Starting phenix.real_space_refine on Mon Apr 6 04:17:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ki4_22884/04_2026/7ki4_22884.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ki4_22884/04_2026/7ki4_22884.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ki4_22884/04_2026/7ki4_22884.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ki4_22884/04_2026/7ki4_22884.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ki4_22884/04_2026/7ki4_22884.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ki4_22884/04_2026/7ki4_22884.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.087 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 78 5.16 5 C 9978 2.51 5 N 2553 2.21 5 O 3129 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 71 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15738 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 3404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3404 Classifications: {'peptide': 448} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 15, 'TRANS': 432} Chain breaks: 1 Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 2, 'GLN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 31 Chain: "L" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 790 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 99} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "H" Number of atoms: 886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 886 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 4, 'TRANS': 112} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 3404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3404 Classifications: {'peptide': 448} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 15, 'TRANS': 432} Chain breaks: 1 Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 2, 'GLN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 31 Chain: "C" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 790 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 99} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "D" Number of atoms: 886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 886 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 4, 'TRANS': 112} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 3404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3404 Classifications: {'peptide': 448} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 15, 'TRANS': 432} Chain breaks: 1 Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 2, 'GLN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 31 Chain: "F" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 790 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 99} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "G" Number of atoms: 886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 886 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 4, 'TRANS': 112} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 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: 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: "K" 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: "M" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 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: 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: "P" 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: "Q" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "R" 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: "S" 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: "T" 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: "U" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 3.74, per 1000 atoms: 0.24 Number of scatterers: 15738 At special positions: 0 Unit cell: (111.3, 113.4, 152.25, 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 78 16.00 O 3129 8.00 N 2553 7.00 C 9978 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS A 71 " - pdb=" SG CYS A 192 " distance=2.04 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 340 " distance=2.03 Simple disulfide: pdb=" SG CYS A 355 " - pdb=" SG CYS A 363 " distance=2.02 Simple disulfide: pdb=" SG CYS A 387 " - pdb=" SG CYS A 392 " distance=2.03 Simple disulfide: pdb=" SG CYS A 394 " - pdb=" SG CYS A 417 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.03 Simple disulfide: pdb=" SG CYS B 71 " - pdb=" SG CYS B 192 " distance=2.04 Simple disulfide: pdb=" SG CYS B 331 " - pdb=" SG CYS B 340 " distance=2.03 Simple disulfide: pdb=" SG CYS B 355 " - pdb=" SG CYS B 363 " distance=2.02 Simple disulfide: pdb=" SG CYS B 387 " - pdb=" SG CYS B 392 " distance=2.03 Simple disulfide: pdb=" SG CYS B 394 " - pdb=" SG CYS B 417 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 88 " distance=2.02 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 95 " distance=2.03 Simple disulfide: pdb=" SG CYS E 71 " - pdb=" SG CYS E 192 " distance=2.04 Simple disulfide: pdb=" SG CYS E 331 " - pdb=" SG CYS E 340 " distance=2.03 Simple disulfide: pdb=" SG CYS E 355 " - pdb=" SG CYS E 363 " distance=2.02 Simple disulfide: pdb=" SG CYS E 387 " - pdb=" SG CYS E 392 " distance=2.03 Simple disulfide: pdb=" SG CYS E 394 " - pdb=" SG CYS E 417 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.02 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 95 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA M 3 " - " MAN M 4 " " BMA Q 3 " - " MAN Q 4 " " BMA U 3 " - " MAN U 4 " ALPHA1-6 " BMA M 3 " - " MAN M 5 " " BMA Q 3 " - " MAN Q 5 " " BMA U 3 " - " MAN U 5 " BETA1-4 " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " BETA1-6 " NAG M 1 " - " FUC M 6 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG Q 1 " - " FUC Q 6 " " NAG U 1 " - " FUC U 6 " NAG-ASN " NAG I 1 " - " ASN A 99 " " NAG J 1 " - " ASN A 464 " " NAG K 1 " - " ASN A 414 " " NAG M 1 " - " ASN A 67 " " NAG N 1 " - " ASN B 99 " " NAG O 1 " - " ASN B 464 " " NAG P 1 " - " ASN B 414 " " NAG Q 1 " - " ASN B 67 " " NAG R 1 " - " ASN E 99 " " NAG S 1 " - " ASN E 464 " " NAG T 1 " - " ASN E 414 " " NAG U 1 " - " ASN E 67 " Time building additional restraints: 1.68 Conformation dependent library (CDL) restraints added in 736.0 milliseconds 3972 Ramachandran restraints generated. 1986 Oldfield, 0 Emsley, 1986 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3720 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 33 sheets defined 30.3% alpha, 38.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.83 Creating SS restraints... Processing helix chain 'A' and resid 29 through 35 Processing helix chain 'A' and resid 65 through 72 removed outlier: 3.628A pdb=" N SER A 69 " --> pdb=" O SER A 66 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N GLN A 70 " --> pdb=" O ASN A 67 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N THR A 72 " --> pdb=" O SER A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 99 removed outlier: 3.537A pdb=" N ILE A 86 " --> pdb=" O ARG A 82 " (cutoff:3.500A) Proline residue: A 89 - end of helix removed outlier: 4.062A pdb=" N TYR A 97 " --> pdb=" O ALA A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 121 Processing helix chain 'A' and resid 125 through 145 removed outlier: 3.896A pdb=" N LYS A 139 " --> pdb=" O TYR A 135 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ASN A 140 " --> pdb=" O GLU A 136 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ASN A 143 " --> pdb=" O LYS A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 154 Processing helix chain 'A' and resid 175 through 183 Processing helix chain 'A' and resid 184 through 187 removed outlier: 3.504A pdb=" N ILE A 187 " --> pdb=" O VAL A 184 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 184 through 187' Processing helix chain 'A' and resid 191 through 215 removed outlier: 4.323A pdb=" N PHE A 212 " --> pdb=" O SER A 208 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N VAL A 213 " --> pdb=" O ASP A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 232 Processing helix chain 'A' and resid 233 through 236 Processing helix chain 'A' and resid 238 through 246 Processing helix chain 'A' and resid 252 through 259 Processing helix chain 'A' and resid 328 through 331 Processing helix chain 'A' and resid 349 through 357 Processing helix chain 'A' and resid 359 through 363 Processing helix chain 'A' and resid 437 through 442 removed outlier: 4.320A pdb=" N GLY A 442 " --> pdb=" O TYR A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 481 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.537A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 86 through 90 Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'B' and resid 65 through 72 removed outlier: 3.627A pdb=" N SER B 69 " --> pdb=" O SER B 66 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N GLN B 70 " --> pdb=" O ASN B 67 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N THR B 72 " --> pdb=" O SER B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 99 removed outlier: 3.537A pdb=" N ILE B 86 " --> pdb=" O ARG B 82 " (cutoff:3.500A) Proline residue: B 89 - end of helix removed outlier: 4.061A pdb=" N TYR B 97 " --> pdb=" O ALA B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 121 Processing helix chain 'B' and resid 125 through 145 removed outlier: 3.896A pdb=" N LYS B 139 " --> pdb=" O TYR B 135 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ASN B 140 " --> pdb=" O GLU B 136 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ASN B 143 " --> pdb=" O LYS B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 154 Processing helix chain 'B' and resid 175 through 183 Processing helix chain 'B' and resid 184 through 187 removed outlier: 3.504A pdb=" N ILE B 187 " --> pdb=" O VAL B 184 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 184 through 187' Processing helix chain 'B' and resid 191 through 215 removed outlier: 4.322A pdb=" N PHE B 212 " --> pdb=" O SER B 208 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N VAL B 213 " --> pdb=" O ASP B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 232 Processing helix chain 'B' and resid 233 through 236 Processing helix chain 'B' and resid 238 through 246 Processing helix chain 'B' and resid 252 through 259 Processing helix chain 'B' and resid 328 through 331 Processing helix chain 'B' and resid 349 through 357 Processing helix chain 'B' and resid 359 through 363 Processing helix chain 'B' and resid 437 through 442 removed outlier: 4.320A pdb=" N GLY B 442 " --> pdb=" O TYR B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 481 Processing helix chain 'C' and resid 79 through 83 removed outlier: 3.537A pdb=" N PHE C 83 " --> pdb=" O PRO C 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 90 Processing helix chain 'E' and resid 29 through 35 Processing helix chain 'E' and resid 65 through 72 removed outlier: 3.627A pdb=" N SER E 69 " --> pdb=" O SER E 66 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N GLN E 70 " --> pdb=" O ASN E 67 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N THR E 72 " --> pdb=" O SER E 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 99 removed outlier: 3.537A pdb=" N ILE E 86 " --> pdb=" O ARG E 82 " (cutoff:3.500A) Proline residue: E 89 - end of helix removed outlier: 4.061A pdb=" N TYR E 97 " --> pdb=" O ALA E 93 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 121 Processing helix chain 'E' and resid 125 through 145 removed outlier: 3.896A pdb=" N LYS E 139 " --> pdb=" O TYR E 135 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ASN E 140 " --> pdb=" O GLU E 136 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ASN E 143 " --> pdb=" O LYS E 139 " (cutoff:3.500A) Processing helix chain 'E' and resid 147 through 154 Processing helix chain 'E' and resid 175 through 183 Processing helix chain 'E' and resid 184 through 187 removed outlier: 3.504A pdb=" N ILE E 187 " --> pdb=" O VAL E 184 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 184 through 187' Processing helix chain 'E' and resid 191 through 215 removed outlier: 4.323A pdb=" N PHE E 212 " --> pdb=" O SER E 208 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N VAL E 213 " --> pdb=" O ASP E 209 " (cutoff:3.500A) Processing helix chain 'E' and resid 228 through 232 Processing helix chain 'E' and resid 233 through 236 Processing helix chain 'E' and resid 238 through 246 Processing helix chain 'E' and resid 252 through 259 Processing helix chain 'E' and resid 328 through 331 Processing helix chain 'E' and resid 349 through 357 Processing helix chain 'E' and resid 359 through 363 Processing helix chain 'E' and resid 437 through 442 removed outlier: 4.320A pdb=" N GLY E 442 " --> pdb=" O TYR E 438 " (cutoff:3.500A) Processing helix chain 'E' and resid 452 through 481 Processing helix chain 'F' and resid 79 through 83 removed outlier: 3.537A pdb=" N PHE F 83 " --> pdb=" O PRO F 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 86 through 90 Processing sheet with id=AA1, first strand: chain 'A' and resid 158 through 162 removed outlier: 10.218A pdb=" N THR A 168 " --> pdb=" O THR A 54 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ASP A 56 " --> pdb=" O THR A 168 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N TYR A 170 " --> pdb=" O ASP A 56 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N VAL A 39 " --> pdb=" O LEU A 296 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N LEU A 296 " --> pdb=" O VAL A 39 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N GLY A 41 " --> pdb=" O GLN A 294 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N GLN A 294 " --> pdb=" O GLY A 41 " (cutoff:3.500A) removed outlier: 8.921A pdb=" N THR A 43 " --> pdb=" O TYR A 292 " (cutoff:3.500A) removed outlier: 8.869A pdb=" N TYR A 292 " --> pdb=" O THR A 43 " (cutoff:3.500A) removed outlier: 9.994A pdb=" N LYS A 45 " --> pdb=" O GLN A 290 " (cutoff:3.500A) removed outlier: 10.194A pdb=" N GLN A 290 " --> pdb=" O LYS A 45 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N LYS A 47 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N ILE A 288 " --> pdb=" O LYS A 47 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N LYS A 49 " --> pdb=" O THR A 286 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N THR A 286 " --> pdb=" O LYS A 49 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N ASN A 51 " --> pdb=" O ILE A 284 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ILE A 284 " --> pdb=" O ASN A 51 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 275 through 298 current: chain 'A' and resid 332 through 333 Processing sheet with id=AA2, first strand: chain 'A' and resid 226 through 227 removed outlier: 3.795A pdb=" N MET A 226 " --> pdb=" O GLY A 264 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR A 263 " --> pdb=" O TYR A 281 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ILE A 277 " --> pdb=" O ILE A 267 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N VAL A 269 " --> pdb=" O TYR A 275 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N TYR A 275 " --> pdb=" O VAL A 269 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ILE A 284 " --> pdb=" O ASN A 51 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N ASN A 51 " --> pdb=" O ILE A 284 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N THR A 286 " --> pdb=" O LYS A 49 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N LYS A 49 " --> pdb=" O THR A 286 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N ILE A 288 " --> pdb=" O LYS A 47 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N LYS A 47 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 10.194A pdb=" N GLN A 290 " --> pdb=" O LYS A 45 " (cutoff:3.500A) removed outlier: 9.994A pdb=" N LYS A 45 " --> pdb=" O GLN A 290 " (cutoff:3.500A) removed outlier: 8.869A pdb=" N TYR A 292 " --> pdb=" O THR A 43 " (cutoff:3.500A) removed outlier: 8.921A pdb=" N THR A 43 " --> pdb=" O TYR A 292 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N GLN A 294 " --> pdb=" O GLY A 41 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N GLY A 41 " --> pdb=" O GLN A 294 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N LEU A 296 " --> pdb=" O VAL A 39 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N VAL A 39 " --> pdb=" O LEU A 296 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 38 through 60 current: chain 'A' and resid 322 through 326 Processing sheet with id=AA3, first strand: chain 'A' and resid 101 through 102 removed outlier: 6.574A pdb=" N MET A 115 " --> pdb=" O SER E 428 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 122 through 124 Processing sheet with id=AA5, first strand: chain 'A' and resid 301 through 303 removed outlier: 5.938A pdb=" N ARG A 365 " --> pdb=" O VAL A 449 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 410 through 412 Processing sheet with id=AA7, first strand: chain 'A' and resid 392 through 394 Processing sheet with id=AA8, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AA9, first strand: chain 'L' and resid 10 through 11 removed outlier: 6.385A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 10 through 11 Processing sheet with id=AB2, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB3, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.899A pdb=" N TRP H 36 " --> pdb=" O LEU H 48 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N VAL H 50 " --> pdb=" O VAL H 34 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N VAL H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 12.118A pdb=" N TYR H 93 " --> pdb=" O TRP H 109 " (cutoff:3.500A) removed outlier: 10.666A pdb=" N TRP H 109 " --> pdb=" O TYR H 93 " (cutoff:3.500A) removed outlier: 11.414A pdb=" N CYS H 95 " --> pdb=" O ALA H 107 " (cutoff:3.500A) removed outlier: 9.062A pdb=" N ALA H 107 " --> pdb=" O CYS H 95 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ARG H 97 " --> pdb=" O GLY H 105 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N GLY H 105 " --> pdb=" O ARG H 97 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.899A pdb=" N TRP H 36 " --> pdb=" O LEU H 48 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N VAL H 50 " --> pdb=" O VAL H 34 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N VAL H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 158 through 162 removed outlier: 10.219A pdb=" N THR B 168 " --> pdb=" O THR B 54 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ASP B 56 " --> pdb=" O THR B 168 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N TYR B 170 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N VAL B 39 " --> pdb=" O LEU B 296 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N LEU B 296 " --> pdb=" O VAL B 39 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N GLY B 41 " --> pdb=" O GLN B 294 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N GLN B 294 " --> pdb=" O GLY B 41 " (cutoff:3.500A) removed outlier: 8.921A pdb=" N THR B 43 " --> pdb=" O TYR B 292 " (cutoff:3.500A) removed outlier: 8.869A pdb=" N TYR B 292 " --> pdb=" O THR B 43 " (cutoff:3.500A) removed outlier: 9.994A pdb=" N LYS B 45 " --> pdb=" O GLN B 290 " (cutoff:3.500A) removed outlier: 10.194A pdb=" N GLN B 290 " --> pdb=" O LYS B 45 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N LYS B 47 " --> pdb=" O ILE B 288 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N ILE B 288 " --> pdb=" O LYS B 47 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N LYS B 49 " --> pdb=" O THR B 286 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N THR B 286 " --> pdb=" O LYS B 49 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N ASN B 51 " --> pdb=" O ILE B 284 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ILE B 284 " --> pdb=" O ASN B 51 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 275 through 298 current: chain 'B' and resid 332 through 333 Processing sheet with id=AB6, first strand: chain 'B' and resid 226 through 227 removed outlier: 3.795A pdb=" N MET B 226 " --> pdb=" O GLY B 264 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR B 263 " --> pdb=" O TYR B 281 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ILE B 277 " --> pdb=" O ILE B 267 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N VAL B 269 " --> pdb=" O TYR B 275 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N TYR B 275 " --> pdb=" O VAL B 269 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ILE B 284 " --> pdb=" O ASN B 51 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N ASN B 51 " --> pdb=" O ILE B 284 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N THR B 286 " --> pdb=" O LYS B 49 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N LYS B 49 " --> pdb=" O THR B 286 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N ILE B 288 " --> pdb=" O LYS B 47 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N LYS B 47 " --> pdb=" O ILE B 288 " (cutoff:3.500A) removed outlier: 10.194A pdb=" N GLN B 290 " --> pdb=" O LYS B 45 " (cutoff:3.500A) removed outlier: 9.994A pdb=" N LYS B 45 " --> pdb=" O GLN B 290 " (cutoff:3.500A) removed outlier: 8.869A pdb=" N TYR B 292 " --> pdb=" O THR B 43 " (cutoff:3.500A) removed outlier: 8.921A pdb=" N THR B 43 " --> pdb=" O TYR B 292 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N GLN B 294 " --> pdb=" O GLY B 41 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N GLY B 41 " --> pdb=" O GLN B 294 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N LEU B 296 " --> pdb=" O VAL B 39 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N VAL B 39 " --> pdb=" O LEU B 296 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 38 through 60 current: chain 'B' and resid 322 through 326 Processing sheet with id=AB7, first strand: chain 'B' and resid 301 through 303 removed outlier: 5.938A pdb=" N ARG B 365 " --> pdb=" O VAL B 449 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 410 through 412 Processing sheet with id=AB9, first strand: chain 'B' and resid 392 through 394 Processing sheet with id=AC1, first strand: chain 'C' and resid 4 through 7 Processing sheet with id=AC2, first strand: chain 'C' and resid 10 through 11 removed outlier: 6.386A pdb=" N LEU C 33 " --> pdb=" O TYR C 49 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N TYR C 49 " --> pdb=" O LEU C 33 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N TRP C 35 " --> pdb=" O LEU C 47 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 10 through 11 Processing sheet with id=AC4, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AC5, first strand: chain 'D' and resid 57 through 59 removed outlier: 6.900A pdb=" N TRP D 36 " --> pdb=" O LEU D 48 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N VAL D 50 " --> pdb=" O VAL D 34 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N VAL D 34 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 12.118A pdb=" N TYR D 93 " --> pdb=" O TRP D 109 " (cutoff:3.500A) removed outlier: 10.665A pdb=" N TRP D 109 " --> pdb=" O TYR D 93 " (cutoff:3.500A) removed outlier: 11.414A pdb=" N CYS D 95 " --> pdb=" O ALA D 107 " (cutoff:3.500A) removed outlier: 9.062A pdb=" N ALA D 107 " --> pdb=" O CYS D 95 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ARG D 97 " --> pdb=" O GLY D 105 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N GLY D 105 " --> pdb=" O ARG D 97 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 57 through 59 removed outlier: 6.900A pdb=" N TRP D 36 " --> pdb=" O LEU D 48 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N VAL D 50 " --> pdb=" O VAL D 34 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N VAL D 34 " --> pdb=" O VAL D 50 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 158 through 162 removed outlier: 10.218A pdb=" N THR E 168 " --> pdb=" O THR E 54 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ASP E 56 " --> pdb=" O THR E 168 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N TYR E 170 " --> pdb=" O ASP E 56 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N VAL E 39 " --> pdb=" O LEU E 296 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N LEU E 296 " --> pdb=" O VAL E 39 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N GLY E 41 " --> pdb=" O GLN E 294 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N GLN E 294 " --> pdb=" O GLY E 41 " (cutoff:3.500A) removed outlier: 8.921A pdb=" N THR E 43 " --> pdb=" O TYR E 292 " (cutoff:3.500A) removed outlier: 8.869A pdb=" N TYR E 292 " --> pdb=" O THR E 43 " (cutoff:3.500A) removed outlier: 9.995A pdb=" N LYS E 45 " --> pdb=" O GLN E 290 " (cutoff:3.500A) removed outlier: 10.194A pdb=" N GLN E 290 " --> pdb=" O LYS E 45 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N LYS E 47 " --> pdb=" O ILE E 288 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N ILE E 288 " --> pdb=" O LYS E 47 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N LYS E 49 " --> pdb=" O THR E 286 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N THR E 286 " --> pdb=" O LYS E 49 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N ASN E 51 " --> pdb=" O ILE E 284 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ILE E 284 " --> pdb=" O ASN E 51 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 275 through 298 current: chain 'E' and resid 332 through 333 Processing sheet with id=AC8, first strand: chain 'E' and resid 226 through 227 removed outlier: 3.795A pdb=" N MET E 226 " --> pdb=" O GLY E 264 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR E 263 " --> pdb=" O TYR E 281 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ILE E 277 " --> pdb=" O ILE E 267 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N VAL E 269 " --> pdb=" O TYR E 275 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N TYR E 275 " --> pdb=" O VAL E 269 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ILE E 284 " --> pdb=" O ASN E 51 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N ASN E 51 " --> pdb=" O ILE E 284 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N THR E 286 " --> pdb=" O LYS E 49 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N LYS E 49 " --> pdb=" O THR E 286 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N ILE E 288 " --> pdb=" O LYS E 47 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N LYS E 47 " --> pdb=" O ILE E 288 " (cutoff:3.500A) removed outlier: 10.194A pdb=" N GLN E 290 " --> pdb=" O LYS E 45 " (cutoff:3.500A) removed outlier: 9.995A pdb=" N LYS E 45 " --> pdb=" O GLN E 290 " (cutoff:3.500A) removed outlier: 8.869A pdb=" N TYR E 292 " --> pdb=" O THR E 43 " (cutoff:3.500A) removed outlier: 8.921A pdb=" N THR E 43 " --> pdb=" O TYR E 292 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N GLN E 294 " --> pdb=" O GLY E 41 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N GLY E 41 " --> pdb=" O GLN E 294 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N LEU E 296 " --> pdb=" O VAL E 39 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N VAL E 39 " --> pdb=" O LEU E 296 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 38 through 60 current: chain 'E' and resid 322 through 326 Processing sheet with id=AC9, first strand: chain 'E' and resid 301 through 303 removed outlier: 5.938A pdb=" N ARG E 365 " --> pdb=" O VAL E 449 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 4 through 7 Processing sheet with id=AD2, first strand: chain 'F' and resid 10 through 11 removed outlier: 6.385A pdb=" N LEU F 33 " --> pdb=" O TYR F 49 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N TYR F 49 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 10 through 11 Processing sheet with id=AD4, first strand: chain 'G' and resid 3 through 7 Processing sheet with id=AD5, first strand: chain 'G' and resid 57 through 59 removed outlier: 6.899A pdb=" N TRP G 36 " --> pdb=" O LEU G 48 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N VAL G 50 " --> pdb=" O VAL G 34 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N VAL G 34 " --> pdb=" O VAL G 50 " (cutoff:3.500A) removed outlier: 12.117A pdb=" N TYR G 93 " --> pdb=" O TRP G 109 " (cutoff:3.500A) removed outlier: 10.665A pdb=" N TRP G 109 " --> pdb=" O TYR G 93 " (cutoff:3.500A) removed outlier: 11.414A pdb=" N CYS G 95 " --> pdb=" O ALA G 107 " (cutoff:3.500A) removed outlier: 9.062A pdb=" N ALA G 107 " --> pdb=" O CYS G 95 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ARG G 97 " --> pdb=" O GLY G 105 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N GLY G 105 " --> pdb=" O ARG G 97 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 57 through 59 removed outlier: 6.899A pdb=" N TRP G 36 " --> pdb=" O LEU G 48 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N VAL G 50 " --> pdb=" O VAL G 34 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N VAL G 34 " --> pdb=" O VAL G 50 " (cutoff:3.500A) 763 hydrogen bonds defined for protein. 2001 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: 3.05 Time building geometry restraints manager: 2.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 3758 1.33 - 1.46: 4468 1.46 - 1.59: 7656 1.59 - 1.72: 18 1.72 - 1.85: 114 Bond restraints: 16014 Sorted by residual: bond pdb=" CB ILE B 27 " pdb=" CG1 ILE B 27 " ideal model delta sigma weight residual 1.530 1.609 -0.079 2.00e-02 2.50e+03 1.56e+01 bond pdb=" CB ILE A 27 " pdb=" CG1 ILE A 27 " ideal model delta sigma weight residual 1.530 1.609 -0.079 2.00e-02 2.50e+03 1.55e+01 bond pdb=" CB ILE E 27 " pdb=" CG1 ILE E 27 " ideal model delta sigma weight residual 1.530 1.608 -0.078 2.00e-02 2.50e+03 1.53e+01 bond pdb=" CA ASP A 188 " pdb=" C ASP A 188 " ideal model delta sigma weight residual 1.526 1.575 -0.049 1.28e-02 6.10e+03 1.48e+01 bond pdb=" CB LEU B 481 " pdb=" CG LEU B 481 " ideal model delta sigma weight residual 1.530 1.607 -0.077 2.00e-02 2.50e+03 1.48e+01 ... (remaining 16009 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 19426 2.05 - 4.10: 1992 4.10 - 6.15: 294 6.15 - 8.20: 62 8.20 - 10.25: 6 Bond angle restraints: 21780 Sorted by residual: angle pdb=" C GLN D 39 " pdb=" N PRO D 40 " pdb=" CA PRO D 40 " ideal model delta sigma weight residual 119.66 125.84 -6.18 7.30e-01 1.88e+00 7.16e+01 angle pdb=" C GLN H 39 " pdb=" N PRO H 40 " pdb=" CA PRO H 40 " ideal model delta sigma weight residual 119.66 125.83 -6.17 7.30e-01 1.88e+00 7.15e+01 angle pdb=" C GLN G 39 " pdb=" N PRO G 40 " pdb=" CA PRO G 40 " ideal model delta sigma weight residual 119.66 125.80 -6.14 7.30e-01 1.88e+00 7.08e+01 angle pdb=" N LYS A 189 " pdb=" CA LYS A 189 " pdb=" C LYS A 189 " ideal model delta sigma weight residual 113.55 103.30 10.25 1.26e+00 6.30e-01 6.62e+01 angle pdb=" N LYS B 189 " pdb=" CA LYS B 189 " pdb=" C LYS B 189 " ideal model delta sigma weight residual 113.55 103.31 10.24 1.26e+00 6.30e-01 6.61e+01 ... (remaining 21775 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.48: 9771 21.48 - 42.95: 198 42.95 - 64.43: 63 64.43 - 85.90: 54 85.90 - 107.38: 24 Dihedral angle restraints: 10110 sinusoidal: 4293 harmonic: 5817 Sorted by residual: dihedral pdb=" O4 BMA U 3 " pdb=" C4 BMA U 3 " pdb=" C5 BMA U 3 " pdb=" O5 BMA U 3 " ideal model delta sinusoidal sigma weight residual -71.29 -178.67 107.38 1 3.00e+01 1.11e-03 1.39e+01 dihedral pdb=" O4 BMA M 3 " pdb=" C4 BMA M 3 " pdb=" C5 BMA M 3 " pdb=" O5 BMA M 3 " ideal model delta sinusoidal sigma weight residual -71.29 -178.67 107.38 1 3.00e+01 1.11e-03 1.39e+01 dihedral pdb=" O4 BMA Q 3 " pdb=" C4 BMA Q 3 " pdb=" C5 BMA Q 3 " pdb=" O5 BMA Q 3 " ideal model delta sinusoidal sigma weight residual -71.29 -178.64 107.35 1 3.00e+01 1.11e-03 1.38e+01 ... (remaining 10107 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 1716 0.076 - 0.152: 697 0.152 - 0.229: 206 0.229 - 0.305: 48 0.305 - 0.381: 18 Chirality restraints: 2685 Sorted by residual: chirality pdb=" C1 BMA O 3 " pdb=" O4 NAG O 2 " pdb=" C2 BMA O 3 " pdb=" O5 BMA O 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.49 0.09 2.00e-02 2.50e+03 1.89e+01 chirality pdb=" C1 BMA S 3 " pdb=" O4 NAG S 2 " pdb=" C2 BMA S 3 " pdb=" O5 BMA S 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.49 0.09 2.00e-02 2.50e+03 1.87e+01 chirality pdb=" C1 BMA J 3 " pdb=" O4 NAG J 2 " pdb=" C2 BMA J 3 " pdb=" O5 BMA J 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.49 0.09 2.00e-02 2.50e+03 1.85e+01 ... (remaining 2682 not shown) Planarity restraints: 2715 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN E 67 " -0.051 2.00e-02 2.50e+03 5.10e-02 3.26e+01 pdb=" CG ASN E 67 " 0.028 2.00e-02 2.50e+03 pdb=" OD1 ASN E 67 " 0.009 2.00e-02 2.50e+03 pdb=" ND2 ASN E 67 " 0.076 2.00e-02 2.50e+03 pdb=" C1 NAG U 1 " -0.062 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 67 " 0.051 2.00e-02 2.50e+03 5.10e-02 3.25e+01 pdb=" CG ASN A 67 " -0.028 2.00e-02 2.50e+03 pdb=" OD1 ASN A 67 " -0.009 2.00e-02 2.50e+03 pdb=" ND2 ASN A 67 " -0.076 2.00e-02 2.50e+03 pdb=" C1 NAG M 1 " 0.062 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 67 " 0.051 2.00e-02 2.50e+03 5.09e-02 3.24e+01 pdb=" CG ASN B 67 " -0.028 2.00e-02 2.50e+03 pdb=" OD1 ASN B 67 " -0.009 2.00e-02 2.50e+03 pdb=" ND2 ASN B 67 " -0.075 2.00e-02 2.50e+03 pdb=" C1 NAG Q 1 " 0.062 2.00e-02 2.50e+03 ... (remaining 2712 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.87: 5260 2.87 - 3.38: 14474 3.38 - 3.88: 27386 3.88 - 4.39: 31469 4.39 - 4.90: 52563 Nonbonded interactions: 131152 Sorted by model distance: nonbonded pdb=" O ASP B 188 " pdb=" OD1 ASP B 188 " model vdw 2.361 3.040 nonbonded pdb=" O ASP A 188 " pdb=" OD1 ASP A 188 " model vdw 2.361 3.040 nonbonded pdb=" O ASP E 188 " pdb=" OD1 ASP E 188 " model vdw 2.361 3.040 nonbonded pdb=" OH TYR L 32 " pdb=" O ILE B 187 " model vdw 2.438 3.040 nonbonded pdb=" OH TYR C 32 " pdb=" O ILE E 187 " model vdw 2.438 3.040 ... (remaining 131147 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'L' } ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'K' selection = chain 'N' selection = chain 'P' selection = chain 'R' selection = chain 'T' } ncs_group { reference = chain 'J' selection = chain 'O' selection = chain 'S' } ncs_group { reference = chain 'M' selection = chain 'Q' selection = chain 'U' } 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 individual isotropic 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: 3.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 16.070 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 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 : 0.013 0.085 16074 Z= 0.702 Angle : 1.392 10.249 21939 Z= 0.916 Chirality : 0.094 0.381 2685 Planarity : 0.006 0.042 2703 Dihedral : 13.468 107.380 6327 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 1.70 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.57 % Favored : 97.28 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.18), residues: 1986 helix: 0.03 (0.21), residues: 456 sheet: 0.90 (0.21), residues: 561 loop : 0.43 (0.21), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 82 TYR 0.048 0.005 TYR F 32 PHE 0.023 0.004 PHE B 253 TRP 0.039 0.007 TRP D 47 HIS 0.005 0.001 HIS F 90 Details of bonding type rmsd covalent geometry : bond 0.01296 (16014) covalent geometry : angle 1.37184 (21780) SS BOND : bond 0.00684 ( 21) SS BOND : angle 2.72722 ( 42) hydrogen bonds : bond 0.15980 ( 691) hydrogen bonds : angle 8.38176 ( 2001) link_ALPHA1-3 : bond 0.05089 ( 3) link_ALPHA1-3 : angle 2.51005 ( 9) link_ALPHA1-6 : bond 0.04443 ( 3) link_ALPHA1-6 : angle 1.73180 ( 9) link_BETA1-4 : bond 0.05668 ( 18) link_BETA1-4 : angle 3.92254 ( 54) link_BETA1-6 : bond 0.04660 ( 3) link_BETA1-6 : angle 1.66898 ( 9) link_NAG-ASN : bond 0.05467 ( 12) link_NAG-ASN : angle 2.80219 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3972 Ramachandran restraints generated. 1986 Oldfield, 0 Emsley, 1986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3972 Ramachandran restraints generated. 1986 Oldfield, 0 Emsley, 1986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 380 time to evaluate : 0.600 Fit side-chains REVERT: A 205 LYS cc_start: 0.8454 (tptp) cc_final: 0.8177 (tptp) outliers start: 0 outliers final: 0 residues processed: 380 average time/residue: 0.5235 time to fit residues: 222.1049 Evaluate side-chains 195 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 195 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 0.7980 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.2980 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 ASN A 194 GLN A 224 ASN L 90 HIS L 91 HIS H 1 GLN B 64 ASN B 224 ASN C 90 HIS C 91 HIS D 1 GLN E 64 ASN E 224 ASN F 50 ASN ** F 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 1 GLN G 111 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.145064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.122164 restraints weight = 19932.620| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 2.12 r_work: 0.3381 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3255 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 16074 Z= 0.169 Angle : 0.678 9.283 21939 Z= 0.344 Chirality : 0.051 0.444 2685 Planarity : 0.004 0.034 2703 Dihedral : 9.537 67.658 2928 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.15 % Allowed : 1.46 % Favored : 98.39 % Rotamer: Outliers : 3.44 % Allowed : 10.49 % Favored : 86.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.19), residues: 1986 helix: 1.35 (0.24), residues: 471 sheet: 0.89 (0.20), residues: 594 loop : 0.07 (0.21), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 399 TYR 0.041 0.002 TYR F 32 PHE 0.016 0.002 PHE E 253 TRP 0.012 0.002 TRP D 47 HIS 0.006 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00392 (16014) covalent geometry : angle 0.64316 (21780) SS BOND : bond 0.00174 ( 21) SS BOND : angle 0.79849 ( 42) hydrogen bonds : bond 0.04866 ( 691) hydrogen bonds : angle 5.87552 ( 2001) link_ALPHA1-3 : bond 0.01426 ( 3) link_ALPHA1-3 : angle 2.78364 ( 9) link_ALPHA1-6 : bond 0.00707 ( 3) link_ALPHA1-6 : angle 1.52443 ( 9) link_BETA1-4 : bond 0.00573 ( 18) link_BETA1-4 : angle 3.10420 ( 54) link_BETA1-6 : bond 0.00486 ( 3) link_BETA1-6 : angle 1.43745 ( 9) link_NAG-ASN : bond 0.00399 ( 12) link_NAG-ASN : angle 3.41920 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3972 Ramachandran restraints generated. 1986 Oldfield, 0 Emsley, 1986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3972 Ramachandran restraints generated. 1986 Oldfield, 0 Emsley, 1986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 235 time to evaluate : 0.481 Fit side-chains revert: symmetry clash REVERT: A 136 GLU cc_start: 0.7508 (mt-10) cc_final: 0.7212 (mm-30) REVERT: A 167 LYS cc_start: 0.8185 (mtmt) cc_final: 0.7610 (mttt) REVERT: A 240 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.7340 (tm-30) REVERT: A 395 GLN cc_start: 0.7513 (tp40) cc_final: 0.6971 (tm-30) REVERT: L 52 LYS cc_start: 0.8062 (ptpp) cc_final: 0.7455 (mtpp) REVERT: H 11 LEU cc_start: 0.7012 (tp) cc_final: 0.6700 (tm) REVERT: B 138 MET cc_start: 0.6378 (mmm) cc_final: 0.5870 (mmm) REVERT: B 240 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.7417 (tm-30) REVERT: D 6 GLU cc_start: 0.7586 (mp0) cc_final: 0.7367 (mp0) REVERT: E 138 MET cc_start: 0.6265 (mmm) cc_final: 0.5843 (mmm) REVERT: E 156 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.8199 (tp30) REVERT: E 240 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.7605 (tm-30) REVERT: E 244 ARG cc_start: 0.7646 (ttp-110) cc_final: 0.7028 (ttp-110) REVERT: E 395 GLN cc_start: 0.7461 (tp40) cc_final: 0.7107 (tm-30) REVERT: E 406 GLU cc_start: 0.7282 (pp20) cc_final: 0.6798 (tm-30) REVERT: F 11 LEU cc_start: 0.7261 (OUTLIER) cc_final: 0.6675 (tp) REVERT: F 22 THR cc_start: 0.7978 (m) cc_final: 0.7609 (p) REVERT: F 52 LYS cc_start: 0.8111 (ptpp) cc_final: 0.7817 (ptmt) outliers start: 57 outliers final: 19 residues processed: 263 average time/residue: 0.5684 time to fit residues: 165.5006 Evaluate side-chains 221 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 197 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 ASP Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 53 SER Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain B residue 240 GLU Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 465 GLN Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain D residue 64 MET Chi-restraints excluded: chain D residue 70 ASN Chi-restraints excluded: chain E residue 156 GLU Chi-restraints excluded: chain E residue 240 GLU Chi-restraints excluded: chain E residue 415 THR Chi-restraints excluded: chain E residue 416 THR Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 53 SER Chi-restraints excluded: chain G residue 64 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 73 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 5 optimal weight: 0.5980 chunk 152 optimal weight: 0.7980 chunk 71 optimal weight: 0.9990 chunk 96 optimal weight: 0.9980 chunk 182 optimal weight: 0.6980 chunk 136 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 9 optimal weight: 0.5980 chunk 132 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN H 1 GLN B 393 GLN D 1 GLN E 224 ASN E 380 ASN E 469 GLN ** F 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 91 HIS G 1 GLN G 111 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.140210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.117559 restraints weight = 20185.833| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 2.09 r_work: 0.3335 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3207 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.2849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 16074 Z= 0.159 Angle : 0.615 7.961 21939 Z= 0.308 Chirality : 0.049 0.337 2685 Planarity : 0.005 0.042 2703 Dihedral : 7.344 49.551 2928 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.72 % Favored : 97.23 % Rotamer: Outliers : 4.16 % Allowed : 11.45 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.19), residues: 1986 helix: 1.60 (0.24), residues: 486 sheet: 0.76 (0.20), residues: 597 loop : -0.22 (0.20), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 399 TYR 0.016 0.002 TYR F 32 PHE 0.015 0.002 PHE A 376 TRP 0.015 0.001 TRP H 47 HIS 0.008 0.001 HIS C 91 Details of bonding type rmsd covalent geometry : bond 0.00371 (16014) covalent geometry : angle 0.58270 (21780) SS BOND : bond 0.00423 ( 21) SS BOND : angle 0.97126 ( 42) hydrogen bonds : bond 0.04038 ( 691) hydrogen bonds : angle 5.22674 ( 2001) link_ALPHA1-3 : bond 0.01470 ( 3) link_ALPHA1-3 : angle 1.43045 ( 9) link_ALPHA1-6 : bond 0.00630 ( 3) link_ALPHA1-6 : angle 1.47772 ( 9) link_BETA1-4 : bond 0.00737 ( 18) link_BETA1-4 : angle 2.78437 ( 54) link_BETA1-6 : bond 0.00556 ( 3) link_BETA1-6 : angle 1.03696 ( 9) link_NAG-ASN : bond 0.00418 ( 12) link_NAG-ASN : angle 3.32327 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3972 Ramachandran restraints generated. 1986 Oldfield, 0 Emsley, 1986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3972 Ramachandran restraints generated. 1986 Oldfield, 0 Emsley, 1986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 227 time to evaluate : 0.448 Fit side-chains REVERT: A 82 ARG cc_start: 0.8679 (tpt90) cc_final: 0.8329 (tmt-80) REVERT: A 115 MET cc_start: 0.8652 (OUTLIER) cc_final: 0.8266 (mtp) REVERT: A 167 LYS cc_start: 0.7885 (mtmt) cc_final: 0.7568 (mttt) REVERT: A 240 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.7447 (tm-30) REVERT: A 244 ARG cc_start: 0.7824 (ttp-110) cc_final: 0.7538 (ttp-110) REVERT: A 395 GLN cc_start: 0.7268 (tp40) cc_final: 0.7001 (tm-30) REVERT: L 52 LYS cc_start: 0.8076 (ptpp) cc_final: 0.7490 (mtpp) REVERT: H 11 LEU cc_start: 0.7044 (tp) cc_final: 0.6772 (tm) REVERT: H 46 GLU cc_start: 0.8317 (tt0) cc_final: 0.8116 (pt0) REVERT: H 70 ASN cc_start: 0.7968 (t0) cc_final: 0.7529 (m-40) REVERT: B 138 MET cc_start: 0.6212 (mmm) cc_final: 0.5689 (mmm) REVERT: B 307 GLU cc_start: 0.8342 (mt-10) cc_final: 0.8082 (mt-10) REVERT: B 413 ASP cc_start: 0.8319 (p0) cc_final: 0.8041 (p0) REVERT: E 138 MET cc_start: 0.6339 (mmm) cc_final: 0.5882 (mmm) REVERT: E 156 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.8008 (tp30) REVERT: E 240 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.7582 (tm-30) REVERT: E 395 GLN cc_start: 0.7465 (tp40) cc_final: 0.7158 (tm-30) REVERT: E 399 ARG cc_start: 0.6715 (ptp-110) cc_final: 0.6102 (ptp-170) REVERT: F 52 LYS cc_start: 0.8147 (ptpp) cc_final: 0.7871 (ptmt) outliers start: 69 outliers final: 36 residues processed: 262 average time/residue: 0.5222 time to fit residues: 152.7370 Evaluate side-chains 237 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 197 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 392 CYS Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 53 SER Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 85 SER Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 351 ASN Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 90 HIS Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain E residue 142 ASP Chi-restraints excluded: chain E residue 156 GLU Chi-restraints excluded: chain E residue 240 GLU Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain E residue 415 THR Chi-restraints excluded: chain E residue 416 THR Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 53 SER Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 68 SER Chi-restraints excluded: chain G residue 116 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 12 optimal weight: 1.9990 chunk 183 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 179 optimal weight: 0.0570 chunk 42 optimal weight: 0.9980 chunk 135 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 60 optimal weight: 0.0170 chunk 57 optimal weight: 0.6980 chunk 97 optimal weight: 2.9990 overall best weight: 0.3936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN A 393 GLN H 1 GLN B 393 GLN B 469 GLN D 1 GLN E 224 ASN E 380 ASN E 469 GLN ** F 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 1 GLN G 111 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.142882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.119575 restraints weight = 19962.678| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 2.14 r_work: 0.3345 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.3111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16074 Z= 0.116 Angle : 0.569 8.055 21939 Z= 0.281 Chirality : 0.047 0.348 2685 Planarity : 0.004 0.041 2703 Dihedral : 6.143 39.651 2928 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.74 % Allowed : 13.62 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.19), residues: 1986 helix: 2.12 (0.25), residues: 468 sheet: 0.73 (0.21), residues: 579 loop : -0.21 (0.20), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 24 TYR 0.014 0.001 TYR A 239 PHE 0.012 0.001 PHE B 253 TRP 0.013 0.001 TRP G 47 HIS 0.003 0.001 HIS F 91 Details of bonding type rmsd covalent geometry : bond 0.00262 (16014) covalent geometry : angle 0.53668 (21780) SS BOND : bond 0.00351 ( 21) SS BOND : angle 0.86464 ( 42) hydrogen bonds : bond 0.03385 ( 691) hydrogen bonds : angle 4.92349 ( 2001) link_ALPHA1-3 : bond 0.01352 ( 3) link_ALPHA1-3 : angle 1.76096 ( 9) link_ALPHA1-6 : bond 0.00533 ( 3) link_ALPHA1-6 : angle 1.50037 ( 9) link_BETA1-4 : bond 0.00562 ( 18) link_BETA1-4 : angle 2.57052 ( 54) link_BETA1-6 : bond 0.00473 ( 3) link_BETA1-6 : angle 1.13088 ( 9) link_NAG-ASN : bond 0.00368 ( 12) link_NAG-ASN : angle 3.26962 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3972 Ramachandran restraints generated. 1986 Oldfield, 0 Emsley, 1986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3972 Ramachandran restraints generated. 1986 Oldfield, 0 Emsley, 1986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 227 time to evaluate : 0.561 Fit side-chains revert: symmetry clash REVERT: A 82 ARG cc_start: 0.8649 (tpt90) cc_final: 0.8390 (tmt-80) REVERT: A 115 MET cc_start: 0.8599 (mtm) cc_final: 0.8153 (mtp) REVERT: A 167 LYS cc_start: 0.7820 (mtmt) cc_final: 0.7520 (mttt) REVERT: A 240 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.7320 (tm-30) REVERT: A 244 ARG cc_start: 0.7831 (ttp-110) cc_final: 0.7609 (ttp-110) REVERT: A 395 GLN cc_start: 0.7233 (tp40) cc_final: 0.6983 (tm-30) REVERT: L 52 LYS cc_start: 0.8042 (ptpp) cc_final: 0.7672 (ptmt) REVERT: H 11 LEU cc_start: 0.6970 (tp) cc_final: 0.6710 (tm) REVERT: H 38 ARG cc_start: 0.8861 (OUTLIER) cc_final: 0.8477 (ptt180) REVERT: B 138 MET cc_start: 0.6212 (mmm) cc_final: 0.5633 (mmm) REVERT: B 167 LYS cc_start: 0.7868 (mtmm) cc_final: 0.7485 (mttt) REVERT: B 240 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.7539 (tm-30) REVERT: B 399 ARG cc_start: 0.6585 (ptp-110) cc_final: 0.6188 (ptp-170) REVERT: B 406 GLU cc_start: 0.7793 (pm20) cc_final: 0.7559 (pm20) REVERT: B 413 ASP cc_start: 0.8245 (p0) cc_final: 0.7952 (p0) REVERT: C 52 LYS cc_start: 0.8069 (ptpp) cc_final: 0.7756 (ptmt) REVERT: D 11 LEU cc_start: 0.7605 (tt) cc_final: 0.7294 (tm) REVERT: D 66 ARG cc_start: 0.8093 (mtp180) cc_final: 0.7883 (mtp180) REVERT: E 115 MET cc_start: 0.8833 (mtm) cc_final: 0.8472 (mtm) REVERT: E 138 MET cc_start: 0.6215 (mmm) cc_final: 0.5732 (mmm) REVERT: E 142 ASP cc_start: 0.7907 (OUTLIER) cc_final: 0.7288 (t0) REVERT: E 156 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.8030 (tp30) REVERT: E 240 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7541 (tm-30) REVERT: E 395 GLN cc_start: 0.7532 (tp40) cc_final: 0.7201 (tm-30) REVERT: E 399 ARG cc_start: 0.6879 (ptp-110) cc_final: 0.6294 (ptp-170) REVERT: F 52 LYS cc_start: 0.8019 (ptpp) cc_final: 0.7720 (ptmt) REVERT: G 38 ARG cc_start: 0.9075 (OUTLIER) cc_final: 0.8424 (ptt180) outliers start: 62 outliers final: 31 residues processed: 267 average time/residue: 0.5263 time to fit residues: 156.8843 Evaluate side-chains 234 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 196 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 392 CYS Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 53 SER Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain B residue 240 GLU Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 351 ASN Chi-restraints excluded: chain B residue 392 CYS Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 90 HIS Chi-restraints excluded: chain D residue 64 MET Chi-restraints excluded: chain E residue 142 ASP Chi-restraints excluded: chain E residue 156 GLU Chi-restraints excluded: chain E residue 240 GLU Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain E residue 392 CYS Chi-restraints excluded: chain E residue 415 THR Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 53 SER Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 38 ARG Chi-restraints excluded: chain G residue 53 THR Chi-restraints excluded: chain G residue 64 MET Chi-restraints excluded: chain G residue 116 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 31 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 190 optimal weight: 0.0980 chunk 37 optimal weight: 0.9990 chunk 186 optimal weight: 3.9990 chunk 161 optimal weight: 0.9980 chunk 40 optimal weight: 0.8980 chunk 156 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 120 optimal weight: 0.0040 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN A 469 GLN H 1 GLN B 194 GLN B 469 GLN E 224 ASN E 380 ASN E 393 GLN ** F 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 1 GLN G 111 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.141014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.118042 restraints weight = 20593.340| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 2.09 r_work: 0.3319 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.3384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16074 Z= 0.138 Angle : 0.578 8.437 21939 Z= 0.285 Chirality : 0.047 0.341 2685 Planarity : 0.004 0.044 2703 Dihedral : 5.612 34.266 2928 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.32 % Allowed : 14.83 % Favored : 81.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.19), residues: 1986 helix: 1.92 (0.25), residues: 486 sheet: 0.59 (0.21), residues: 567 loop : -0.27 (0.20), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 24 TYR 0.021 0.001 TYR L 32 PHE 0.011 0.001 PHE B 330 TRP 0.015 0.001 TRP G 47 HIS 0.006 0.001 HIS L 91 Details of bonding type rmsd covalent geometry : bond 0.00322 (16014) covalent geometry : angle 0.54622 (21780) SS BOND : bond 0.00341 ( 21) SS BOND : angle 1.06556 ( 42) hydrogen bonds : bond 0.03383 ( 691) hydrogen bonds : angle 4.80157 ( 2001) link_ALPHA1-3 : bond 0.01254 ( 3) link_ALPHA1-3 : angle 1.60091 ( 9) link_ALPHA1-6 : bond 0.00488 ( 3) link_ALPHA1-6 : angle 1.47080 ( 9) link_BETA1-4 : bond 0.00584 ( 18) link_BETA1-4 : angle 2.43763 ( 54) link_BETA1-6 : bond 0.00430 ( 3) link_BETA1-6 : angle 1.12934 ( 9) link_NAG-ASN : bond 0.00323 ( 12) link_NAG-ASN : angle 3.32894 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3972 Ramachandran restraints generated. 1986 Oldfield, 0 Emsley, 1986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3972 Ramachandran restraints generated. 1986 Oldfield, 0 Emsley, 1986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 203 time to evaluate : 0.692 Fit side-chains revert: symmetry clash REVERT: A 115 MET cc_start: 0.8600 (mtm) cc_final: 0.8169 (mtp) REVERT: A 142 ASP cc_start: 0.7954 (OUTLIER) cc_final: 0.7650 (m-30) REVERT: A 167 LYS cc_start: 0.7887 (mtmt) cc_final: 0.7543 (mttt) REVERT: A 240 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7324 (tm-30) REVERT: A 244 ARG cc_start: 0.7902 (ttp-110) cc_final: 0.7683 (ttp-110) REVERT: A 399 ARG cc_start: 0.6723 (ptp-110) cc_final: 0.6468 (ptp-110) REVERT: A 406 GLU cc_start: 0.7870 (pm20) cc_final: 0.7464 (pm20) REVERT: L 52 LYS cc_start: 0.8079 (ptpp) cc_final: 0.7871 (ptmt) REVERT: H 11 LEU cc_start: 0.6969 (tp) cc_final: 0.6720 (tm) REVERT: H 38 ARG cc_start: 0.8890 (OUTLIER) cc_final: 0.8599 (ptt180) REVERT: B 138 MET cc_start: 0.6311 (mmm) cc_final: 0.5804 (mmm) REVERT: B 167 LYS cc_start: 0.7935 (mtmm) cc_final: 0.7584 (mttt) REVERT: B 399 ARG cc_start: 0.6614 (ptp-110) cc_final: 0.6192 (ptp-170) REVERT: B 413 ASP cc_start: 0.8257 (p0) cc_final: 0.7910 (p0) REVERT: C 52 LYS cc_start: 0.8144 (ptpp) cc_final: 0.7859 (ptmt) REVERT: D 66 ARG cc_start: 0.8104 (mtp180) cc_final: 0.7868 (mtp180) REVERT: D 72 ASP cc_start: 0.8670 (OUTLIER) cc_final: 0.8292 (t70) REVERT: E 115 MET cc_start: 0.8827 (mtm) cc_final: 0.8506 (mtm) REVERT: E 138 MET cc_start: 0.6314 (mmm) cc_final: 0.5891 (mmm) REVERT: E 142 ASP cc_start: 0.7978 (OUTLIER) cc_final: 0.7378 (t0) REVERT: E 156 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.7987 (tp30) REVERT: E 240 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7541 (tm-30) REVERT: E 399 ARG cc_start: 0.6851 (ptp-110) cc_final: 0.6250 (ptp-170) REVERT: E 413 ASP cc_start: 0.8475 (p0) cc_final: 0.8177 (p0) REVERT: F 52 LYS cc_start: 0.8035 (ptpp) cc_final: 0.7763 (ptmm) REVERT: G 46 GLU cc_start: 0.8454 (tt0) cc_final: 0.8181 (pt0) outliers start: 55 outliers final: 32 residues processed: 242 average time/residue: 0.5089 time to fit residues: 138.1718 Evaluate side-chains 227 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 188 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 142 ASP Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 392 CYS Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 53 SER Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 351 ASN Chi-restraints excluded: chain B residue 392 CYS Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 90 HIS Chi-restraints excluded: chain D residue 64 MET Chi-restraints excluded: chain D residue 70 ASN Chi-restraints excluded: chain D residue 72 ASP Chi-restraints excluded: chain E residue 142 ASP Chi-restraints excluded: chain E residue 156 GLU Chi-restraints excluded: chain E residue 240 GLU Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain E residue 392 CYS Chi-restraints excluded: chain E residue 415 THR Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 53 SER Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 53 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 183 optimal weight: 0.9980 chunk 155 optimal weight: 0.9980 chunk 174 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 191 optimal weight: 1.9990 chunk 45 optimal weight: 9.9990 chunk 172 optimal weight: 1.9990 chunk 167 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 100 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN A 393 GLN A 469 GLN H 1 GLN B 393 GLN B 459 GLN B 469 GLN E 224 ASN G 1 GLN G 111 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.137792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.114643 restraints weight = 20037.893| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 2.09 r_work: 0.3284 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.3592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 16074 Z= 0.176 Angle : 0.605 8.862 21939 Z= 0.299 Chirality : 0.048 0.351 2685 Planarity : 0.004 0.042 2703 Dihedral : 5.518 30.040 2928 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 3.74 % Allowed : 14.47 % Favored : 81.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.19), residues: 1986 helix: 1.82 (0.24), residues: 486 sheet: 0.48 (0.21), residues: 564 loop : -0.37 (0.20), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 24 TYR 0.017 0.002 TYR A 239 PHE 0.012 0.001 PHE B 330 TRP 0.017 0.002 TRP D 47 HIS 0.007 0.001 HIS C 91 Details of bonding type rmsd covalent geometry : bond 0.00420 (16014) covalent geometry : angle 0.57366 (21780) SS BOND : bond 0.00430 ( 21) SS BOND : angle 1.04603 ( 42) hydrogen bonds : bond 0.03569 ( 691) hydrogen bonds : angle 4.86253 ( 2001) link_ALPHA1-3 : bond 0.01149 ( 3) link_ALPHA1-3 : angle 1.74574 ( 9) link_ALPHA1-6 : bond 0.00455 ( 3) link_ALPHA1-6 : angle 1.44423 ( 9) link_BETA1-4 : bond 0.00561 ( 18) link_BETA1-4 : angle 2.48832 ( 54) link_BETA1-6 : bond 0.00390 ( 3) link_BETA1-6 : angle 1.11977 ( 9) link_NAG-ASN : bond 0.00299 ( 12) link_NAG-ASN : angle 3.40249 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3972 Ramachandran restraints generated. 1986 Oldfield, 0 Emsley, 1986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3972 Ramachandran restraints generated. 1986 Oldfield, 0 Emsley, 1986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 193 time to evaluate : 0.572 Fit side-chains revert: symmetry clash REVERT: A 115 MET cc_start: 0.8586 (OUTLIER) cc_final: 0.8154 (mtp) REVERT: A 167 LYS cc_start: 0.7891 (mtmt) cc_final: 0.7513 (mttt) REVERT: A 240 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.7346 (tm-30) REVERT: A 307 GLU cc_start: 0.8450 (mt-10) cc_final: 0.8222 (mt-10) REVERT: A 399 ARG cc_start: 0.6879 (ptp-110) cc_final: 0.6648 (ptp-110) REVERT: A 406 GLU cc_start: 0.7778 (pm20) cc_final: 0.7463 (pm20) REVERT: L 21 ILE cc_start: 0.7710 (OUTLIER) cc_final: 0.7455 (mm) REVERT: L 52 LYS cc_start: 0.8063 (ptpp) cc_final: 0.7778 (ptmt) REVERT: H 11 LEU cc_start: 0.7027 (tp) cc_final: 0.6748 (tm) REVERT: H 46 GLU cc_start: 0.8451 (tt0) cc_final: 0.8239 (pt0) REVERT: B 138 MET cc_start: 0.6395 (mmm) cc_final: 0.5876 (mmm) REVERT: B 167 LYS cc_start: 0.7919 (mtmm) cc_final: 0.7555 (mttt) REVERT: B 399 ARG cc_start: 0.6658 (ptp-110) cc_final: 0.6194 (ptp-170) REVERT: B 413 ASP cc_start: 0.8392 (p0) cc_final: 0.8121 (p0) REVERT: D 66 ARG cc_start: 0.8133 (mtp180) cc_final: 0.7880 (mtp180) REVERT: D 72 ASP cc_start: 0.8667 (OUTLIER) cc_final: 0.8270 (t70) REVERT: E 115 MET cc_start: 0.8836 (mtm) cc_final: 0.8506 (mtm) REVERT: E 138 MET cc_start: 0.6315 (mmm) cc_final: 0.5970 (mmm) REVERT: E 142 ASP cc_start: 0.7984 (OUTLIER) cc_final: 0.7386 (t0) REVERT: E 240 GLU cc_start: 0.8257 (OUTLIER) cc_final: 0.7582 (tm-30) REVERT: E 399 ARG cc_start: 0.6830 (ptp-110) cc_final: 0.6244 (ptp-170) REVERT: F 52 LYS cc_start: 0.8133 (ptpp) cc_final: 0.7852 (ptmt) REVERT: G 43 LYS cc_start: 0.8135 (mmtt) cc_final: 0.7790 (mptt) REVERT: G 46 GLU cc_start: 0.8485 (tt0) cc_final: 0.8178 (pt0) outliers start: 62 outliers final: 38 residues processed: 235 average time/residue: 0.4544 time to fit residues: 120.8788 Evaluate side-chains 227 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 183 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 392 CYS Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 53 SER Chi-restraints excluded: chain L residue 85 SER Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 351 ASN Chi-restraints excluded: chain B residue 392 CYS Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 90 HIS Chi-restraints excluded: chain D residue 70 ASN Chi-restraints excluded: chain D residue 72 ASP Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain E residue 142 ASP Chi-restraints excluded: chain E residue 240 GLU Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain E residue 300 SER Chi-restraints excluded: chain E residue 392 CYS Chi-restraints excluded: chain E residue 415 THR Chi-restraints excluded: chain E residue 416 THR Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain G residue 53 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 145 optimal weight: 0.5980 chunk 178 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 chunk 158 optimal weight: 0.8980 chunk 110 optimal weight: 5.9990 chunk 35 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 177 optimal weight: 0.7980 chunk 26 optimal weight: 0.5980 chunk 194 optimal weight: 0.4980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN A 393 GLN H 1 GLN B 469 GLN E 224 ASN G 1 GLN G 111 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.138405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.115427 restraints weight = 19940.320| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 2.07 r_work: 0.3294 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.3697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16074 Z= 0.146 Angle : 0.576 7.877 21939 Z= 0.286 Chirality : 0.047 0.332 2685 Planarity : 0.004 0.044 2703 Dihedral : 5.368 27.511 2928 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.50 % Allowed : 15.13 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.19), residues: 1986 helix: 1.87 (0.24), residues: 486 sheet: 0.43 (0.21), residues: 567 loop : -0.42 (0.20), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 24 TYR 0.015 0.001 TYR A 239 PHE 0.016 0.001 PHE E 330 TRP 0.016 0.001 TRP G 47 HIS 0.006 0.001 HIS C 91 Details of bonding type rmsd covalent geometry : bond 0.00344 (16014) covalent geometry : angle 0.54588 (21780) SS BOND : bond 0.00345 ( 21) SS BOND : angle 0.86783 ( 42) hydrogen bonds : bond 0.03365 ( 691) hydrogen bonds : angle 4.80287 ( 2001) link_ALPHA1-3 : bond 0.01218 ( 3) link_ALPHA1-3 : angle 1.50947 ( 9) link_ALPHA1-6 : bond 0.00486 ( 3) link_ALPHA1-6 : angle 1.42837 ( 9) link_BETA1-4 : bond 0.00556 ( 18) link_BETA1-4 : angle 2.40076 ( 54) link_BETA1-6 : bond 0.00452 ( 3) link_BETA1-6 : angle 1.09136 ( 9) link_NAG-ASN : bond 0.00323 ( 12) link_NAG-ASN : angle 3.35051 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3972 Ramachandran restraints generated. 1986 Oldfield, 0 Emsley, 1986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3972 Ramachandran restraints generated. 1986 Oldfield, 0 Emsley, 1986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 191 time to evaluate : 0.545 Fit side-chains revert: symmetry clash REVERT: A 167 LYS cc_start: 0.7914 (mtmt) cc_final: 0.7528 (mttt) REVERT: A 240 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7327 (tm-30) REVERT: A 307 GLU cc_start: 0.8500 (mt-10) cc_final: 0.8295 (mt-10) REVERT: A 406 GLU cc_start: 0.7904 (pm20) cc_final: 0.7549 (pm20) REVERT: H 11 LEU cc_start: 0.6974 (tp) cc_final: 0.6710 (tm) REVERT: H 38 ARG cc_start: 0.8876 (OUTLIER) cc_final: 0.8576 (ptt180) REVERT: B 138 MET cc_start: 0.6335 (mmm) cc_final: 0.5878 (mmm) REVERT: B 167 LYS cc_start: 0.7913 (mtmm) cc_final: 0.7585 (mttt) REVERT: B 399 ARG cc_start: 0.6727 (ptp-110) cc_final: 0.6390 (ptp-170) REVERT: C 52 LYS cc_start: 0.8261 (ptmm) cc_final: 0.7812 (ptmt) REVERT: D 66 ARG cc_start: 0.8123 (mtp180) cc_final: 0.7902 (mtp180) REVERT: D 72 ASP cc_start: 0.8640 (OUTLIER) cc_final: 0.8258 (t70) REVERT: E 115 MET cc_start: 0.8819 (mtm) cc_final: 0.8547 (mtm) REVERT: E 142 ASP cc_start: 0.7964 (OUTLIER) cc_final: 0.7365 (t0) REVERT: E 219 GLN cc_start: 0.7832 (OUTLIER) cc_final: 0.7244 (pt0) REVERT: E 240 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7527 (tm-30) REVERT: E 399 ARG cc_start: 0.6797 (ptp-110) cc_final: 0.6262 (ptp-170) REVERT: F 52 LYS cc_start: 0.8140 (ptpp) cc_final: 0.7866 (ptmt) REVERT: G 46 GLU cc_start: 0.8473 (tt0) cc_final: 0.8163 (pt0) outliers start: 58 outliers final: 34 residues processed: 226 average time/residue: 0.4700 time to fit residues: 119.9835 Evaluate side-chains 226 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 186 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 392 CYS Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 53 SER Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 351 ASN Chi-restraints excluded: chain B residue 392 CYS Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 90 HIS Chi-restraints excluded: chain D residue 70 ASN Chi-restraints excluded: chain D residue 72 ASP Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain E residue 142 ASP Chi-restraints excluded: chain E residue 219 GLN Chi-restraints excluded: chain E residue 240 GLU Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain E residue 392 CYS Chi-restraints excluded: chain E residue 415 THR Chi-restraints excluded: chain E residue 416 THR Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 53 SER Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain G residue 53 THR Chi-restraints excluded: chain G residue 64 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 65 optimal weight: 2.9990 chunk 108 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 chunk 144 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 85 optimal weight: 0.9990 chunk 96 optimal weight: 0.6980 chunk 122 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN H 1 GLN D 1 GLN E 224 ASN G 1 GLN G 111 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.137320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.114313 restraints weight = 20165.197| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 2.08 r_work: 0.3278 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.3797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 16074 Z= 0.173 Angle : 0.603 8.570 21939 Z= 0.298 Chirality : 0.047 0.334 2685 Planarity : 0.004 0.043 2703 Dihedral : 5.463 28.568 2928 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.62 % Allowed : 15.67 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.19), residues: 1986 helix: 1.86 (0.24), residues: 486 sheet: 0.43 (0.21), residues: 576 loop : -0.52 (0.20), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 24 TYR 0.016 0.002 TYR B 239 PHE 0.016 0.001 PHE E 330 TRP 0.016 0.002 TRP D 47 HIS 0.007 0.001 HIS C 91 Details of bonding type rmsd covalent geometry : bond 0.00413 (16014) covalent geometry : angle 0.57363 (21780) SS BOND : bond 0.00335 ( 21) SS BOND : angle 0.94822 ( 42) hydrogen bonds : bond 0.03506 ( 691) hydrogen bonds : angle 4.85323 ( 2001) link_ALPHA1-3 : bond 0.01074 ( 3) link_ALPHA1-3 : angle 1.56214 ( 9) link_ALPHA1-6 : bond 0.00437 ( 3) link_ALPHA1-6 : angle 1.45709 ( 9) link_BETA1-4 : bond 0.00536 ( 18) link_BETA1-4 : angle 2.44467 ( 54) link_BETA1-6 : bond 0.00422 ( 3) link_BETA1-6 : angle 1.12161 ( 9) link_NAG-ASN : bond 0.00279 ( 12) link_NAG-ASN : angle 3.36021 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3972 Ramachandran restraints generated. 1986 Oldfield, 0 Emsley, 1986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3972 Ramachandran restraints generated. 1986 Oldfield, 0 Emsley, 1986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 190 time to evaluate : 0.401 Fit side-chains revert: symmetry clash REVERT: A 167 LYS cc_start: 0.7932 (mtmt) cc_final: 0.7528 (mttt) REVERT: A 240 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7341 (tm-30) REVERT: A 406 GLU cc_start: 0.7833 (pm20) cc_final: 0.7493 (pm20) REVERT: L 52 LYS cc_start: 0.8132 (ptpp) cc_final: 0.7825 (ptmt) REVERT: H 11 LEU cc_start: 0.6915 (tp) cc_final: 0.6681 (tm) REVERT: H 38 ARG cc_start: 0.8910 (OUTLIER) cc_final: 0.8640 (ptt180) REVERT: B 138 MET cc_start: 0.6370 (mmm) cc_final: 0.5898 (mmm) REVERT: B 167 LYS cc_start: 0.7917 (mtmm) cc_final: 0.7582 (mttt) REVERT: B 399 ARG cc_start: 0.6637 (ptp-110) cc_final: 0.6372 (ptp-170) REVERT: C 52 LYS cc_start: 0.8231 (ptmm) cc_final: 0.7833 (ptmt) REVERT: D 72 ASP cc_start: 0.8624 (OUTLIER) cc_final: 0.8241 (t70) REVERT: E 115 MET cc_start: 0.8836 (mtm) cc_final: 0.8524 (mtm) REVERT: E 138 MET cc_start: 0.6475 (mmm) cc_final: 0.6086 (mmm) REVERT: E 219 GLN cc_start: 0.7862 (OUTLIER) cc_final: 0.7252 (pt0) REVERT: E 240 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.7592 (tm-30) REVERT: E 399 ARG cc_start: 0.6775 (ptp-110) cc_final: 0.6254 (ptp-170) REVERT: F 52 LYS cc_start: 0.8176 (ptpp) cc_final: 0.7885 (ptmt) REVERT: G 46 GLU cc_start: 0.8479 (tt0) cc_final: 0.8175 (pt0) outliers start: 60 outliers final: 39 residues processed: 225 average time/residue: 0.4737 time to fit residues: 120.3826 Evaluate side-chains 223 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 179 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 392 CYS Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 53 SER Chi-restraints excluded: chain L residue 85 SER Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 351 ASN Chi-restraints excluded: chain B residue 392 CYS Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 90 HIS Chi-restraints excluded: chain D residue 70 ASN Chi-restraints excluded: chain D residue 72 ASP Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain E residue 219 GLN Chi-restraints excluded: chain E residue 240 GLU Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain E residue 392 CYS Chi-restraints excluded: chain E residue 415 THR Chi-restraints excluded: chain E residue 416 THR Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 53 SER Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain G residue 53 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 173 optimal weight: 1.9990 chunk 91 optimal weight: 0.6980 chunk 75 optimal weight: 0.8980 chunk 142 optimal weight: 0.6980 chunk 5 optimal weight: 0.5980 chunk 51 optimal weight: 0.9990 chunk 137 optimal weight: 0.5980 chunk 13 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 chunk 90 optimal weight: 0.7980 chunk 189 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN H 1 GLN D 1 GLN E 224 ASN G 1 GLN G 111 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.137701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.114836 restraints weight = 20012.058| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 2.06 r_work: 0.3299 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.3859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 16074 Z= 0.148 Angle : 0.583 8.027 21939 Z= 0.289 Chirality : 0.047 0.334 2685 Planarity : 0.004 0.044 2703 Dihedral : 5.367 31.260 2928 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.13 % Allowed : 16.52 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.19), residues: 1986 helix: 1.90 (0.24), residues: 486 sheet: 0.43 (0.21), residues: 576 loop : -0.52 (0.20), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 24 TYR 0.014 0.001 TYR A 239 PHE 0.015 0.001 PHE E 330 TRP 0.015 0.001 TRP G 47 HIS 0.006 0.001 HIS C 91 Details of bonding type rmsd covalent geometry : bond 0.00350 (16014) covalent geometry : angle 0.55370 (21780) SS BOND : bond 0.00329 ( 21) SS BOND : angle 0.82944 ( 42) hydrogen bonds : bond 0.03341 ( 691) hydrogen bonds : angle 4.78848 ( 2001) link_ALPHA1-3 : bond 0.01145 ( 3) link_ALPHA1-3 : angle 1.40669 ( 9) link_ALPHA1-6 : bond 0.00462 ( 3) link_ALPHA1-6 : angle 1.43222 ( 9) link_BETA1-4 : bond 0.00535 ( 18) link_BETA1-4 : angle 2.37837 ( 54) link_BETA1-6 : bond 0.00427 ( 3) link_BETA1-6 : angle 1.12582 ( 9) link_NAG-ASN : bond 0.00284 ( 12) link_NAG-ASN : angle 3.33898 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3972 Ramachandran restraints generated. 1986 Oldfield, 0 Emsley, 1986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3972 Ramachandran restraints generated. 1986 Oldfield, 0 Emsley, 1986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 184 time to evaluate : 0.544 Fit side-chains revert: symmetry clash REVERT: A 167 LYS cc_start: 0.7917 (mtmt) cc_final: 0.7518 (mttt) REVERT: A 240 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.7341 (tm-30) REVERT: A 406 GLU cc_start: 0.7944 (pm20) cc_final: 0.7510 (pm20) REVERT: A 416 THR cc_start: 0.7664 (p) cc_final: 0.7213 (t) REVERT: L 52 LYS cc_start: 0.8052 (ptpp) cc_final: 0.7829 (ptmt) REVERT: H 11 LEU cc_start: 0.6931 (tp) cc_final: 0.6706 (tm) REVERT: H 38 ARG cc_start: 0.8894 (OUTLIER) cc_final: 0.8610 (ptt180) REVERT: B 138 MET cc_start: 0.6396 (mmm) cc_final: 0.5934 (mmm) REVERT: B 167 LYS cc_start: 0.7896 (mtmm) cc_final: 0.7569 (mttt) REVERT: B 399 ARG cc_start: 0.6691 (ptp-110) cc_final: 0.6381 (ptp-170) REVERT: C 52 LYS cc_start: 0.8186 (ptmm) cc_final: 0.7791 (ptmt) REVERT: D 46 GLU cc_start: 0.8432 (tt0) cc_final: 0.8119 (pt0) REVERT: E 115 MET cc_start: 0.8853 (mtm) cc_final: 0.8513 (mtm) REVERT: E 138 MET cc_start: 0.6379 (mmm) cc_final: 0.5993 (mmm) REVERT: E 219 GLN cc_start: 0.7867 (OUTLIER) cc_final: 0.7256 (pt0) REVERT: E 240 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.7581 (tm-30) REVERT: E 399 ARG cc_start: 0.6795 (ptp-110) cc_final: 0.6268 (ptp-170) REVERT: F 52 LYS cc_start: 0.8144 (ptpp) cc_final: 0.7831 (ptmt) REVERT: G 46 GLU cc_start: 0.8504 (tt0) cc_final: 0.8195 (pt0) outliers start: 52 outliers final: 36 residues processed: 213 average time/residue: 0.4868 time to fit residues: 116.7465 Evaluate side-chains 219 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 179 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 392 CYS Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 53 SER Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 351 ASN Chi-restraints excluded: chain B residue 392 CYS Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 90 HIS Chi-restraints excluded: chain D residue 70 ASN Chi-restraints excluded: chain E residue 219 GLN Chi-restraints excluded: chain E residue 224 ASN Chi-restraints excluded: chain E residue 240 GLU Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain E residue 388 ILE Chi-restraints excluded: chain E residue 392 CYS Chi-restraints excluded: chain E residue 415 THR Chi-restraints excluded: chain E residue 416 THR Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 53 SER Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain G residue 53 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 107 optimal weight: 0.7980 chunk 141 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 125 optimal weight: 0.0570 chunk 17 optimal weight: 0.5980 chunk 90 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 83 optimal weight: 0.7980 chunk 114 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 150 optimal weight: 0.5980 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN H 1 GLN D 1 GLN ** F 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 1 GLN G 111 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.137857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.115053 restraints weight = 19898.439| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 2.06 r_work: 0.3302 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.3848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 16074 Z= 0.163 Angle : 0.769 59.198 21939 Z= 0.432 Chirality : 0.048 0.551 2685 Planarity : 0.005 0.079 2703 Dihedral : 5.385 31.264 2928 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.07 % Favored : 96.88 % Rotamer: Outliers : 2.65 % Allowed : 16.70 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.19), residues: 1986 helix: 1.91 (0.24), residues: 486 sheet: 0.43 (0.21), residues: 576 loop : -0.53 (0.20), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 66 TYR 0.014 0.001 TYR A 239 PHE 0.015 0.001 PHE E 330 TRP 0.015 0.001 TRP G 47 HIS 0.005 0.001 HIS C 91 Details of bonding type rmsd covalent geometry : bond 0.00366 (16014) covalent geometry : angle 0.74825 (21780) SS BOND : bond 0.00325 ( 21) SS BOND : angle 0.81742 ( 42) hydrogen bonds : bond 0.03337 ( 691) hydrogen bonds : angle 4.78862 ( 2001) link_ALPHA1-3 : bond 0.01029 ( 3) link_ALPHA1-3 : angle 1.39775 ( 9) link_ALPHA1-6 : bond 0.00464 ( 3) link_ALPHA1-6 : angle 1.43461 ( 9) link_BETA1-4 : bond 0.00535 ( 18) link_BETA1-4 : angle 2.37244 ( 54) link_BETA1-6 : bond 0.00423 ( 3) link_BETA1-6 : angle 1.12435 ( 9) link_NAG-ASN : bond 0.00288 ( 12) link_NAG-ASN : angle 3.34145 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3972 Ramachandran restraints generated. 1986 Oldfield, 0 Emsley, 1986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3972 Ramachandran restraints generated. 1986 Oldfield, 0 Emsley, 1986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 180 time to evaluate : 0.542 Fit side-chains revert: symmetry clash REVERT: A 167 LYS cc_start: 0.7937 (mtmt) cc_final: 0.7538 (mttt) REVERT: A 240 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7315 (tm-30) REVERT: A 406 GLU cc_start: 0.7907 (pm20) cc_final: 0.7450 (pm20) REVERT: A 416 THR cc_start: 0.7677 (p) cc_final: 0.7232 (t) REVERT: L 52 LYS cc_start: 0.8060 (ptpp) cc_final: 0.7807 (ptmt) REVERT: H 11 LEU cc_start: 0.6925 (tp) cc_final: 0.6704 (tm) REVERT: H 38 ARG cc_start: 0.8878 (OUTLIER) cc_final: 0.8595 (ptt180) REVERT: B 138 MET cc_start: 0.6398 (mmm) cc_final: 0.5930 (mmm) REVERT: B 167 LYS cc_start: 0.7917 (mtmm) cc_final: 0.7588 (mttt) REVERT: B 399 ARG cc_start: 0.6696 (ptp-110) cc_final: 0.6384 (ptp-170) REVERT: C 52 LYS cc_start: 0.8211 (ptmm) cc_final: 0.7809 (ptmt) REVERT: E 115 MET cc_start: 0.8829 (mtm) cc_final: 0.8494 (mtm) REVERT: E 138 MET cc_start: 0.6390 (mmm) cc_final: 0.5994 (mmm) REVERT: E 219 GLN cc_start: 0.7856 (OUTLIER) cc_final: 0.7242 (pt0) REVERT: E 240 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7567 (tm-30) REVERT: E 399 ARG cc_start: 0.6779 (ptp-110) cc_final: 0.6256 (ptp-170) REVERT: F 52 LYS cc_start: 0.8141 (ptpp) cc_final: 0.7833 (ptmt) REVERT: G 46 GLU cc_start: 0.8475 (tt0) cc_final: 0.8178 (pt0) outliers start: 44 outliers final: 34 residues processed: 207 average time/residue: 0.4768 time to fit residues: 111.2540 Evaluate side-chains 216 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 178 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 392 CYS Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 53 SER Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 351 ASN Chi-restraints excluded: chain B residue 392 CYS Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 90 HIS Chi-restraints excluded: chain D residue 70 ASN Chi-restraints excluded: chain E residue 219 GLN Chi-restraints excluded: chain E residue 240 GLU Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain E residue 388 ILE Chi-restraints excluded: chain E residue 392 CYS Chi-restraints excluded: chain E residue 415 THR Chi-restraints excluded: chain E residue 416 THR Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 53 SER Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain G residue 53 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 52 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 136 optimal weight: 0.5980 chunk 100 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 143 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN H 1 GLN D 1 GLN ** F 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 1 GLN G 111 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.137878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.115065 restraints weight = 19963.871| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 2.06 r_work: 0.3303 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.3847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 16074 Z= 0.163 Angle : 0.769 59.198 21939 Z= 0.432 Chirality : 0.048 0.551 2685 Planarity : 0.005 0.079 2703 Dihedral : 5.385 31.264 2928 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.07 % Favored : 96.88 % Rotamer: Outliers : 2.47 % Allowed : 16.88 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.19), residues: 1986 helix: 1.91 (0.24), residues: 486 sheet: 0.43 (0.21), residues: 576 loop : -0.53 (0.20), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 66 TYR 0.014 0.001 TYR A 239 PHE 0.015 0.001 PHE E 330 TRP 0.015 0.001 TRP G 47 HIS 0.005 0.001 HIS C 91 Details of bonding type rmsd covalent geometry : bond 0.00366 (16014) covalent geometry : angle 0.74825 (21780) SS BOND : bond 0.00325 ( 21) SS BOND : angle 0.81742 ( 42) hydrogen bonds : bond 0.03337 ( 691) hydrogen bonds : angle 4.78862 ( 2001) link_ALPHA1-3 : bond 0.01029 ( 3) link_ALPHA1-3 : angle 1.39775 ( 9) link_ALPHA1-6 : bond 0.00464 ( 3) link_ALPHA1-6 : angle 1.43461 ( 9) link_BETA1-4 : bond 0.00535 ( 18) link_BETA1-4 : angle 2.37244 ( 54) link_BETA1-6 : bond 0.00423 ( 3) link_BETA1-6 : angle 1.12435 ( 9) link_NAG-ASN : bond 0.00288 ( 12) link_NAG-ASN : angle 3.34145 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4991.17 seconds wall clock time: 85 minutes 52.58 seconds (5152.58 seconds total)