Starting phenix.real_space_refine on Wed Jun 25 17:50:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jn1_36429/06_2025/8jn1_36429.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jn1_36429/06_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_36429/06_2025/8jn1_36429.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jn1_36429/06_2025/8jn1_36429.map" model { file = "/net/cci-nas-00/data/ceres_data/8jn1_36429/06_2025/8jn1_36429.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jn1_36429/06_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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 16.97, per 1000 atoms: 0.57 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: 7.11 Conformation dependent library (CDL) restraints added in 3.7 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: 4.48 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: 11.34 Time building geometry restraints manager: 8.51 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: 0.640 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: 0.030 Extract box with map and model: 1.080 Check model and map are aligned: 0.230 Set scattering table: 0.250 Process input model: 65.890 Find NCS groups from input model: 1.130 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:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.080 ------------------------------------------------------------------------------- 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 : 3.366 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: 0.4398 time to fit residues: 512.6245 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 : 3.592 ------------------------------------------------------------------------------- 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 = 0.108083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.095855 restraints weight = 42977.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.096334 restraints weight = 30714.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.098055 restraints weight = 25900.420| |-----------------------------------------------------------------------------| r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 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 13.910 41578 Z= 0.370 Chirality : 0.048 0.296 4848 Planarity : 0.004 0.038 5162 Dihedral : 8.039 60.467 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 2.08648 ( 36) link_BETA1-4 : bond 0.00382 ( 16) link_BETA1-4 : angle 2.10801 ( 48) hydrogen bonds : bond 0.04774 ( 1190) hydrogen bonds : angle 6.21121 ( 3354) SS BOND : bond 0.00942 ( 38) SS BOND : angle 2.25770 ( 76) covalent geometry : bond 0.00587 (30572) covalent geometry : angle 0.71154 (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 : 3.352 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: 0.8381 (t-90) cc_final: 0.7783 (t-170) REVERT: A 287 MET cc_start: 0.9152 (OUTLIER) cc_final: 0.8871 (mtp) REVERT: A 324 TYR cc_start: 0.8945 (t80) cc_final: 0.8694 (t80) REVERT: A 438 PHE cc_start: 0.8290 (m-80) cc_final: 0.8086 (m-10) REVERT: A 442 TYR cc_start: 0.9188 (t80) cc_final: 0.8904 (t80) REVERT: B 10 MET cc_start: 0.8143 (mmm) cc_final: 0.7691 (mmp) REVERT: B 17 GLN cc_start: 0.8746 (tt0) cc_final: 0.8487 (tt0) REVERT: D 52 TYR cc_start: 0.7893 (m-80) cc_final: 0.7364 (m-80) REVERT: D 59 GLN cc_start: 0.7463 (mt0) cc_final: 0.6884 (mt0) REVERT: E 49 GLU cc_start: 0.7698 (mt-10) cc_final: 0.7430 (tp30) REVERT: E 318 ILE cc_start: 0.8747 (mm) cc_final: 0.8470 (pt) REVERT: E 400 PHE cc_start: 0.8047 (t80) cc_final: 0.7588 (t80) REVERT: F 10 MET cc_start: 0.8418 (mmp) cc_final: 0.8164 (mmp) REVERT: F 20 MET cc_start: 0.9004 (mtm) cc_final: 0.8644 (mtm) REVERT: F 59 GLN cc_start: 0.8089 (mt0) cc_final: 0.7565 (mt0) REVERT: H 10 GLU cc_start: 0.8257 (tt0) cc_final: 0.7971 (mt-10) REVERT: L 48 LEU cc_start: 0.7752 (tt) cc_final: 0.7536 (tt) REVERT: L 49 MET cc_start: 0.6279 (mmt) cc_final: 0.5717 (mmt) REVERT: L 71 SER cc_start: 0.8691 (m) cc_final: 0.8453 (p) REVERT: L 107 LEU cc_start: 0.6140 (tp) cc_final: 0.5850 (tp) REVERT: O 132 HIS cc_start: 0.8381 (t-90) cc_final: 0.7791 (t-170) REVERT: O 287 MET cc_start: 0.9141 (OUTLIER) cc_final: 0.8865 (mtp) REVERT: O 324 TYR cc_start: 0.8937 (t80) cc_final: 0.8684 (t80) REVERT: O 442 TYR cc_start: 0.9190 (t80) cc_final: 0.8913 (t80) REVERT: P 10 MET cc_start: 0.8127 (mmm) cc_final: 0.7694 (mmp) REVERT: P 17 GLN cc_start: 0.8747 (tt0) cc_final: 0.8482 (tt0) REVERT: R 52 TYR cc_start: 0.7886 (m-80) cc_final: 0.7353 (m-80) REVERT: R 59 GLN cc_start: 0.7467 (mt0) cc_final: 0.6889 (mt0) REVERT: S 49 GLU cc_start: 0.7692 (mt-10) cc_final: 0.7419 (tp30) REVERT: S 318 ILE cc_start: 0.8746 (mm) cc_final: 0.8470 (pt) REVERT: S 400 PHE cc_start: 0.8040 (t80) cc_final: 0.7586 (t80) REVERT: T 10 MET cc_start: 0.8413 (mmp) cc_final: 0.8154 (mmp) REVERT: T 59 GLN cc_start: 0.8083 (mt0) cc_final: 0.7561 (mt0) REVERT: U 10 GLU cc_start: 0.8258 (tt0) cc_final: 0.7975 (mt-10) REVERT: V 48 LEU cc_start: 0.7749 (tt) cc_final: 0.7518 (tt) REVERT: V 49 MET cc_start: 0.6274 (mmt) cc_final: 0.5710 (mmt) REVERT: V 71 SER cc_start: 0.8686 (m) cc_final: 0.8451 (p) outliers start: 70 outliers final: 46 residues processed: 589 average time/residue: 0.3913 time to fit residues: 377.6894 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 : 3.758 ------------------------------------------------------------------------------- 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: 0.0670 chunk 121 optimal weight: 3.9990 chunk 254 optimal weight: 8.9990 chunk 362 optimal weight: 10.0000 chunk 219 optimal weight: 10.0000 chunk 372 optimal weight: 7.9990 chunk 122 optimal weight: 0.8980 chunk 275 optimal weight: 9.9990 chunk 58 optimal weight: 6.9990 chunk 12 optimal weight: 9.9990 chunk 315 optimal weight: 4.9990 overall best weight: 3.3924 ------------------------------------------------------------------------------- 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 = 0.3158 r_free = 0.3158 target = 0.108961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.095136 restraints weight = 42952.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.097244 restraints weight = 26297.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.098657 restraints weight = 18459.213| |-----------------------------------------------------------------------------| r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 30638 Z= 0.188 Angle : 0.647 13.200 41578 Z= 0.331 Chirality : 0.046 0.281 4848 Planarity : 0.004 0.037 5162 Dihedral : 6.784 54.838 4632 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 3.47 % Allowed : 15.06 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.13), residues: 3838 helix: 1.55 (0.18), residues: 876 sheet: -1.47 (0.15), residues: 1070 loop : -1.30 (0.13), residues: 1892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP O 451 HIS 0.008 0.001 HIS E 149 PHE 0.027 0.002 PHE Q 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 0.00321 ( 12) link_NAG-ASN : angle 1.92834 ( 36) link_BETA1-4 : bond 0.00463 ( 16) link_BETA1-4 : angle 1.93006 ( 48) hydrogen bonds : bond 0.04249 ( 1190) hydrogen bonds : angle 5.72691 ( 3354) SS BOND : bond 0.00734 ( 38) SS BOND : angle 1.55205 ( 76) covalent geometry : bond 0.00446 (30572) covalent geometry : angle 0.63939 (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 631 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 520 time to evaluate : 3.257 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: 0.7742 (t-170) REVERT: A 324 TYR cc_start: 0.8934 (t80) cc_final: 0.8623 (t80) REVERT: A 438 PHE cc_start: 0.8291 (m-80) cc_final: 0.8052 (m-10) REVERT: A 442 TYR cc_start: 0.9179 (t80) cc_final: 0.8856 (t80) REVERT: B 10 MET cc_start: 0.8063 (mmm) cc_final: 0.7659 (mmp) REVERT: B 17 GLN cc_start: 0.8813 (tt0) cc_final: 0.8557 (tt0) REVERT: C 2 ARG cc_start: 0.8635 (OUTLIER) cc_final: 0.7488 (ttm-80) REVERT: C 41 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8175 (pp) REVERT: C 181 LEU cc_start: 0.8102 (OUTLIER) cc_final: 0.7745 (pp) REVERT: C 485 LEU cc_start: 0.9078 (mm) cc_final: 0.8872 (mm) REVERT: D 52 TYR cc_start: 0.8004 (m-80) cc_final: 0.7516 (m-80) REVERT: D 59 GLN cc_start: 0.7435 (mt0) cc_final: 0.7203 (mt0) REVERT: E 49 GLU cc_start: 0.7716 (mt-10) cc_final: 0.7448 (tp30) REVERT: E 205 MET cc_start: 0.7943 (OUTLIER) cc_final: 0.7707 (ttm) REVERT: E 297 TYR cc_start: 0.8027 (m-80) cc_final: 0.7701 (m-80) REVERT: E 400 PHE cc_start: 0.8029 (t80) cc_final: 0.7564 (t80) REVERT: F 10 MET cc_start: 0.8372 (mmp) cc_final: 0.8155 (mmp) REVERT: F 68 MET cc_start: 0.8605 (mmm) cc_final: 0.8204 (mmm) REVERT: H 10 GLU cc_start: 0.8145 (tt0) cc_final: 0.7836 (mt-10) REVERT: H 63 ARG cc_start: 0.8590 (ttt180) cc_final: 0.8062 (tmm-80) REVERT: H 100 ARG cc_start: 0.7733 (mmm-85) cc_final: 0.7277 (mmm-85) REVERT: L 49 MET cc_start: 0.6331 (mmt) cc_final: 0.5748 (mmt) REVERT: L 71 SER cc_start: 0.8580 (m) cc_final: 0.8283 (p) REVERT: L 107 LEU cc_start: 0.6496 (tp) cc_final: 0.6226 (tp) REVERT: O 132 HIS cc_start: 0.8354 (t-90) cc_final: 0.7734 (t-170) REVERT: O 324 TYR cc_start: 0.8926 (t80) cc_final: 0.8614 (t80) REVERT: O 442 TYR cc_start: 0.9184 (t80) cc_final: 0.8867 (t80) REVERT: P 10 MET cc_start: 0.8051 (mmm) cc_final: 0.7666 (mmp) REVERT: P 17 GLN cc_start: 0.8811 (tt0) cc_final: 0.8554 (tt0) REVERT: Q 2 ARG cc_start: 0.8634 (OUTLIER) cc_final: 0.7491 (ttm-80) REVERT: Q 41 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8180 (pp) REVERT: Q 181 LEU cc_start: 0.8104 (OUTLIER) cc_final: 0.7756 (pp) REVERT: R 52 TYR cc_start: 0.7999 (m-80) cc_final: 0.7506 (m-80) REVERT: R 59 GLN cc_start: 0.7436 (mt0) cc_final: 0.7201 (mt0) REVERT: S 49 GLU cc_start: 0.7719 (mt-10) cc_final: 0.7446 (tp30) REVERT: S 205 MET cc_start: 0.7935 (OUTLIER) cc_final: 0.7702 (ttm) REVERT: S 297 TYR cc_start: 0.8026 (m-80) cc_final: 0.7699 (m-80) REVERT: S 400 PHE cc_start: 0.8026 (t80) cc_final: 0.7565 (t80) REVERT: T 10 MET cc_start: 0.8372 (mmp) cc_final: 0.8147 (mmp) REVERT: T 20 MET cc_start: 0.9025 (mtm) cc_final: 0.8683 (mtm) REVERT: T 68 MET cc_start: 0.8621 (mmm) cc_final: 0.8210 (mmm) REVERT: U 10 GLU cc_start: 0.8145 (tt0) cc_final: 0.7840 (mt-10) REVERT: U 63 ARG cc_start: 0.8585 (ttt180) cc_final: 0.8061 (tmm-80) REVERT: U 100 ARG cc_start: 0.7727 (mmm-85) cc_final: 0.7284 (mmm-85) REVERT: V 49 MET cc_start: 0.6327 (mmt) cc_final: 0.5741 (mmt) REVERT: V 71 SER cc_start: 0.8576 (m) cc_final: 0.8278 (p) outliers start: 111 outliers final: 69 residues processed: 592 average time/residue: 0.3834 time to fit residues: 375.5161 Evaluate side-chains 565 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 488 time to evaluate : 3.343 ------------------------------------------------------------------------------- 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 319 LEU Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain B residue 20 MET Chi-restraints excluded: chain C residue 2 ARG Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 295 MET Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 401 GLU Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 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 O residue 1 MET Chi-restraints excluded: chain O residue 48 THR Chi-restraints excluded: chain O residue 115 THR Chi-restraints excluded: chain O residue 124 LEU Chi-restraints excluded: chain O residue 134 ASN Chi-restraints excluded: chain O residue 163 THR Chi-restraints excluded: chain O residue 182 GLU Chi-restraints excluded: chain O residue 183 CYS Chi-restraints excluded: chain O residue 251 LEU Chi-restraints excluded: chain O residue 258 MET Chi-restraints excluded: chain O residue 269 GLN Chi-restraints excluded: chain O residue 319 LEU Chi-restraints excluded: chain O residue 336 SER Chi-restraints excluded: chain O residue 355 VAL Chi-restraints excluded: chain O residue 491 VAL Chi-restraints excluded: chain P residue 20 MET Chi-restraints excluded: chain Q residue 2 ARG Chi-restraints excluded: chain Q residue 41 LEU Chi-restraints excluded: chain Q residue 43 ILE Chi-restraints excluded: chain Q residue 65 ILE Chi-restraints excluded: chain Q residue 70 THR Chi-restraints excluded: chain Q residue 92 CYS Chi-restraints excluded: chain Q residue 151 VAL Chi-restraints excluded: chain Q residue 181 LEU Chi-restraints excluded: chain Q residue 262 LEU Chi-restraints excluded: chain Q residue 281 LEU Chi-restraints excluded: chain Q residue 295 MET Chi-restraints excluded: chain Q residue 319 LEU Chi-restraints excluded: chain Q residue 337 THR Chi-restraints excluded: chain Q residue 401 GLU Chi-restraints excluded: chain S residue 33 THR Chi-restraints excluded: chain S residue 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 181 optimal weight: 30.0000 chunk 241 optimal weight: 10.0000 chunk 117 optimal weight: 4.9990 chunk 261 optimal weight: 10.0000 chunk 157 optimal weight: 6.9990 chunk 332 optimal weight: 10.0000 chunk 357 optimal weight: 0.9980 chunk 198 optimal weight: 3.9990 chunk 217 optimal weight: 5.9990 chunk 19 optimal weight: 5.9990 chunk 164 optimal weight: 9.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- 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** ** E 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 39 HIS O 134 ASN O 364 ASN ** Q 302 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 = 0.3141 r_free = 0.3141 target = 0.107634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.093755 restraints weight = 43115.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.095839 restraints weight = 26350.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.097249 restraints weight = 18520.500| |-----------------------------------------------------------------------------| r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 30638 Z= 0.223 Angle : 0.662 13.143 41578 Z= 0.339 Chirality : 0.046 0.283 4848 Planarity : 0.004 0.038 5162 Dihedral : 6.506 54.853 4632 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 4.78 % Allowed : 16.38 % Favored : 78.84 % 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: -1.08 (0.13), residues: 3838 helix: 1.49 (0.18), residues: 876 sheet: -1.43 (0.15), residues: 1066 loop : -1.32 (0.13), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP U 50 HIS 0.006 0.001 HIS E 149 PHE 0.026 0.002 PHE C 420 TYR 0.014 0.002 TYR O 297 ARG 0.004 0.001 ARG A 284 Details of bonding type rmsd link_NAG-ASN : bond 0.00365 ( 12) link_NAG-ASN : angle 1.95965 ( 36) link_BETA1-4 : bond 0.00409 ( 16) link_BETA1-4 : angle 1.77278 ( 48) hydrogen bonds : bond 0.04121 ( 1190) hydrogen bonds : angle 5.59863 ( 3354) SS BOND : bond 0.00760 ( 38) SS BOND : angle 1.57283 ( 76) covalent geometry : bond 0.00535 (30572) covalent geometry : angle 0.65477 (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 659 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 506 time to evaluate : 3.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 324 TYR cc_start: 0.8869 (t80) cc_final: 0.8558 (t80) REVERT: A 438 PHE cc_start: 0.8305 (m-80) cc_final: 0.8063 (m-10) REVERT: A 442 TYR cc_start: 0.9181 (t80) cc_final: 0.8841 (t80) REVERT: B 10 MET cc_start: 0.8112 (mmm) cc_final: 0.7686 (mmp) REVERT: B 12 LEU cc_start: 0.8476 (mt) cc_final: 0.8247 (mp) REVERT: B 17 GLN cc_start: 0.8762 (tt0) cc_final: 0.8508 (tt0) REVERT: C 2 ARG cc_start: 0.8640 (OUTLIER) cc_final: 0.7313 (ttm-80) REVERT: C 41 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8236 (pp) REVERT: C 181 LEU cc_start: 0.8203 (OUTLIER) cc_final: 0.7848 (pp) REVERT: C 485 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8843 (mm) REVERT: D 52 TYR cc_start: 0.7940 (m-80) cc_final: 0.7463 (m-80) REVERT: D 59 GLN cc_start: 0.7675 (mt0) cc_final: 0.7314 (mt0) REVERT: E 49 GLU cc_start: 0.7828 (mt-10) cc_final: 0.7405 (tp30) REVERT: E 297 TYR cc_start: 0.7979 (m-80) cc_final: 0.7605 (m-80) REVERT: E 400 PHE cc_start: 0.7938 (t80) cc_final: 0.7441 (t80) REVERT: F 20 MET cc_start: 0.9064 (mtm) cc_final: 0.8709 (mtm) REVERT: F 68 MET cc_start: 0.8740 (mmm) cc_final: 0.8399 (mmm) REVERT: H 10 GLU cc_start: 0.8115 (tt0) cc_final: 0.7786 (mt-10) REVERT: H 81 MET cc_start: 0.6769 (OUTLIER) cc_final: 0.6537 (tpp) REVERT: H 100 ARG cc_start: 0.7760 (mmm-85) cc_final: 0.7388 (mmm-85) REVERT: L 48 LEU cc_start: 0.7501 (tt) cc_final: 0.7180 (tt) REVERT: L 49 MET cc_start: 0.6145 (mmt) cc_final: 0.5786 (mmt) REVERT: L 71 SER cc_start: 0.8564 (m) cc_final: 0.8279 (p) REVERT: L 107 LEU cc_start: 0.6560 (tp) cc_final: 0.6352 (tp) REVERT: O 324 TYR cc_start: 0.8860 (t80) cc_final: 0.8550 (t80) REVERT: O 442 TYR cc_start: 0.9189 (t80) cc_final: 0.8840 (t80) REVERT: P 10 MET cc_start: 0.8095 (mmm) cc_final: 0.7623 (mmp) REVERT: P 12 LEU cc_start: 0.8472 (mt) cc_final: 0.8245 (mp) REVERT: P 17 GLN cc_start: 0.8755 (tt0) cc_final: 0.8505 (tt0) REVERT: Q 2 ARG cc_start: 0.8639 (OUTLIER) cc_final: 0.7319 (ttm-80) REVERT: Q 41 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8244 (pp) REVERT: Q 181 LEU cc_start: 0.8207 (OUTLIER) cc_final: 0.7860 (pp) REVERT: R 52 TYR cc_start: 0.7935 (m-80) cc_final: 0.7456 (m-80) REVERT: R 59 GLN cc_start: 0.7675 (mt0) cc_final: 0.7312 (mt0) REVERT: S 49 GLU cc_start: 0.7835 (mt-10) cc_final: 0.7403 (tp30) REVERT: S 297 TYR cc_start: 0.7973 (m-80) cc_final: 0.7606 (m-80) REVERT: S 400 PHE cc_start: 0.7933 (t80) cc_final: 0.7440 (t80) REVERT: T 20 MET cc_start: 0.9025 (mtm) cc_final: 0.8729 (mtm) REVERT: T 68 MET cc_start: 0.8753 (mmm) cc_final: 0.8399 (mmm) REVERT: U 10 GLU cc_start: 0.8115 (tt0) cc_final: 0.7790 (mt-10) REVERT: U 81 MET cc_start: 0.6772 (OUTLIER) cc_final: 0.6540 (tpp) REVERT: U 100 ARG cc_start: 0.7753 (mmm-85) cc_final: 0.7390 (mmm-85) REVERT: V 48 LEU cc_start: 0.7670 (tt) cc_final: 0.7289 (tt) REVERT: V 49 MET cc_start: 0.6130 (mmt) cc_final: 0.5775 (mmt) REVERT: V 71 SER cc_start: 0.8560 (m) cc_final: 0.8273 (p) outliers start: 153 outliers final: 102 residues processed: 612 average time/residue: 0.4163 time to fit residues: 426.0552 Evaluate side-chains 590 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 479 time to evaluate : 3.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 134 ASN Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 183 CYS Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 258 MET Chi-restraints excluded: chain A residue 269 GLN Chi-restraints excluded: chain A residue 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 485 LEU Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 20 MET Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 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 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 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 F residue 21 SER Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 69 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 363 VAL Chi-restraints excluded: chain O residue 485 LEU Chi-restraints excluded: chain O residue 491 VAL Chi-restraints excluded: chain P residue 8 VAL Chi-restraints excluded: chain P residue 20 MET Chi-restraints excluded: chain P residue 49 LEU 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 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 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 T residue 21 SER Chi-restraints excluded: chain T residue 70 VAL Chi-restraints excluded: chain U residue 28 THR Chi-restraints excluded: chain U residue 69 THR Chi-restraints excluded: chain U residue 81 MET Chi-restraints excluded: chain U residue 116 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 36 optimal weight: 5.9990 chunk 299 optimal weight: 4.9990 chunk 6 optimal weight: 5.9990 chunk 174 optimal weight: 0.7980 chunk 106 optimal weight: 4.9990 chunk 35 optimal weight: 4.9990 chunk 102 optimal weight: 10.0000 chunk 248 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 371 optimal weight: 5.9990 chunk 350 optimal weight: 8.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 ASN ** C 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 134 ASN ** Q 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.108993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.096783 restraints weight = 42644.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.097221 restraints weight = 30322.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.098804 restraints weight = 25913.035| |-----------------------------------------------------------------------------| r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 30638 Z= 0.171 Angle : 0.624 13.262 41578 Z= 0.318 Chirality : 0.045 0.323 4848 Planarity : 0.004 0.040 5162 Dihedral : 6.242 54.602 4632 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 5.34 % Allowed : 17.47 % Favored : 77.19 % 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: 1098 loop : -1.27 (0.13), residues: 1864 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 0.018 0.002 TYR U 27 ARG 0.005 0.001 ARG F 15 Details of bonding type rmsd link_NAG-ASN : bond 0.00317 ( 12) link_NAG-ASN : angle 1.81605 ( 36) link_BETA1-4 : bond 0.00390 ( 16) link_BETA1-4 : angle 1.68165 ( 48) hydrogen bonds : bond 0.03913 ( 1190) hydrogen bonds : angle 5.42597 ( 3354) SS BOND : bond 0.00632 ( 38) SS BOND : angle 1.37135 ( 76) covalent geometry : bond 0.00407 (30572) covalent geometry : angle 0.61782 (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 691 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 171 poor density : 520 time to evaluate : 3.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 324 TYR cc_start: 0.8825 (t80) cc_final: 0.8507 (t80) REVERT: A 438 PHE cc_start: 0.8284 (m-80) cc_final: 0.8048 (m-10) REVERT: A 442 TYR cc_start: 0.9189 (t80) cc_final: 0.8790 (t80) REVERT: B 10 MET cc_start: 0.8041 (mmm) cc_final: 0.7653 (mmp) REVERT: B 17 GLN cc_start: 0.8724 (tt0) cc_final: 0.8487 (tt0) REVERT: C 41 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8229 (pp) REVERT: C 181 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.8113 (pp) REVERT: C 485 LEU cc_start: 0.9125 (OUTLIER) cc_final: 0.8826 (mm) REVERT: D 52 TYR cc_start: 0.7944 (m-80) cc_final: 0.7609 (m-80) REVERT: D 59 GLN cc_start: 0.7918 (mt0) cc_final: 0.7583 (mt0) REVERT: E 49 GLU cc_start: 0.7728 (mt-10) cc_final: 0.7298 (tp30) REVERT: E 282 LYS cc_start: 0.8361 (ttpt) cc_final: 0.7957 (ttpp) REVERT: E 297 TYR cc_start: 0.7876 (m-80) cc_final: 0.7479 (m-80) REVERT: E 400 PHE cc_start: 0.7944 (t80) cc_final: 0.7462 (t80) REVERT: F 20 MET cc_start: 0.8999 (mtm) cc_final: 0.8675 (mtm) REVERT: F 68 MET cc_start: 0.8649 (mmm) cc_final: 0.8259 (mmm) REVERT: H 10 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7724 (mt-10) REVERT: H 100 ARG cc_start: 0.7761 (mmm-85) cc_final: 0.7423 (mmm-85) REVERT: H 106 TYR cc_start: 0.8454 (OUTLIER) cc_final: 0.7981 (m-80) REVERT: L 4 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.7867 (pp) REVERT: L 48 LEU cc_start: 0.7892 (tt) cc_final: 0.7561 (tt) REVERT: L 49 MET cc_start: 0.6310 (mmt) cc_final: 0.5957 (mmt) REVERT: L 71 SER cc_start: 0.8471 (m) cc_final: 0.8208 (p) REVERT: L 107 LEU cc_start: 0.6483 (tp) cc_final: 0.6223 (tp) REVERT: O 324 TYR cc_start: 0.8819 (t80) cc_final: 0.8501 (t80) REVERT: O 442 TYR cc_start: 0.9185 (t80) cc_final: 0.8804 (t80) REVERT: P 10 MET cc_start: 0.8048 (mmm) cc_final: 0.7669 (mmp) REVERT: P 17 GLN cc_start: 0.8718 (tt0) cc_final: 0.8474 (tt0) REVERT: Q 41 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8234 (pp) REVERT: Q 181 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.8126 (pp) REVERT: Q 485 LEU cc_start: 0.9057 (mm) cc_final: 0.8808 (mm) REVERT: R 52 TYR cc_start: 0.7944 (m-80) cc_final: 0.7605 (m-80) REVERT: R 59 GLN cc_start: 0.7920 (mt0) cc_final: 0.7585 (mt0) REVERT: S 49 GLU cc_start: 0.7723 (mt-10) cc_final: 0.7286 (tp30) REVERT: S 282 LYS cc_start: 0.8357 (ttpt) cc_final: 0.7952 (ttpp) REVERT: S 297 TYR cc_start: 0.7875 (m-80) cc_final: 0.7477 (m-80) REVERT: S 400 PHE cc_start: 0.7942 (t80) cc_final: 0.7460 (t80) REVERT: T 68 MET cc_start: 0.8667 (mmm) cc_final: 0.8272 (mmm) REVERT: U 10 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7727 (mt-10) REVERT: U 100 ARG cc_start: 0.7753 (mmm-85) cc_final: 0.7425 (mmm-85) REVERT: U 106 TYR cc_start: 0.8460 (OUTLIER) cc_final: 0.7987 (m-80) REVERT: V 4 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.7884 (pp) REVERT: V 48 LEU cc_start: 0.7902 (tt) cc_final: 0.7570 (tt) REVERT: V 49 MET cc_start: 0.6097 (mmt) cc_final: 0.5766 (mmt) REVERT: V 71 SER cc_start: 0.8469 (m) cc_final: 0.8212 (p) outliers start: 171 outliers final: 105 residues processed: 632 average time/residue: 0.3634 time to fit residues: 380.3308 Evaluate side-chains 608 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 492 time to evaluate : 3.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 134 ASN Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 183 CYS Chi-restraints excluded: chain A residue 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 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 181 LEU Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 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 311 SER Chi-restraints excluded: chain E residue 343 LYS Chi-restraints excluded: chain E residue 361 GLU Chi-restraints excluded: chain E residue 464 ILE Chi-restraints excluded: chain E residue 487 LEU Chi-restraints excluded: chain F residue 21 SER Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 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 115 THR Chi-restraints excluded: chain O residue 124 LEU Chi-restraints excluded: chain O residue 134 ASN Chi-restraints excluded: chain O residue 163 THR Chi-restraints excluded: chain O residue 183 CYS Chi-restraints excluded: chain O residue 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 485 LEU Chi-restraints excluded: chain O residue 491 VAL Chi-restraints excluded: chain P residue 8 VAL Chi-restraints excluded: chain P residue 20 MET Chi-restraints excluded: chain 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 181 LEU Chi-restraints excluded: chain Q residue 197 LEU Chi-restraints excluded: chain Q residue 262 LEU Chi-restraints excluded: chain Q residue 266 THR Chi-restraints excluded: chain Q residue 281 LEU Chi-restraints excluded: chain Q residue 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 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 311 SER Chi-restraints excluded: chain S residue 343 LYS Chi-restraints excluded: chain S residue 361 GLU Chi-restraints excluded: chain S residue 464 ILE Chi-restraints excluded: chain S residue 487 LEU Chi-restraints excluded: chain T residue 21 SER Chi-restraints excluded: chain T residue 70 VAL Chi-restraints excluded: chain U residue 10 GLU Chi-restraints excluded: chain U residue 28 THR Chi-restraints excluded: chain U residue 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 187 optimal weight: 8.9990 chunk 214 optimal weight: 0.8980 chunk 98 optimal weight: 10.0000 chunk 95 optimal weight: 4.9990 chunk 47 optimal weight: 8.9990 chunk 377 optimal weight: 30.0000 chunk 138 optimal weight: 5.9990 chunk 49 optimal weight: 9.9990 chunk 305 optimal weight: 3.9990 chunk 325 optimal weight: 6.9990 chunk 152 optimal weight: 5.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- 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** O 134 ASN O 364 ASN ** Q 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.107431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.095117 restraints weight = 43302.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.095789 restraints weight = 29938.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.097362 restraints weight = 24381.738| |-----------------------------------------------------------------------------| r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 30638 Z= 0.221 Angle : 0.651 13.102 41578 Z= 0.333 Chirality : 0.047 0.288 4848 Planarity : 0.004 0.072 5162 Dihedral : 6.261 54.874 4632 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 5.47 % Allowed : 18.81 % Favored : 75.72 % 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: 876 sheet: -1.44 (0.15), residues: 1086 loop : -1.40 (0.13), residues: 1876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP U 50 HIS 0.005 0.001 HIS S 144 PHE 0.024 0.002 PHE C 420 TYR 0.021 0.002 TYR U 27 ARG 0.005 0.001 ARG F 15 Details of bonding type rmsd link_NAG-ASN : bond 0.00419 ( 12) link_NAG-ASN : angle 1.88653 ( 36) link_BETA1-4 : bond 0.00387 ( 16) link_BETA1-4 : angle 1.65751 ( 48) hydrogen bonds : bond 0.03984 ( 1190) hydrogen bonds : angle 5.41563 ( 3354) SS BOND : bond 0.00726 ( 38) SS BOND : angle 1.44675 ( 76) covalent geometry : bond 0.00528 (30572) covalent geometry : angle 0.64479 (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 674 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 175 poor density : 499 time to evaluate : 3.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 324 TYR cc_start: 0.8832 (t80) cc_final: 0.8522 (t80) REVERT: A 438 PHE cc_start: 0.8303 (m-80) cc_final: 0.8066 (m-10) REVERT: A 442 TYR cc_start: 0.9174 (t80) cc_final: 0.8803 (t80) REVERT: B 10 MET cc_start: 0.8103 (mmm) cc_final: 0.7678 (mmp) REVERT: C 41 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8325 (pp) REVERT: C 181 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8186 (pp) REVERT: C 485 LEU cc_start: 0.9132 (OUTLIER) cc_final: 0.8824 (mm) REVERT: D 59 GLN cc_start: 0.7970 (mt0) cc_final: 0.7620 (mt0) REVERT: E 49 GLU cc_start: 0.7822 (mt-10) cc_final: 0.7343 (tp30) REVERT: E 282 LYS cc_start: 0.8458 (ttpt) cc_final: 0.8047 (ttpp) REVERT: E 297 TYR cc_start: 0.7923 (m-80) cc_final: 0.7625 (m-80) REVERT: E 400 PHE cc_start: 0.7958 (t80) cc_final: 0.7460 (t80) REVERT: F 20 MET cc_start: 0.9004 (mtm) cc_final: 0.8708 (mtm) REVERT: F 68 MET cc_start: 0.8739 (mmm) cc_final: 0.8442 (mmm) REVERT: H 10 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7690 (mt-10) REVERT: H 106 TYR cc_start: 0.8494 (OUTLIER) cc_final: 0.8041 (m-80) REVERT: L 4 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.8008 (pp) REVERT: L 48 LEU cc_start: 0.7901 (tt) cc_final: 0.7597 (tt) REVERT: L 49 MET cc_start: 0.6119 (mmt) cc_final: 0.5730 (mmt) REVERT: L 71 SER cc_start: 0.8510 (m) cc_final: 0.8253 (p) REVERT: L 107 LEU cc_start: 0.6561 (tp) cc_final: 0.6313 (tp) REVERT: O 324 TYR cc_start: 0.8824 (t80) cc_final: 0.8513 (t80) REVERT: O 442 TYR cc_start: 0.9186 (t80) cc_final: 0.8814 (t80) REVERT: P 10 MET cc_start: 0.8094 (mmm) cc_final: 0.7695 (mmp) REVERT: Q 41 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8323 (pp) REVERT: Q 181 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.8190 (pp) REVERT: Q 485 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8792 (mm) REVERT: R 59 GLN cc_start: 0.7974 (mt0) cc_final: 0.7622 (mt0) REVERT: S 49 GLU cc_start: 0.7815 (mt-10) cc_final: 0.7338 (tp30) REVERT: S 282 LYS cc_start: 0.8456 (ttpt) cc_final: 0.8042 (ttpp) REVERT: S 297 TYR cc_start: 0.7925 (m-80) cc_final: 0.7628 (m-80) REVERT: S 400 PHE cc_start: 0.7953 (t80) cc_final: 0.7457 (t80) REVERT: T 20 MET cc_start: 0.9024 (mtm) cc_final: 0.8675 (mtm) REVERT: T 68 MET cc_start: 0.8756 (mmm) cc_final: 0.8453 (mmm) REVERT: U 10 GLU cc_start: 0.8039 (OUTLIER) cc_final: 0.7697 (mt-10) REVERT: U 106 TYR cc_start: 0.8501 (OUTLIER) cc_final: 0.8049 (m-80) REVERT: V 4 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8009 (pp) REVERT: V 48 LEU cc_start: 0.7921 (tt) cc_final: 0.7589 (tt) REVERT: V 49 MET cc_start: 0.6108 (mmt) cc_final: 0.5719 (mmt) REVERT: V 71 SER cc_start: 0.8502 (m) cc_final: 0.8227 (p) outliers start: 175 outliers final: 126 residues processed: 620 average time/residue: 0.3656 time to fit residues: 378.2638 Evaluate side-chains 629 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 491 time to evaluate : 3.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 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 283 CYS Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 371 PHE Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 20 MET Chi-restraints excluded: chain 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 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 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 144 HIS Chi-restraints excluded: chain E residue 205 MET Chi-restraints excluded: chain E residue 268 ILE Chi-restraints excluded: chain E residue 270 THR Chi-restraints excluded: chain E residue 311 SER Chi-restraints excluded: chain E residue 343 LYS Chi-restraints excluded: chain E residue 361 GLU Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 380 ILE Chi-restraints excluded: chain E residue 464 ILE Chi-restraints excluded: chain E residue 487 LEU Chi-restraints excluded: chain F residue 21 SER Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 78 VAL 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 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 283 CYS Chi-restraints excluded: chain O residue 319 LEU Chi-restraints excluded: chain O residue 336 SER Chi-restraints excluded: chain O residue 355 VAL Chi-restraints excluded: chain O residue 363 VAL Chi-restraints excluded: chain O residue 371 PHE Chi-restraints excluded: chain O residue 485 LEU Chi-restraints excluded: chain O residue 491 VAL Chi-restraints excluded: chain P residue 8 VAL Chi-restraints excluded: chain P residue 20 MET Chi-restraints excluded: chain 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 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 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 311 SER Chi-restraints excluded: chain S residue 343 LYS Chi-restraints excluded: chain S residue 361 GLU Chi-restraints excluded: chain S residue 363 VAL Chi-restraints excluded: chain S residue 380 ILE Chi-restraints excluded: chain S residue 464 ILE Chi-restraints excluded: chain S residue 487 LEU Chi-restraints excluded: chain T residue 21 SER Chi-restraints excluded: chain T residue 70 VAL Chi-restraints excluded: chain U residue 10 GLU Chi-restraints excluded: chain U residue 28 THR Chi-restraints excluded: chain U residue 69 THR Chi-restraints excluded: chain U residue 78 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 120 optimal weight: 0.9990 chunk 202 optimal weight: 8.9990 chunk 182 optimal weight: 7.9990 chunk 213 optimal weight: 7.9990 chunk 131 optimal weight: 7.9990 chunk 41 optimal weight: 0.9990 chunk 326 optimal weight: 0.8980 chunk 256 optimal weight: 0.9980 chunk 285 optimal weight: 4.9990 chunk 152 optimal weight: 7.9990 chunk 227 optimal weight: 9.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 ASN ** C 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 134 ASN ** Q 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.110215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.096401 restraints weight = 42781.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.098502 restraints weight = 26206.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.099913 restraints weight = 18385.065| |-----------------------------------------------------------------------------| r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 30638 Z= 0.136 Angle : 0.601 13.407 41578 Z= 0.306 Chirality : 0.044 0.275 4848 Planarity : 0.004 0.065 5162 Dihedral : 6.004 54.335 4632 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 4.16 % Allowed : 20.94 % Favored : 74.91 % 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: -0.94 (0.13), residues: 3838 helix: 1.76 (0.18), residues: 876 sheet: -1.32 (0.15), residues: 1078 loop : -1.32 (0.13), residues: 1884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP U 50 HIS 0.005 0.001 HIS R 39 PHE 0.019 0.001 PHE Q 420 TYR 0.020 0.002 TYR H 27 ARG 0.007 0.000 ARG H 100 Details of bonding type rmsd link_NAG-ASN : bond 0.00297 ( 12) link_NAG-ASN : angle 1.62280 ( 36) link_BETA1-4 : bond 0.00391 ( 16) link_BETA1-4 : angle 1.60911 ( 48) hydrogen bonds : bond 0.03726 ( 1190) hydrogen bonds : angle 5.23240 ( 3354) SS BOND : bond 0.00530 ( 38) SS BOND : angle 1.78857 ( 76) covalent geometry : bond 0.00315 (30572) covalent geometry : angle 0.59257 (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 657 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 524 time to evaluate : 3.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 324 TYR cc_start: 0.8801 (t80) cc_final: 0.8504 (t80) REVERT: A 438 PHE cc_start: 0.8258 (m-80) cc_final: 0.8015 (m-10) REVERT: A 442 TYR cc_start: 0.9154 (t80) cc_final: 0.8778 (t80) REVERT: B 10 MET cc_start: 0.7986 (mmm) cc_final: 0.7626 (mmp) REVERT: C 1 MET cc_start: 0.9222 (tpp) cc_final: 0.9018 (tpp) REVERT: C 13 GLU cc_start: 0.8033 (tm-30) cc_final: 0.7546 (tm-30) REVERT: C 41 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8163 (pp) REVERT: C 181 LEU cc_start: 0.8316 (OUTLIER) cc_final: 0.8036 (pp) REVERT: C 485 LEU cc_start: 0.9124 (OUTLIER) cc_final: 0.8819 (mm) REVERT: D 52 TYR cc_start: 0.7964 (m-80) cc_final: 0.7683 (m-80) REVERT: D 59 GLN cc_start: 0.7933 (mt0) cc_final: 0.7578 (mt0) REVERT: E 49 GLU cc_start: 0.7529 (mt-10) cc_final: 0.7006 (tp30) REVERT: E 282 LYS cc_start: 0.8378 (ttpt) cc_final: 0.7910 (ttpp) REVERT: E 297 TYR cc_start: 0.7907 (m-80) cc_final: 0.7652 (m-80) REVERT: E 400 PHE cc_start: 0.7905 (t80) cc_final: 0.7442 (t80) REVERT: F 20 MET cc_start: 0.8950 (mtm) cc_final: 0.8629 (mtm) REVERT: F 68 MET cc_start: 0.8748 (mmm) cc_final: 0.8379 (mmm) REVERT: H 10 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7698 (mt-10) REVERT: H 106 TYR cc_start: 0.8443 (OUTLIER) cc_final: 0.7920 (m-80) REVERT: L 4 LEU cc_start: 0.8346 (OUTLIER) cc_final: 0.7685 (pp) REVERT: L 37 TYR cc_start: 0.8471 (m-80) cc_final: 0.8211 (m-80) REVERT: L 49 MET cc_start: 0.6066 (mmt) cc_final: 0.5671 (mmt) REVERT: L 71 SER cc_start: 0.8653 (m) cc_final: 0.8315 (p) REVERT: L 107 LEU cc_start: 0.6548 (tp) cc_final: 0.6317 (tp) REVERT: O 324 TYR cc_start: 0.8794 (t80) cc_final: 0.8495 (t80) REVERT: O 442 TYR cc_start: 0.9165 (t80) cc_final: 0.8778 (t80) REVERT: P 10 MET cc_start: 0.7972 (mmm) cc_final: 0.7639 (mmp) REVERT: Q 1 MET cc_start: 0.9232 (tpp) cc_final: 0.9031 (tpp) REVERT: Q 13 GLU cc_start: 0.8020 (tm-30) cc_final: 0.7538 (tm-30) REVERT: Q 41 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8150 (pp) REVERT: Q 181 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.8042 (pp) REVERT: Q 485 LEU cc_start: 0.9121 (OUTLIER) cc_final: 0.8842 (mm) REVERT: R 52 TYR cc_start: 0.7958 (m-80) cc_final: 0.7674 (m-80) REVERT: R 59 GLN cc_start: 0.7939 (mt0) cc_final: 0.7586 (mt0) REVERT: S 49 GLU cc_start: 0.7527 (mt-10) cc_final: 0.7000 (tp30) REVERT: S 282 LYS cc_start: 0.8378 (ttpt) cc_final: 0.7907 (ttpp) REVERT: S 297 TYR cc_start: 0.7906 (m-80) cc_final: 0.7652 (m-80) REVERT: S 400 PHE cc_start: 0.7901 (t80) cc_final: 0.7445 (t80) REVERT: T 20 MET cc_start: 0.9016 (mtm) cc_final: 0.8663 (mtm) REVERT: T 68 MET cc_start: 0.8762 (mmm) cc_final: 0.8387 (mmm) REVERT: U 10 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7697 (mt-10) REVERT: U 106 TYR cc_start: 0.8448 (OUTLIER) cc_final: 0.7926 (m-80) REVERT: V 4 LEU cc_start: 0.8354 (OUTLIER) cc_final: 0.7703 (pp) REVERT: V 48 LEU cc_start: 0.7755 (tt) cc_final: 0.7514 (tt) REVERT: V 49 MET cc_start: 0.6055 (mmt) cc_final: 0.5651 (mmt) REVERT: V 71 SER cc_start: 0.8652 (m) cc_final: 0.8328 (p) outliers start: 133 outliers final: 93 residues processed: 615 average time/residue: 0.3668 time to fit residues: 374.4090 Evaluate side-chains 599 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 494 time to evaluate : 3.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 134 ASN Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 183 CYS Chi-restraints excluded: chain A residue 244 LYS Chi-restraints excluded: chain A residue 258 MET Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 371 PHE Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 20 MET Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 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 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 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 121 CYS Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 205 MET Chi-restraints excluded: chain E residue 268 ILE Chi-restraints excluded: chain E residue 311 SER Chi-restraints excluded: chain E residue 361 GLU 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 10 GLU 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 O residue 1 MET Chi-restraints excluded: chain O residue 48 THR Chi-restraints excluded: chain O residue 66 THR Chi-restraints excluded: chain O residue 115 THR Chi-restraints excluded: chain O residue 134 ASN Chi-restraints excluded: chain O residue 163 THR Chi-restraints excluded: chain O residue 179 LEU Chi-restraints excluded: chain O residue 182 GLU Chi-restraints excluded: chain O residue 183 CYS Chi-restraints excluded: chain O residue 244 LYS Chi-restraints excluded: chain O residue 258 MET Chi-restraints excluded: chain O residue 336 SER Chi-restraints excluded: chain O residue 371 PHE Chi-restraints excluded: chain O residue 491 VAL Chi-restraints excluded: chain P residue 8 VAL Chi-restraints excluded: chain P residue 20 MET Chi-restraints excluded: chain Q residue 19 THR Chi-restraints excluded: chain Q residue 41 LEU Chi-restraints excluded: chain Q residue 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 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 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 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 311 SER Chi-restraints excluded: chain S residue 361 GLU 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 10 GLU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 114 optimal weight: 10.0000 chunk 319 optimal weight: 6.9990 chunk 149 optimal weight: 10.0000 chunk 157 optimal weight: 6.9990 chunk 342 optimal weight: 10.0000 chunk 89 optimal weight: 5.9990 chunk 270 optimal weight: 10.0000 chunk 36 optimal weight: 7.9990 chunk 306 optimal weight: 9.9990 chunk 226 optimal weight: 5.9990 chunk 137 optimal weight: 9.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 ASN ** C 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 375 ASN ** L 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 134 ASN ** Q 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 375 ASN ** V 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.105031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.091022 restraints weight = 43641.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.093068 restraints weight = 27076.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.094426 restraints weight = 19229.853| |-----------------------------------------------------------------------------| r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.2642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.078 30638 Z= 0.316 Angle : 0.729 12.859 41578 Z= 0.375 Chirality : 0.050 0.282 4848 Planarity : 0.005 0.066 5162 Dihedral : 6.400 55.584 4632 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 5.44 % Allowed : 20.19 % Favored : 74.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.13), residues: 3838 helix: 1.34 (0.18), residues: 876 sheet: -1.60 (0.14), residues: 1222 loop : -1.40 (0.14), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP U 50 HIS 0.006 0.001 HIS Q 94 PHE 0.026 0.002 PHE Q 420 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 0.00548 ( 12) link_NAG-ASN : angle 2.07084 ( 36) link_BETA1-4 : bond 0.00425 ( 16) link_BETA1-4 : angle 1.64792 ( 48) hydrogen bonds : bond 0.04200 ( 1190) hydrogen bonds : angle 5.47210 ( 3354) SS BOND : bond 0.00916 ( 38) SS BOND : angle 1.89850 ( 76) covalent geometry : bond 0.00758 (30572) covalent geometry : angle 0.72077 (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 680 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 174 poor density : 506 time to evaluate : 3.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 324 TYR cc_start: 0.8791 (t80) cc_final: 0.8516 (t80) REVERT: A 438 PHE cc_start: 0.8329 (m-80) cc_final: 0.8091 (m-10) REVERT: A 442 TYR cc_start: 0.9078 (t80) cc_final: 0.8665 (t80) REVERT: B 10 MET cc_start: 0.8269 (mmm) cc_final: 0.7753 (mmp) REVERT: C 13 GLU cc_start: 0.8138 (tm-30) cc_final: 0.7688 (tm-30) REVERT: C 41 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8352 (pp) REVERT: C 181 LEU cc_start: 0.8485 (OUTLIER) cc_final: 0.8231 (pp) REVERT: C 485 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8811 (mm) REVERT: D 59 GLN cc_start: 0.8001 (mt0) cc_final: 0.7579 (mt0) REVERT: E 282 LYS cc_start: 0.8513 (ttpt) cc_final: 0.7926 (ttpp) REVERT: E 359 LYS cc_start: 0.8349 (OUTLIER) cc_final: 0.7904 (tptt) REVERT: E 400 PHE cc_start: 0.7783 (t80) cc_final: 0.7333 (t80) REVERT: F 20 MET cc_start: 0.9072 (mtm) cc_final: 0.8809 (mtm) REVERT: H 10 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7727 (mt-10) REVERT: H 106 TYR cc_start: 0.8588 (OUTLIER) cc_final: 0.8007 (m-80) REVERT: L 4 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.7899 (pp) REVERT: L 48 LEU cc_start: 0.8450 (tt) cc_final: 0.8101 (tt) REVERT: L 49 MET cc_start: 0.6359 (mmt) cc_final: 0.5677 (mmt) REVERT: L 63 PHE cc_start: 0.7563 (m-80) cc_final: 0.7354 (m-10) REVERT: L 71 SER cc_start: 0.8677 (m) cc_final: 0.8312 (p) REVERT: L 107 LEU cc_start: 0.6737 (tp) cc_final: 0.6527 (tp) REVERT: O 324 TYR cc_start: 0.8781 (t80) cc_final: 0.8511 (t80) REVERT: O 442 TYR cc_start: 0.9126 (t80) cc_final: 0.8730 (t80) REVERT: P 10 MET cc_start: 0.8241 (mmm) cc_final: 0.7776 (mmp) REVERT: Q 13 GLU cc_start: 0.8173 (tm-30) cc_final: 0.7779 (tm-30) REVERT: Q 41 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8352 (pp) REVERT: Q 181 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8239 (pp) REVERT: Q 485 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8839 (mm) REVERT: R 59 GLN cc_start: 0.8006 (mt0) cc_final: 0.7586 (mt0) REVERT: S 282 LYS cc_start: 0.8514 (ttpt) cc_final: 0.7926 (ttpp) REVERT: S 359 LYS cc_start: 0.8356 (OUTLIER) cc_final: 0.7914 (tptt) REVERT: S 400 PHE cc_start: 0.7782 (t80) cc_final: 0.7337 (t80) REVERT: T 20 MET cc_start: 0.9090 (mtm) cc_final: 0.8777 (mtm) REVERT: U 10 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7728 (mt-10) REVERT: U 106 TYR cc_start: 0.8610 (OUTLIER) cc_final: 0.8036 (m-80) REVERT: V 4 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.7906 (pp) REVERT: V 49 MET cc_start: 0.6095 (mmt) cc_final: 0.5628 (mmt) REVERT: V 55 ARG cc_start: 0.8303 (mtm110) cc_final: 0.7860 (mtm110) REVERT: V 71 SER cc_start: 0.8672 (m) cc_final: 0.8304 (p) outliers start: 174 outliers final: 134 residues processed: 625 average time/residue: 0.3808 time to fit residues: 397.4070 Evaluate side-chains 631 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 483 time to evaluate : 3.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 183 CYS Chi-restraints excluded: chain A residue 244 LYS Chi-restraints excluded: chain A residue 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 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 53 LEU Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 295 MET Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 394 SER Chi-restraints excluded: chain C residue 401 GLU Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain E residue 16 SER Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 34 MET Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 121 CYS Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 205 MET Chi-restraints excluded: chain E residue 251 LEU 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 359 LYS Chi-restraints excluded: chain E residue 361 GLU Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 380 ILE Chi-restraints excluded: chain E residue 464 ILE Chi-restraints excluded: chain E residue 487 LEU Chi-restraints excluded: chain F residue 21 SER Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 70 MET Chi-restraints excluded: chain H residue 78 VAL 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 115 THR Chi-restraints excluded: chain O residue 124 LEU Chi-restraints excluded: chain O residue 163 THR Chi-restraints excluded: chain O residue 179 LEU Chi-restraints excluded: chain O residue 182 GLU Chi-restraints excluded: chain O residue 183 CYS Chi-restraints excluded: chain O residue 244 LYS Chi-restraints excluded: chain O residue 258 MET Chi-restraints excluded: chain O residue 269 GLN Chi-restraints excluded: chain O residue 283 CYS Chi-restraints excluded: chain O residue 319 LEU Chi-restraints excluded: chain O residue 336 SER Chi-restraints excluded: chain O residue 355 VAL Chi-restraints excluded: chain O residue 363 VAL Chi-restraints excluded: chain O residue 371 PHE Chi-restraints excluded: chain O residue 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 53 LEU Chi-restraints excluded: chain Q residue 65 ILE Chi-restraints excluded: chain Q residue 70 THR Chi-restraints excluded: chain Q residue 92 CYS Chi-restraints excluded: chain Q residue 126 GLU Chi-restraints excluded: chain Q residue 139 VAL Chi-restraints excluded: chain Q residue 158 VAL Chi-restraints excluded: chain Q residue 181 LEU Chi-restraints excluded: chain Q residue 197 LEU Chi-restraints excluded: chain Q residue 262 LEU Chi-restraints excluded: chain Q residue 266 THR Chi-restraints excluded: chain Q residue 281 LEU Chi-restraints excluded: chain Q residue 285 LEU Chi-restraints excluded: chain Q residue 295 MET Chi-restraints excluded: chain Q residue 319 LEU Chi-restraints excluded: chain Q residue 337 THR Chi-restraints excluded: chain Q residue 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 32 THR Chi-restraints excluded: chain S residue 33 THR Chi-restraints excluded: chain S residue 34 MET Chi-restraints excluded: chain S residue 51 THR Chi-restraints excluded: chain S residue 121 CYS Chi-restraints excluded: chain S residue 130 VAL Chi-restraints excluded: chain S residue 205 MET Chi-restraints excluded: chain S residue 251 LEU 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 359 LYS Chi-restraints excluded: chain S residue 361 GLU Chi-restraints excluded: chain S residue 363 VAL Chi-restraints excluded: chain S residue 380 ILE 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 69 THR Chi-restraints excluded: chain U residue 70 MET Chi-restraints excluded: chain U residue 78 VAL 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: 5.9990 chunk 217 optimal weight: 10.0000 chunk 262 optimal weight: 0.9980 chunk 354 optimal weight: 9.9990 chunk 12 optimal weight: 5.9990 chunk 144 optimal weight: 5.9990 chunk 148 optimal weight: 6.9990 chunk 2 optimal weight: 4.9990 chunk 290 optimal weight: 5.9990 chunk 375 optimal weight: 10.0000 overall best weight: 4.7988 ------------------------------------------------------------------------------- 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** ** L 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.106133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.092258 restraints weight = 43309.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.094315 restraints weight = 26659.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.095701 restraints weight = 18851.192| |-----------------------------------------------------------------------------| r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.2689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 30638 Z= 0.240 Angle : 0.679 13.173 41578 Z= 0.347 Chirality : 0.047 0.281 4848 Planarity : 0.004 0.064 5162 Dihedral : 6.332 55.048 4632 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 4.75 % Allowed : 20.94 % 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: -1.31 (0.13), residues: 3838 helix: 1.40 (0.18), residues: 876 sheet: -1.61 (0.14), residues: 1222 loop : -1.43 (0.14), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP H 50 HIS 0.005 0.001 HIS C 94 PHE 0.026 0.002 PHE Q 420 TYR 0.024 0.002 TYR U 27 ARG 0.007 0.001 ARG U 100 Details of bonding type rmsd link_NAG-ASN : bond 0.00493 ( 12) link_NAG-ASN : angle 1.95607 ( 36) link_BETA1-4 : bond 0.00380 ( 16) link_BETA1-4 : angle 1.57998 ( 48) hydrogen bonds : bond 0.04011 ( 1190) hydrogen bonds : angle 5.38330 ( 3354) SS BOND : bond 0.00794 ( 38) SS BOND : angle 1.69188 ( 76) covalent geometry : bond 0.00578 (30572) covalent geometry : angle 0.67149 (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 639 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 487 time to evaluate : 3.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 324 TYR cc_start: 0.8775 (t80) cc_final: 0.8493 (t80) REVERT: A 438 PHE cc_start: 0.8316 (m-80) cc_final: 0.8079 (m-10) REVERT: A 442 TYR cc_start: 0.9101 (t80) cc_final: 0.8688 (t80) REVERT: B 10 MET cc_start: 0.8217 (mmm) cc_final: 0.7759 (mmp) REVERT: C 13 GLU cc_start: 0.8110 (tm-30) cc_final: 0.7677 (tm-30) REVERT: C 41 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8274 (pp) REVERT: C 181 LEU cc_start: 0.8302 (OUTLIER) cc_final: 0.8096 (pp) REVERT: C 485 LEU cc_start: 0.9132 (OUTLIER) cc_final: 0.8809 (mm) REVERT: D 59 GLN cc_start: 0.7988 (mt0) cc_final: 0.7576 (mt0) REVERT: E 170 GLU cc_start: 0.6388 (mp0) cc_final: 0.6151 (mp0) REVERT: E 282 LYS cc_start: 0.8485 (ttpt) cc_final: 0.7862 (ttpp) REVERT: E 400 PHE cc_start: 0.7914 (t80) cc_final: 0.7416 (t80) REVERT: F 20 MET cc_start: 0.9099 (mtm) cc_final: 0.8823 (mtm) REVERT: H 10 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7755 (mt-10) REVERT: H 106 TYR cc_start: 0.8585 (OUTLIER) cc_final: 0.8023 (m-80) REVERT: L 4 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.7941 (pp) REVERT: L 48 LEU cc_start: 0.8392 (tt) cc_final: 0.8133 (tt) REVERT: L 49 MET cc_start: 0.6296 (mmt) cc_final: 0.5614 (mmt) REVERT: L 71 SER cc_start: 0.8661 (m) cc_final: 0.8297 (p) REVERT: L 107 LEU cc_start: 0.7028 (tp) cc_final: 0.6818 (tp) REVERT: O 324 TYR cc_start: 0.8768 (t80) cc_final: 0.8491 (t80) REVERT: O 442 TYR cc_start: 0.9100 (t80) cc_final: 0.8688 (t80) REVERT: P 10 MET cc_start: 0.8199 (mmm) cc_final: 0.7767 (mmp) REVERT: Q 13 GLU cc_start: 0.8145 (tm-30) cc_final: 0.7732 (tm-30) REVERT: Q 41 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8276 (pp) REVERT: Q 485 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8841 (mm) REVERT: R 59 GLN cc_start: 0.7991 (mt0) cc_final: 0.7580 (mt0) REVERT: S 170 GLU cc_start: 0.6391 (mp0) cc_final: 0.6156 (mp0) REVERT: S 282 LYS cc_start: 0.8486 (ttpt) cc_final: 0.7865 (ttpp) REVERT: S 400 PHE cc_start: 0.7912 (t80) cc_final: 0.7419 (t80) REVERT: T 20 MET cc_start: 0.9067 (mtm) cc_final: 0.8764 (mtm) REVERT: U 10 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7756 (mt-10) REVERT: U 102 PHE cc_start: 0.8603 (p90) cc_final: 0.8398 (p90) REVERT: U 106 TYR cc_start: 0.8591 (OUTLIER) cc_final: 0.8026 (m-80) REVERT: V 4 LEU cc_start: 0.8415 (OUTLIER) cc_final: 0.7947 (pp) REVERT: V 48 LEU cc_start: 0.7778 (tt) cc_final: 0.7199 (tt) REVERT: V 49 MET cc_start: 0.6041 (mmt) cc_final: 0.5745 (mmt) REVERT: V 55 ARG cc_start: 0.8213 (mtm110) cc_final: 0.7794 (mtm110) REVERT: V 71 SER cc_start: 0.8653 (m) cc_final: 0.8289 (p) outliers start: 152 outliers final: 133 residues processed: 591 average time/residue: 0.3633 time to fit residues: 359.3218 Evaluate side-chains 627 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 483 time to evaluate : 3.237 ------------------------------------------------------------------------------- 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 115 THR Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 183 CYS Chi-restraints excluded: chain A residue 244 LYS Chi-restraints excluded: chain A residue 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 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 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 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 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 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 380 ILE Chi-restraints excluded: chain E residue 464 ILE Chi-restraints excluded: chain E residue 487 LEU Chi-restraints excluded: chain F residue 21 SER Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 70 MET Chi-restraints excluded: chain H residue 78 VAL 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 115 THR Chi-restraints excluded: chain O residue 124 LEU Chi-restraints excluded: chain O residue 163 THR Chi-restraints excluded: chain O residue 179 LEU Chi-restraints excluded: chain O residue 182 GLU Chi-restraints excluded: chain O residue 183 CYS Chi-restraints excluded: chain O residue 244 LYS Chi-restraints excluded: chain O residue 258 MET 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 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 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 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 270 THR 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 380 ILE 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 69 THR Chi-restraints excluded: chain U residue 70 MET Chi-restraints excluded: chain U residue 78 VAL 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 343 optimal weight: 0.0870 chunk 163 optimal weight: 8.9990 chunk 12 optimal weight: 3.9990 chunk 135 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 8 optimal weight: 7.9990 chunk 149 optimal weight: 10.0000 chunk 258 optimal weight: 5.9990 chunk 278 optimal weight: 6.9990 chunk 45 optimal weight: 0.8980 chunk 379 optimal weight: 0.0670 overall best weight: 1.6100 ------------------------------------------------------------------------------- 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** C 314 GLN ** E 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 134 ASN ** Q 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 35 HIS ** V 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.110653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.097029 restraints weight = 42658.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.099643 restraints weight = 27872.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.100935 restraints weight = 16760.758| |-----------------------------------------------------------------------------| r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.2771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 30638 Z= 0.132 Angle : 0.605 13.317 41578 Z= 0.308 Chirality : 0.044 0.243 4848 Planarity : 0.004 0.057 5162 Dihedral : 5.964 54.230 4632 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 3.91 % Allowed : 21.88 % 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: -1.03 (0.13), residues: 3838 helix: 1.77 (0.18), residues: 870 sheet: -1.45 (0.16), residues: 1014 loop : -1.38 (0.13), residues: 1954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP U 50 HIS 0.004 0.001 HIS R 39 PHE 0.026 0.001 PHE L 63 TYR 0.022 0.002 TYR U 27 ARG 0.007 0.000 ARG U 100 Details of bonding type rmsd link_NAG-ASN : bond 0.00335 ( 12) link_NAG-ASN : angle 1.62421 ( 36) link_BETA1-4 : bond 0.00385 ( 16) link_BETA1-4 : angle 1.61215 ( 48) hydrogen bonds : bond 0.03665 ( 1190) hydrogen bonds : angle 5.13164 ( 3354) SS BOND : bond 0.00507 ( 38) SS BOND : angle 1.36745 ( 76) covalent geometry : bond 0.00305 (30572) covalent geometry : angle 0.59923 (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 643 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 518 time to evaluate : 3.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 324 TYR cc_start: 0.8789 (t80) cc_final: 0.8481 (t80) REVERT: A 438 PHE cc_start: 0.8261 (m-80) cc_final: 0.8022 (m-10) REVERT: A 442 TYR cc_start: 0.9156 (t80) cc_final: 0.8802 (t80) REVERT: C 1 MET cc_start: 0.9232 (tpp) cc_final: 0.9029 (tpp) REVERT: C 13 GLU cc_start: 0.8041 (tm-30) cc_final: 0.7557 (tm-30) REVERT: C 41 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8039 (pp) REVERT: C 181 LEU cc_start: 0.8146 (OUTLIER) cc_final: 0.7897 (pp) REVERT: C 485 LEU cc_start: 0.9123 (OUTLIER) cc_final: 0.8818 (mm) REVERT: D 52 TYR cc_start: 0.7930 (m-80) cc_final: 0.7644 (m-80) REVERT: D 59 GLN cc_start: 0.7958 (mt0) cc_final: 0.7601 (mt0) REVERT: E 47 LYS cc_start: 0.8261 (ptmt) cc_final: 0.7892 (pttm) REVERT: E 282 LYS cc_start: 0.8396 (ttpt) cc_final: 0.7923 (ttpp) REVERT: E 297 TYR cc_start: 0.8033 (m-80) cc_final: 0.7808 (m-80) REVERT: E 400 PHE cc_start: 0.7902 (t80) cc_final: 0.7479 (t80) REVERT: F 20 MET cc_start: 0.9036 (mtm) cc_final: 0.8716 (mtm) REVERT: H 10 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7700 (mt-10) REVERT: H 100 ARG cc_start: 0.7842 (mmm-85) cc_final: 0.7473 (mmm-85) REVERT: H 106 TYR cc_start: 0.8436 (OUTLIER) cc_final: 0.7954 (m-80) REVERT: L 4 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.7670 (pp) REVERT: L 48 LEU cc_start: 0.8268 (tt) cc_final: 0.7915 (tt) REVERT: L 49 MET cc_start: 0.6359 (mmt) cc_final: 0.5604 (mmt) REVERT: L 71 SER cc_start: 0.8623 (m) cc_final: 0.8318 (p) REVERT: L 107 LEU cc_start: 0.6811 (tp) cc_final: 0.6596 (tp) REVERT: O 324 TYR cc_start: 0.8782 (t80) cc_final: 0.8472 (t80) REVERT: O 442 TYR cc_start: 0.9151 (t80) cc_final: 0.8800 (t80) REVERT: P 10 MET cc_start: 0.8034 (mmm) cc_final: 0.7629 (mmp) REVERT: Q 1 MET cc_start: 0.9242 (tpp) cc_final: 0.9039 (tpp) REVERT: Q 13 GLU cc_start: 0.8026 (tm-30) cc_final: 0.7551 (tm-30) REVERT: Q 41 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8019 (pp) REVERT: Q 485 LEU cc_start: 0.9118 (OUTLIER) cc_final: 0.8845 (mm) REVERT: R 52 TYR cc_start: 0.7931 (m-80) cc_final: 0.7646 (m-80) REVERT: R 59 GLN cc_start: 0.7966 (mt0) cc_final: 0.7614 (mt0) REVERT: S 47 LYS cc_start: 0.8274 (ptmt) cc_final: 0.7892 (pttm) REVERT: S 282 LYS cc_start: 0.8397 (ttpt) cc_final: 0.7925 (ttpp) REVERT: S 400 PHE cc_start: 0.7905 (t80) cc_final: 0.7479 (t80) REVERT: T 20 MET cc_start: 0.9034 (mtm) cc_final: 0.8716 (mtm) REVERT: U 10 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.7697 (mt-10) REVERT: U 106 TYR cc_start: 0.8477 (OUTLIER) cc_final: 0.7951 (m-80) REVERT: V 4 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.7749 (pp) REVERT: V 48 LEU cc_start: 0.7661 (tt) cc_final: 0.7326 (tt) REVERT: V 49 MET cc_start: 0.6088 (mmt) cc_final: 0.5755 (mmt) REVERT: V 55 ARG cc_start: 0.8344 (mtm110) cc_final: 0.7841 (mtm110) REVERT: V 71 SER cc_start: 0.8629 (m) cc_final: 0.8328 (p) outliers start: 125 outliers final: 103 residues processed: 602 average time/residue: 0.3788 time to fit residues: 375.8600 Evaluate side-chains 598 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 484 time to evaluate : 3.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 134 ASN Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 183 CYS Chi-restraints excluded: chain A residue 244 LYS Chi-restraints excluded: chain A residue 258 MET Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 371 PHE Chi-restraints excluded: chain A residue 491 VAL 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 199 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 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 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 380 ILE Chi-restraints excluded: chain E residue 464 ILE Chi-restraints excluded: chain E residue 487 LEU Chi-restraints excluded: chain F residue 21 SER Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 70 MET Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 106 TYR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 20 ILE Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 30 CYS Chi-restraints excluded: chain O residue 48 THR Chi-restraints excluded: chain O residue 66 THR Chi-restraints excluded: chain O residue 115 THR Chi-restraints excluded: chain O residue 134 ASN Chi-restraints excluded: chain O residue 163 THR Chi-restraints excluded: chain O residue 179 LEU Chi-restraints excluded: chain O residue 182 GLU Chi-restraints excluded: chain O residue 183 CYS Chi-restraints excluded: chain O residue 244 LYS Chi-restraints excluded: chain O residue 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 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 197 LEU Chi-restraints excluded: chain Q residue 199 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 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 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 361 GLU Chi-restraints excluded: chain S residue 380 ILE Chi-restraints excluded: chain S residue 464 ILE Chi-restraints excluded: chain S residue 487 LEU Chi-restraints excluded: chain T residue 21 SER Chi-restraints excluded: chain T residue 70 VAL Chi-restraints excluded: chain U residue 10 GLU Chi-restraints excluded: chain U residue 28 THR Chi-restraints excluded: chain U residue 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 330 optimal weight: 10.0000 chunk 100 optimal weight: 10.0000 chunk 257 optimal weight: 8.9990 chunk 274 optimal weight: 7.9990 chunk 301 optimal weight: 9.9990 chunk 31 optimal weight: 0.8980 chunk 180 optimal weight: 20.0000 chunk 244 optimal weight: 8.9990 chunk 58 optimal weight: 10.0000 chunk 13 optimal weight: 10.0000 chunk 294 optimal weight: 2.9990 overall best weight: 5.9788 ------------------------------------------------------------------------------- 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** ** L 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 134 ASN ** O 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.105895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.091418 restraints weight = 43326.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.093651 restraints weight = 25834.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.095148 restraints weight = 17875.877| |-----------------------------------------------------------------------------| r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.2811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.073 30638 Z= 0.286 Angle : 0.705 12.794 41578 Z= 0.361 Chirality : 0.048 0.223 4848 Planarity : 0.005 0.079 5162 Dihedral : 6.249 55.289 4632 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 4.38 % Allowed : 21.78 % Favored : 73.84 % 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: -1.20 (0.13), residues: 3838 helix: 1.51 (0.18), residues: 870 sheet: -1.49 (0.15), residues: 1102 loop : -1.44 (0.13), residues: 1866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP U 50 HIS 0.005 0.001 HIS C 94 PHE 0.025 0.002 PHE Q 420 TYR 0.030 0.002 TYR H 27 ARG 0.013 0.001 ARG F 15 Details of bonding type rmsd link_NAG-ASN : bond 0.00555 ( 12) link_NAG-ASN : angle 2.01682 ( 36) link_BETA1-4 : bond 0.00413 ( 16) link_BETA1-4 : angle 1.66989 ( 48) hydrogen bonds : bond 0.04019 ( 1190) hydrogen bonds : angle 5.33088 ( 3354) SS BOND : bond 0.00857 ( 38) SS BOND : angle 1.64463 ( 76) covalent geometry : bond 0.00689 (30572) covalent geometry : angle 0.69825 (41418) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10577.02 seconds wall clock time: 184 minutes 6.90 seconds (11046.90 seconds total)