C 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 375 ASN O 52 GLN O 364 ASN ** Q 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 375 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.106475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.091989 restraints weight = 43548.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.094232 restraints weight = 25767.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.095748 restraints weight = 17748.732| |-----------------------------------------------------------------------------| r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 30638 Z= 0.270 Angle : 0.690 12.547 41578 Z= 0.354 Chirality : 0.048 0.276 4848 Planarity : 0.004 0.070 5162 Dihedral : 6.275 55.314 4632 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 5.16 % Allowed : 18.94 % Favored : 75.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.13), residues: 3838 helix: 1.51 (0.18), residues: 876 sheet: -1.26 (0.15), residues: 1052 loop : -1.46 (0.13), residues: 1910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP H 50 HIS 0.006 0.001 HIS E 149 PHE 0.024 0.002 PHE Q 420 TYR 0.023 0.002 TYR H 27 ARG 0.006 0.001 ARG T 15 Details of bonding type rmsd link_NAG-ASN : bond 0.00466 ( 12) link_NAG-ASN : angle 1.99980 ( 36) link_BETA1-4 : bond 0.00393 ( 16) link_BETA1-4 : angle 1.66553 ( 48) hydrogen bonds : bond 0.04100 ( 1190) hydrogen bonds : angle 5.42570 ( 3354) SS BOND : bond 0.00838 ( 38) SS BOND : angle 1.62469 ( 76) covalent geometry : bond 0.00647 (30572) covalent geometry : angle 0.68302 (41418) *********************** 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 662 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 165 poor density : 497 time to evaluate : 3.586 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 201 ASN cc_start: 0.9223 (OUTLIER) cc_final: 0.8850 (p0) REVERT: A 324 TYR cc_start: 0.8784 (t80) cc_final: 0.8467 (t80) REVERT: A 438 PHE cc_start: 0.8312 (m-80) cc_final: 0.8070 (m-10) REVERT: A 442 TYR cc_start: 0.9167 (t80) cc_final: 0.8794 (t80) REVERT: B 10 MET cc_start: 0.8194 (mmm) cc_final: 0.7737 (mmp) REVERT: C 41 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8331 (pp) REVERT: C 181 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.8227 (pp) REVERT: C 485 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8747 (mm) REVERT: D 59 GLN cc_start: 0.7957 (mt0) cc_final: 0.7588 (mt0) REVERT: E 49 GLU cc_start: 0.7785 (mt-10) cc_final: 0.7066 (tp30) REVERT: E 282 LYS cc_start: 0.8548 (ttpt) cc_final: 0.7938 (ttpp) REVERT: E 400 PHE cc_start: 0.7917 (t80) cc_final: 0.7419 (t80) REVERT: F 20 MET cc_start: 0.9081 (mtm) cc_final: 0.8761 (mtm) REVERT: H 10 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7753 (mt-10) REVERT: H 106 TYR cc_start: 0.8581 (OUTLIER) cc_final: 0.7981 (m-80) REVERT: L 4 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.7857 (pp) REVERT: L 49 MET cc_start: 0.6020 (mmt) cc_final: 0.5541 (mmt) REVERT: L 107 LEU cc_start: 0.6655 (tp) cc_final: 0.6412 (tp) REVERT: O 201 ASN cc_start: 0.9224 (OUTLIER) cc_final: 0.8845 (p0) REVERT: O 324 TYR cc_start: 0.8863 (t80) cc_final: 0.8540 (t80) REVERT: O 438 PHE cc_start: 0.8304 (m-80) cc_final: 0.8064 (m-10) REVERT: O 442 TYR cc_start: 0.9167 (t80) cc_final: 0.8794 (t80) REVERT: P 10 MET cc_start: 0.8174 (mmm) cc_final: 0.7675 (mmp) REVERT: Q 41 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8339 (pp) REVERT: Q 181 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8226 (pp) REVERT: Q 485 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8778 (mm) REVERT: R 59 GLN cc_start: 0.7959 (mt0) cc_final: 0.7591 (mt0) REVERT: S 49 GLU cc_start: 0.7787 (mt-10) cc_final: 0.7066 (tp30) REVERT: S 282 LYS cc_start: 0.8542 (ttpt) cc_final: 0.7937 (ttpp) REVERT: S 400 PHE cc_start: 0.7928 (t80) cc_final: 0.7430 (t80) REVERT: T 20 MET cc_start: 0.9032 (mtm) cc_final: 0.8797 (mtm) REVERT: U 10 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7756 (mt-10) REVERT: U 106 TYR cc_start: 0.8589 (OUTLIER) cc_final: 0.7992 (m-80) REVERT: V 4 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.7864 (pp) REVERT: V 48 LEU cc_start: 0.8362 (tt) cc_final: 0.8005 (tt) REVERT: V 49 MET cc_start: 0.6302 (mmt) cc_final: 0.5617 (mmt) outliers start: 165 outliers final: 110 residues processed: 611 average time/residue: 0.3601 time to fit residues: 366.1668 Evaluate side-chains 598 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 474 time to evaluate : 3.111 ------------------------------------------------------------------------------- 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 124 LEU Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 183 CYS Chi-restraints excluded: chain A residue 201 ASN 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 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 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 158 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 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 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 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 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 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 124 LEU Chi-restraints excluded: chain O residue 182 GLU Chi-restraints excluded: chain O residue 183 CYS Chi-restraints excluded: chain O residue 201 ASN 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 491 VAL Chi-restraints excluded: chain P residue 8 VAL Chi-restraints excluded: chain P residue 20 MET Chi-restraints excluded: chain P residue 49 LEU 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 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 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 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 311 SER Chi-restraints excluded: chain S residue 336 SER Chi-restraints excluded: chain S residue 464 ILE 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 120 optimal weight: 0.9980 chunk 202 optimal weight: 6.9990 chunk 182 optimal weight: 8.9990 chunk 213 optimal weight: 3.9990 chunk 131 optimal weight: 4.9990 chunk 41 optimal weight: 0.9990 chunk 326 optimal weight: 0.5980 chunk 256 optimal weight: 3.9990 chunk 285 optimal weight: 9.9990 chunk 152 optimal weight: 8.9990 chunk 227 optimal weight: 9.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.109904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.096165 restraints weight = 42866.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.098261 restraints weight = 26105.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.099667 restraints weight = 18291.606| |-----------------------------------------------------------------------------| r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 30638 Z= 0.145 Angle : 0.604 13.179 41578 Z= 0.307 Chirality : 0.044 0.272 4848 Planarity : 0.004 0.063 5162 Dihedral : 5.999 54.290 4632 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 3.78 % Allowed : 20.78 % Favored : 75.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.13), residues: 3838 helix: 1.76 (0.18), residues: 876 sheet: -1.31 (0.16), residues: 978 loop : -1.31 (0.13), residues: 1984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP H 50 HIS 0.005 0.001 HIS D 39 PHE 0.019 0.001 PHE Q 420 TYR 0.022 0.002 TYR U 27 ARG 0.006 0.000 ARG U 100 Details of bonding type rmsd link_NAG-ASN : bond 0.00322 ( 12) link_NAG-ASN : angle 1.63725 ( 36) link_BETA1-4 : bond 0.00398 ( 16) link_BETA1-4 : angle 1.61020 ( 48) hydrogen bonds : bond 0.03731 ( 1190) hydrogen bonds : angle 5.20664 ( 3354) SS BOND : bond 0.00563 ( 38) SS BOND : angle 1.79049 ( 76) covalent geometry : bond 0.00342 (30572) covalent geometry : angle 0.59534 (41418) *********************** 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 626 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 505 time to evaluate : 3.363 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 201 ASN cc_start: 0.9191 (OUTLIER) cc_final: 0.8923 (p0) REVERT: A 324 TYR cc_start: 0.8809 (t80) cc_final: 0.8507 (t80) REVERT: A 438 PHE cc_start: 0.8272 (m-80) cc_final: 0.8028 (m-10) REVERT: A 442 TYR cc_start: 0.9154 (t80) cc_final: 0.8789 (t80) REVERT: B 10 MET cc_start: 0.7975 (mmm) cc_final: 0.7611 (mmp) REVERT: B 17 GLN cc_start: 0.8845 (tt0) cc_final: 0.8634 (tt0) REVERT: C 1 MET cc_start: 0.9126 (tpp) cc_final: 0.8881 (tpp) REVERT: C 13 GLU cc_start: 0.8034 (tm-30) cc_final: 0.7557 (tm-30) REVERT: C 41 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8143 (pp) REVERT: C 181 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.8043 (pp) REVERT: C 485 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8821 (mm) REVERT: D 52 TYR cc_start: 0.7947 (m-80) cc_final: 0.7642 (m-80) REVERT: D 59 GLN cc_start: 0.7937 (mt0) cc_final: 0.7583 (mt0) REVERT: E 49 GLU cc_start: 0.7748 (mt-10) cc_final: 0.7168 (tp30) REVERT: E 282 LYS cc_start: 0.8378 (ttpt) cc_final: 0.7948 (ttpp) REVERT: E 297 TYR cc_start: 0.7923 (m-80) cc_final: 0.7582 (m-80) REVERT: E 400 PHE cc_start: 0.7914 (t80) cc_final: 0.7454 (t80) REVERT: F 20 MET cc_start: 0.9014 (mtm) cc_final: 0.8692 (mtm) REVERT: H 10 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.7724 (mt-10) REVERT: H 106 TYR cc_start: 0.8455 (OUTLIER) cc_final: 0.7928 (m-80) REVERT: L 4 LEU cc_start: 0.8355 (OUTLIER) cc_final: 0.7719 (pp) REVERT: L 37 TYR cc_start: 0.8475 (m-80) cc_final: 0.8259 (m-80) REVERT: L 48 LEU cc_start: 0.7668 (tt) cc_final: 0.7162 (tt) REVERT: L 49 MET cc_start: 0.6082 (mmt) cc_final: 0.5721 (mmt) REVERT: L 107 LEU cc_start: 0.6256 (tp) cc_final: 0.6028 (tp) REVERT: O 201 ASN cc_start: 0.9188 (OUTLIER) cc_final: 0.8938 (p0) REVERT: O 324 TYR cc_start: 0.8800 (t80) cc_final: 0.8500 (t80) REVERT: O 438 PHE cc_start: 0.8266 (m-80) cc_final: 0.8024 (m-10) REVERT: O 442 TYR cc_start: 0.9148 (t80) cc_final: 0.8784 (t80) REVERT: P 10 MET cc_start: 0.8026 (mmm) cc_final: 0.7638 (mmp) REVERT: P 17 GLN cc_start: 0.8846 (tt0) cc_final: 0.8616 (tt0) REVERT: Q 1 MET cc_start: 0.9133 (tpp) cc_final: 0.8892 (tpp) REVERT: Q 13 GLU cc_start: 0.8035 (tm-30) cc_final: 0.7562 (tm-30) REVERT: Q 41 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8169 (pp) REVERT: Q 181 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.8048 (pp) REVERT: Q 485 LEU cc_start: 0.9062 (OUTLIER) cc_final: 0.8789 (mm) REVERT: R 52 TYR cc_start: 0.7939 (m-80) cc_final: 0.7632 (m-80) REVERT: R 59 GLN cc_start: 0.7945 (mt0) cc_final: 0.7589 (mt0) REVERT: S 49 GLU cc_start: 0.7749 (mt-10) cc_final: 0.7166 (tp30) REVERT: S 282 LYS cc_start: 0.8375 (ttpt) cc_final: 0.7929 (ttpp) REVERT: S 297 TYR cc_start: 0.7918 (m-80) cc_final: 0.7579 (m-80) REVERT: S 400 PHE cc_start: 0.7915 (t80) cc_final: 0.7455 (t80) REVERT: U 10 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.7729 (mt-10) REVERT: U 106 TYR cc_start: 0.8463 (OUTLIER) cc_final: 0.7938 (m-80) REVERT: V 4 LEU cc_start: 0.8302 (OUTLIER) cc_final: 0.7777 (pp) REVERT: V 48 LEU cc_start: 0.8360 (tt) cc_final: 0.7971 (tt) REVERT: V 49 MET cc_start: 0.6383 (mmt) cc_final: 0.5636 (mmt) outliers start: 121 outliers final: 90 residues processed: 591 average time/residue: 0.3639 time to fit residues: 356.0077 Evaluate side-chains 591 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 487 time to evaluate : 3.087 ------------------------------------------------------------------------------- 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 179 LEU Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 183 CYS Chi-restraints excluded: chain A residue 201 ASN 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 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 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 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 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 310 VAL Chi-restraints excluded: chain E residue 311 SER Chi-restraints excluded: chain E residue 361 GLU Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 464 ILE Chi-restraints excluded: chain F residue 21 SER Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 31 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 179 LEU Chi-restraints excluded: chain O residue 182 GLU Chi-restraints excluded: chain O residue 183 CYS Chi-restraints excluded: chain O residue 201 ASN 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 20 MET Chi-restraints excluded: chain P residue 49 LEU 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 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 310 VAL Chi-restraints excluded: chain S residue 311 SER Chi-restraints excluded: chain S residue 361 GLU Chi-restraints excluded: chain S residue 363 VAL Chi-restraints excluded: chain S residue 464 ILE Chi-restraints excluded: chain T residue 21 SER Chi-restraints excluded: chain U residue 10 GLU Chi-restraints excluded: chain U residue 31 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 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 114 optimal weight: 9.9990 chunk 319 optimal weight: 4.9990 chunk 149 optimal weight: 9.9990 chunk 157 optimal weight: 6.9990 chunk 342 optimal weight: 7.9990 chunk 89 optimal weight: 4.9990 chunk 270 optimal weight: 3.9990 chunk 36 optimal weight: 10.0000 chunk 306 optimal weight: 5.9990 chunk 226 optimal weight: 10.0000 chunk 137 optimal weight: 9.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.106079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.091604 restraints weight = 43513.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.093835 restraints weight = 25940.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.095348 restraints weight = 17921.846| |-----------------------------------------------------------------------------| r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.2645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 30638 Z= 0.261 Angle : 0.684 12.885 41578 Z= 0.351 Chirality : 0.048 0.249 4848 Planarity : 0.004 0.065 5162 Dihedral : 6.244 55.400 4632 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 4.56 % Allowed : 20.91 % Favored : 74.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.13), residues: 3838 helix: 1.50 (0.18), residues: 876 sheet: -1.42 (0.15), residues: 1074 loop : -1.39 (0.13), residues: 1888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP H 50 HIS 0.005 0.001 HIS Q 94 PHE 0.025 0.002 PHE V 63 TYR 0.024 0.002 TYR U 27 ARG 0.007 0.001 ARG H 100 Details of bonding type rmsd link_NAG-ASN : bond 0.00489 ( 12) link_NAG-ASN : angle 1.94419 ( 36) link_BETA1-4 : bond 0.00400 ( 16) link_BETA1-4 : angle 1.61725 ( 48) hydrogen bonds : bond 0.04039 ( 1190) hydrogen bonds : angle 5.34491 ( 3354) SS BOND : bond 0.00817 ( 38) SS BOND : angle 1.82405 ( 76) covalent geometry : bond 0.00627 (30572) covalent geometry : angle 0.67603 (41418) *********************** 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 635 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 489 time to evaluate : 3.551 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 201 ASN cc_start: 0.9214 (OUTLIER) cc_final: 0.8727 (p0) REVERT: A 324 TYR cc_start: 0.8764 (t80) cc_final: 0.8497 (t80) REVERT: A 438 PHE cc_start: 0.8310 (m-80) cc_final: 0.8054 (m-10) REVERT: A 442 TYR cc_start: 0.9176 (t80) cc_final: 0.8796 (t80) REVERT: B 10 MET cc_start: 0.8168 (mmm) cc_final: 0.7704 (mmp) REVERT: B 12 LEU cc_start: 0.8720 (mt) cc_final: 0.8485 (mp) REVERT: C 13 GLU cc_start: 0.8118 (tm-30) cc_final: 0.7665 (tm-30) REVERT: C 41 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8313 (pp) REVERT: C 181 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.8129 (pp) REVERT: C 485 LEU cc_start: 0.9141 (OUTLIER) cc_final: 0.8815 (mm) REVERT: D 59 GLN cc_start: 0.7999 (mt0) cc_final: 0.7580 (mt0) REVERT: E 282 LYS cc_start: 0.8483 (ttpt) cc_final: 0.7883 (ttpp) REVERT: E 297 TYR cc_start: 0.7898 (m-80) cc_final: 0.7637 (m-80) REVERT: E 359 LYS cc_start: 0.8358 (OUTLIER) cc_final: 0.7884 (tptt) REVERT: E 400 PHE cc_start: 0.7924 (t80) cc_final: 0.7429 (t80) REVERT: H 10 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7731 (mt-10) REVERT: H 106 TYR cc_start: 0.8566 (OUTLIER) cc_final: 0.7960 (m-80) REVERT: L 4 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.7887 (pp) REVERT: L 48 LEU cc_start: 0.7718 (tt) cc_final: 0.7208 (tt) REVERT: L 49 MET cc_start: 0.6143 (mmt) cc_final: 0.5756 (mmt) REVERT: L 55 ARG cc_start: 0.8319 (mtm110) cc_final: 0.7857 (mtm110) REVERT: L 107 LEU cc_start: 0.6391 (tp) cc_final: 0.6158 (tp) REVERT: O 201 ASN cc_start: 0.9231 (OUTLIER) cc_final: 0.8751 (p0) REVERT: O 324 TYR cc_start: 0.8757 (t80) cc_final: 0.8492 (t80) REVERT: O 438 PHE cc_start: 0.8309 (m-80) cc_final: 0.8053 (m-10) REVERT: O 442 TYR cc_start: 0.9171 (t80) cc_final: 0.8796 (t80) REVERT: P 10 MET cc_start: 0.8223 (mmm) cc_final: 0.7730 (mmp) REVERT: Q 13 GLU cc_start: 0.8112 (tm-30) cc_final: 0.7666 (tm-30) REVERT: Q 41 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8335 (pp) REVERT: Q 181 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8249 (pp) REVERT: Q 485 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8773 (mm) REVERT: R 59 GLN cc_start: 0.7999 (mt0) cc_final: 0.7581 (mt0) REVERT: S 282 LYS cc_start: 0.8474 (ttpt) cc_final: 0.7881 (ttpp) REVERT: S 297 TYR cc_start: 0.7892 (m-80) cc_final: 0.7634 (m-80) REVERT: S 359 LYS cc_start: 0.8361 (OUTLIER) cc_final: 0.7891 (tptt) REVERT: S 400 PHE cc_start: 0.7924 (t80) cc_final: 0.7438 (t80) REVERT: T 20 MET cc_start: 0.9101 (mtm) cc_final: 0.8764 (mtm) REVERT: U 10 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7735 (mt-10) REVERT: U 106 TYR cc_start: 0.8573 (OUTLIER) cc_final: 0.7973 (m-80) REVERT: V 4 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.7862 (pp) REVERT: V 48 LEU cc_start: 0.8315 (tt) cc_final: 0.7931 (tt) REVERT: V 49 MET cc_start: 0.6243 (mmt) cc_final: 0.5515 (mmt) outliers start: 146 outliers final: 111 residues processed: 590 average time/residue: 0.3624 time to fit residues: 354.6264 Evaluate side-chains 600 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 473 time to evaluate : 3.489 ------------------------------------------------------------------------------- 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 124 LEU 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 201 ASN 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 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 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 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 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 140 ILE 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 359 LYS Chi-restraints excluded: chain E residue 361 GLU Chi-restraints excluded: chain E residue 363 VAL 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 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 37 VAL Chi-restraints excluded: chain H residue 69 THR 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 66 THR Chi-restraints excluded: chain O residue 124 LEU 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 201 ASN 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 20 MET Chi-restraints excluded: chain P residue 49 LEU 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 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 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 140 ILE 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 359 LYS Chi-restraints excluded: chain S residue 361 GLU Chi-restraints excluded: chain S residue 363 VAL Chi-restraints excluded: chain S residue 464 ILE Chi-restraints excluded: chain T residue 21 SER Chi-restraints excluded: chain U residue 10 GLU Chi-restraints excluded: chain U residue 37 VAL Chi-restraints excluded: chain U residue 69 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 365 optimal weight: 10.0000 chunk 163 optimal weight: 6.9990 chunk 217 optimal weight: 9.9990 chunk 262 optimal weight: 0.7980 chunk 354 optimal weight: 9.9990 chunk 12 optimal weight: 7.9990 chunk 144 optimal weight: 1.9990 chunk 148 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 290 optimal weight: 8.9990 chunk 375 optimal weight: 6.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.107129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.093368 restraints weight = 43219.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.095387 restraints weight = 26528.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.096779 restraints weight = 18754.327| |-----------------------------------------------------------------------------| r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 30638 Z= 0.207 Angle : 0.644 13.098 41578 Z= 0.329 Chirality : 0.046 0.231 4848 Planarity : 0.004 0.062 5162 Dihedral : 6.165 54.980 4632 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 4.81 % Allowed : 20.97 % Favored : 74.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.13), residues: 3838 helix: 1.53 (0.18), residues: 870 sheet: -1.42 (0.15), residues: 1080 loop : -1.41 (0.13), residues: 1888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP U 50 HIS 0.004 0.001 HIS E 144 PHE 0.025 0.002 PHE V 63 TYR 0.026 0.002 TYR H 27 ARG 0.007 0.001 ARG H 100 Details of bonding type rmsd link_NAG-ASN : bond 0.00436 ( 12) link_NAG-ASN : angle 1.83837 ( 36) link_BETA1-4 : bond 0.00378 ( 16) link_BETA1-4 : angle 1.58250 ( 48) hydrogen bonds : bond 0.03887 ( 1190) hydrogen bonds : angle 5.25806 ( 3354) SS BOND : bond 0.00714 ( 38) SS BOND : angle 1.57326 ( 76) covalent geometry : bond 0.00495 (30572) covalent geometry : angle 0.63765 (41418) *********************** 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 644 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 490 time to evaluate : 3.102 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 132 HIS cc_start: 0.8312 (t-90) cc_final: 0.7716 (t-170) REVERT: A 201 ASN cc_start: 0.9209 (OUTLIER) cc_final: 0.8825 (p0) REVERT: A 324 TYR cc_start: 0.8830 (t80) cc_final: 0.8561 (t80) REVERT: A 438 PHE cc_start: 0.8291 (m-80) cc_final: 0.8054 (m-10) REVERT: A 442 TYR cc_start: 0.9170 (t80) cc_final: 0.8791 (t80) REVERT: B 10 MET cc_start: 0.8101 (mmm) cc_final: 0.7689 (mmp) REVERT: C 13 GLU cc_start: 0.8079 (tm-30) cc_final: 0.7634 (tm-30) REVERT: C 41 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8205 (pp) REVERT: C 181 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.8160 (pp) REVERT: C 312 GLU cc_start: 0.7355 (tt0) cc_final: 0.7097 (tt0) REVERT: C 485 LEU cc_start: 0.9135 (OUTLIER) cc_final: 0.8809 (mm) REVERT: D 30 GLU cc_start: 0.7595 (mm-30) cc_final: 0.7333 (mm-30) REVERT: D 52 TYR cc_start: 0.7941 (m-80) cc_final: 0.7695 (m-80) REVERT: D 59 GLN cc_start: 0.7996 (mt0) cc_final: 0.7588 (mt0) REVERT: E 47 LYS cc_start: 0.8637 (ptmt) cc_final: 0.8437 (pttt) REVERT: E 49 GLU cc_start: 0.7536 (mt-10) cc_final: 0.7059 (tp30) REVERT: E 282 LYS cc_start: 0.8461 (ttpt) cc_final: 0.7897 (ttpp) REVERT: E 289 LYS cc_start: 0.8403 (OUTLIER) cc_final: 0.8158 (ptpp) REVERT: E 297 TYR cc_start: 0.7878 (m-80) cc_final: 0.7580 (m-80) REVERT: E 359 LYS cc_start: 0.8323 (OUTLIER) cc_final: 0.7892 (tptt) REVERT: E 400 PHE cc_start: 0.7930 (t80) cc_final: 0.7453 (t80) REVERT: H 10 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.7709 (mt-10) REVERT: H 106 TYR cc_start: 0.8498 (OUTLIER) cc_final: 0.7970 (m-80) REVERT: L 4 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.7871 (pp) REVERT: L 48 LEU cc_start: 0.7716 (tt) cc_final: 0.7216 (tt) REVERT: L 49 MET cc_start: 0.6169 (mmt) cc_final: 0.5769 (mmt) REVERT: L 55 ARG cc_start: 0.8391 (mtm110) cc_final: 0.7880 (mtm110) REVERT: L 107 LEU cc_start: 0.6347 (tp) cc_final: 0.6123 (tp) REVERT: O 201 ASN cc_start: 0.9217 (OUTLIER) cc_final: 0.8819 (p0) REVERT: O 324 TYR cc_start: 0.8824 (t80) cc_final: 0.8554 (t80) REVERT: O 438 PHE cc_start: 0.8289 (m-80) cc_final: 0.8052 (m-10) REVERT: O 442 TYR cc_start: 0.9165 (t80) cc_final: 0.8793 (t80) REVERT: P 10 MET cc_start: 0.8161 (mmm) cc_final: 0.7681 (mmp) REVERT: Q 13 GLU cc_start: 0.8065 (tm-30) cc_final: 0.7625 (tm-30) REVERT: Q 41 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8248 (pp) REVERT: Q 181 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.8167 (pp) REVERT: Q 312 GLU cc_start: 0.7355 (tt0) cc_final: 0.7096 (tt0) REVERT: Q 485 LEU cc_start: 0.9126 (OUTLIER) cc_final: 0.8842 (mm) REVERT: R 30 GLU cc_start: 0.7598 (mm-30) cc_final: 0.7342 (mm-30) REVERT: R 52 TYR cc_start: 0.7935 (m-80) cc_final: 0.7691 (m-80) REVERT: R 59 GLN cc_start: 0.8005 (mt0) cc_final: 0.7594 (mt0) REVERT: S 47 LYS cc_start: 0.8652 (ptmt) cc_final: 0.8450 (pttt) REVERT: S 49 GLU cc_start: 0.7526 (mt-10) cc_final: 0.7055 (tp30) REVERT: S 282 LYS cc_start: 0.8458 (ttpt) cc_final: 0.7896 (ttpp) REVERT: S 289 LYS cc_start: 0.8402 (OUTLIER) cc_final: 0.8155 (ptpp) REVERT: S 297 TYR cc_start: 0.7875 (m-80) cc_final: 0.7575 (m-80) REVERT: S 359 LYS cc_start: 0.8327 (OUTLIER) cc_final: 0.7891 (tptt) REVERT: S 400 PHE cc_start: 0.7937 (t80) cc_final: 0.7462 (t80) REVERT: T 20 MET cc_start: 0.9065 (mtm) cc_final: 0.8740 (mtm) REVERT: U 10 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7716 (mt-10) REVERT: U 106 TYR cc_start: 0.8507 (OUTLIER) cc_final: 0.7983 (m-80) REVERT: V 4 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.7916 (pp) REVERT: V 49 MET cc_start: 0.6241 (mmt) cc_final: 0.5670 (mmt) outliers start: 154 outliers final: 120 residues processed: 597 average time/residue: 0.3601 time to fit residues: 355.2431 Evaluate side-chains 615 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 477 time to evaluate : 3.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 30 CYS Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 124 LEU 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 201 ASN 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 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 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 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 394 SER 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 140 ILE 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 289 LYS Chi-restraints excluded: chain E residue 310 VAL Chi-restraints excluded: chain E residue 311 SER Chi-restraints excluded: chain E residue 359 LYS Chi-restraints excluded: chain E residue 361 GLU Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 464 ILE Chi-restraints excluded: chain F residue 21 SER 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 37 VAL Chi-restraints excluded: chain H residue 69 THR 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 30 CYS Chi-restraints excluded: chain O residue 48 THR Chi-restraints excluded: chain O residue 66 THR Chi-restraints excluded: chain O residue 124 LEU 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 201 ASN Chi-restraints excluded: chain O residue 258 MET 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 20 MET Chi-restraints excluded: chain P residue 49 LEU 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 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 16 SER 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 140 ILE 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 289 LYS Chi-restraints excluded: chain S residue 310 VAL Chi-restraints excluded: chain S residue 311 SER Chi-restraints excluded: chain S residue 359 LYS Chi-restraints excluded: chain S residue 361 GLU Chi-restraints excluded: chain S residue 363 VAL Chi-restraints excluded: chain S residue 464 ILE Chi-restraints excluded: chain T residue 21 SER 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 37 VAL Chi-restraints excluded: chain U residue 69 THR 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 343 optimal weight: 7.9990 chunk 163 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 135 optimal weight: 1.9990 chunk 4 optimal weight: 6.9990 chunk 8 optimal weight: 6.9990 chunk 149 optimal weight: 9.9990 chunk 258 optimal weight: 3.9990 chunk 278 optimal weight: 4.9990 chunk 45 optimal weight: 0.7980 chunk 379 optimal weight: 0.0970 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 GLN ** E 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 35 HIS O 52 GLN O 134 ASN ** Q 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 35 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.110034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.096655 restraints weight = 42889.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.099141 restraints weight = 28751.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.100010 restraints weight = 17789.658| |-----------------------------------------------------------------------------| r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.2785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 30638 Z= 0.140 Angle : 0.602 13.176 41578 Z= 0.306 Chirality : 0.044 0.184 4848 Planarity : 0.004 0.057 5162 Dihedral : 5.894 54.263 4632 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 4.22 % Allowed : 21.47 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.13), residues: 3838 helix: 1.85 (0.18), residues: 870 sheet: -1.50 (0.15), residues: 1074 loop : -1.23 (0.13), residues: 1894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP U 50 HIS 0.004 0.001 HIS S 144 PHE 0.024 0.001 PHE V 63 TYR 0.023 0.002 TYR H 27 ARG 0.007 0.000 ARG H 100 Details of bonding type rmsd link_NAG-ASN : bond 0.00341 ( 12) link_NAG-ASN : angle 1.61595 ( 36) link_BETA1-4 : bond 0.00385 ( 16) link_BETA1-4 : angle 1.61397 ( 48) hydrogen bonds : bond 0.03660 ( 1190) hydrogen bonds : angle 5.04739 ( 3354) SS BOND : bond 0.00528 ( 38) SS BOND : angle 1.34072 ( 76) covalent geometry : bond 0.00328 (30572) covalent geometry : angle 0.59588 (41418) ********************** 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 662 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 527 time to evaluate : 3.099 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 132 HIS cc_start: 0.8421 (t-90) cc_final: 0.7765 (t-170) REVERT: A 201 ASN cc_start: 0.9194 (OUTLIER) cc_final: 0.8916 (p0) REVERT: A 324 TYR cc_start: 0.8779 (t80) cc_final: 0.8490 (t80) REVERT: A 438 PHE cc_start: 0.8252 (m-80) cc_final: 0.8017 (m-10) REVERT: A 442 TYR cc_start: 0.9150 (t80) cc_final: 0.8780 (t80) REVERT: B 10 MET cc_start: 0.8002 (mmm) cc_final: 0.7704 (mmp) REVERT: C 13 GLU cc_start: 0.8048 (tm-30) cc_final: 0.7544 (tm-30) REVERT: C 41 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.7984 (pp) REVERT: C 181 LEU cc_start: 0.8208 (OUTLIER) cc_final: 0.7964 (pp) REVERT: C 312 GLU cc_start: 0.7147 (tt0) cc_final: 0.6923 (tt0) REVERT: C 485 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8824 (mm) REVERT: D 30 GLU cc_start: 0.7544 (mm-30) cc_final: 0.7176 (mm-30) REVERT: D 52 TYR cc_start: 0.7924 (m-80) cc_final: 0.7672 (m-80) REVERT: D 59 GLN cc_start: 0.7979 (mt0) cc_final: 0.7636 (mt0) REVERT: E 47 LYS cc_start: 0.8607 (ptmt) cc_final: 0.8399 (pttt) REVERT: E 49 GLU cc_start: 0.7342 (mt-10) cc_final: 0.6779 (tp30) REVERT: E 251 LEU cc_start: 0.8668 (mp) cc_final: 0.8354 (mt) REVERT: E 282 LYS cc_start: 0.8389 (ttpt) cc_final: 0.7955 (ttpp) REVERT: E 289 LYS cc_start: 0.8336 (OUTLIER) cc_final: 0.7874 (ptmt) REVERT: E 297 TYR cc_start: 0.7934 (m-80) cc_final: 0.7641 (m-80) REVERT: E 325 LYS cc_start: 0.8329 (mptt) cc_final: 0.8059 (mmtp) REVERT: E 359 LYS cc_start: 0.8320 (OUTLIER) cc_final: 0.7880 (tptt) REVERT: E 400 PHE cc_start: 0.7908 (t80) cc_final: 0.7460 (t80) REVERT: H 10 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7691 (mt-10) REVERT: H 100 ARG cc_start: 0.7843 (mmm-85) cc_final: 0.7474 (mmm-85) REVERT: H 106 TYR cc_start: 0.8325 (OUTLIER) cc_final: 0.7874 (m-80) REVERT: L 4 LEU cc_start: 0.8275 (OUTLIER) cc_final: 0.7782 (pp) REVERT: L 48 LEU cc_start: 0.7669 (tt) cc_final: 0.7309 (tt) REVERT: L 49 MET cc_start: 0.6054 (mmt) cc_final: 0.5672 (mmt) REVERT: L 55 ARG cc_start: 0.8377 (mtm110) cc_final: 0.7882 (mtm110) REVERT: L 107 LEU cc_start: 0.6117 (tp) cc_final: 0.5877 (tp) REVERT: O 125 ILE cc_start: 0.8898 (OUTLIER) cc_final: 0.8685 (mt) REVERT: O 201 ASN cc_start: 0.9190 (OUTLIER) cc_final: 0.8954 (p0) REVERT: O 324 TYR cc_start: 0.8774 (t80) cc_final: 0.8484 (t80) REVERT: O 438 PHE cc_start: 0.8252 (m-80) cc_final: 0.8015 (m-10) REVERT: O 442 TYR cc_start: 0.9141 (t80) cc_final: 0.8781 (t80) REVERT: P 10 MET cc_start: 0.8041 (mmm) cc_final: 0.7618 (mmp) REVERT: Q 1 MET cc_start: 0.9146 (tpp) cc_final: 0.8928 (tpp) REVERT: Q 13 GLU cc_start: 0.8037 (tm-30) cc_final: 0.7544 (tm-30) REVERT: Q 41 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8150 (pp) REVERT: Q 181 LEU cc_start: 0.8318 (OUTLIER) cc_final: 0.8014 (pp) REVERT: Q 312 GLU cc_start: 0.7144 (tt0) cc_final: 0.6910 (tt0) REVERT: Q 485 LEU cc_start: 0.9124 (OUTLIER) cc_final: 0.8851 (mm) REVERT: R 30 GLU cc_start: 0.7540 (mm-30) cc_final: 0.7181 (mm-30) REVERT: R 52 TYR cc_start: 0.7916 (m-80) cc_final: 0.7662 (m-80) REVERT: R 59 GLN cc_start: 0.7985 (mt0) cc_final: 0.7637 (mt0) REVERT: S 47 LYS cc_start: 0.8620 (ptmt) cc_final: 0.8409 (pttt) REVERT: S 49 GLU cc_start: 0.7333 (mt-10) cc_final: 0.6775 (tp30) REVERT: S 251 LEU cc_start: 0.8651 (mp) cc_final: 0.8367 (mt) REVERT: S 282 LYS cc_start: 0.8386 (ttpt) cc_final: 0.7951 (ttpp) REVERT: S 289 LYS cc_start: 0.8340 (OUTLIER) cc_final: 0.7875 (ptmt) REVERT: S 297 TYR cc_start: 0.7926 (m-80) cc_final: 0.7637 (m-80) REVERT: S 359 LYS cc_start: 0.8316 (OUTLIER) cc_final: 0.7871 (tptt) REVERT: S 400 PHE cc_start: 0.7919 (t80) cc_final: 0.7471 (t80) REVERT: T 20 MET cc_start: 0.9026 (mtm) cc_final: 0.8697 (mtm) REVERT: U 10 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.7697 (mt-10) REVERT: U 100 ARG cc_start: 0.7836 (mmm-85) cc_final: 0.7469 (mmm-85) REVERT: U 106 TYR cc_start: 0.8405 (OUTLIER) cc_final: 0.7931 (m-80) REVERT: V 4 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.7723 (pp) REVERT: V 49 MET cc_start: 0.6359 (mmt) cc_final: 0.5742 (mmt) outliers start: 135 outliers final: 108 residues processed: 618 average time/residue: 0.3934 time to fit residues: 400.9995 Evaluate side-chains 632 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 505 time to evaluate : 3.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 30 CYS Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 124 LEU 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 201 ASN Chi-restraints excluded: chain A residue 258 MET Chi-restraints excluded: chain A residue 269 GLN 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 49 LEU 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 126 GLU Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 199 MET 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 33 GLU 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 289 LYS Chi-restraints excluded: chain E residue 310 VAL Chi-restraints excluded: chain E residue 311 SER Chi-restraints excluded: chain E residue 359 LYS Chi-restraints excluded: chain E residue 361 GLU Chi-restraints excluded: chain E residue 363 VAL 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 H residue 5 VAL Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 69 THR 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 30 CYS Chi-restraints excluded: chain O residue 48 THR Chi-restraints excluded: chain O residue 66 THR Chi-restraints excluded: chain O residue 124 LEU Chi-restraints excluded: chain O residue 125 ILE 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 201 ASN Chi-restraints excluded: chain O residue 258 MET 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 49 LEU 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 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 199 MET 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 33 GLU Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain S residue 16 SER 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 205 MET Chi-restraints excluded: chain S residue 268 ILE Chi-restraints excluded: chain S residue 289 LYS Chi-restraints excluded: chain S residue 310 VAL Chi-restraints excluded: chain S residue 311 SER Chi-restraints excluded: chain S residue 359 LYS Chi-restraints excluded: chain S residue 361 GLU Chi-restraints excluded: chain S residue 363 VAL 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 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 37 VAL Chi-restraints excluded: chain U residue 69 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 330 optimal weight: 10.0000 chunk 100 optimal weight: 10.0000 chunk 257 optimal weight: 7.9990 chunk 274 optimal weight: 0.0980 chunk 301 optimal weight: 9.9990 chunk 31 optimal weight: 0.8980 chunk 180 optimal weight: 20.0000 chunk 244 optimal weight: 9.9990 chunk 58 optimal weight: 10.0000 chunk 13 optimal weight: 10.0000 chunk 294 optimal weight: 7.9990 overall best weight: 5.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 52 GLN ** Q 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.105807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.091966 restraints weight = 43252.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.094006 restraints weight = 26735.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.095378 restraints weight = 18892.885| |-----------------------------------------------------------------------------| r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.2812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 30638 Z= 0.262 Angle : 0.690 12.942 41578 Z= 0.353 Chirality : 0.048 0.209 4848 Planarity : 0.004 0.058 5162 Dihedral : 6.222 55.545 4632 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 4.69 % Allowed : 21.69 % Favored : 73.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.13), residues: 3838 helix: 1.52 (0.18), residues: 864 sheet: -1.45 (0.15), residues: 1070 loop : -1.45 (0.13), residues: 1904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP U 50 HIS 0.006 0.001 HIS C 94 PHE 0.024 0.002 PHE C 420 TYR 0.025 0.002 TYR H 27 ARG 0.006 0.001 ARG H 100 Details of bonding type rmsd link_NAG-ASN : bond 0.00496 ( 12) link_NAG-ASN : angle 1.95503 ( 36) link_BETA1-4 : bond 0.00399 ( 16) link_BETA1-4 : angle 1.62536 ( 48) hydrogen bonds : bond 0.04010 ( 1190) hydrogen bonds : angle 5.26002 ( 3354) SS BOND : bond 0.00816 ( 38) SS BOND : angle 1.61640 ( 76) covalent geometry : bond 0.00630 (30572) covalent geometry : angle 0.68293 (41418) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9982.80 seconds wall clock time: 175 minutes 59.56 seconds (10559.56 seconds total)