Starting phenix.real_space_refine on Fri Jul 3 19:42:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ki4_22884/07_2026/7ki4_22884.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ki4_22884/07_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7ki4_22884/07_2026/7ki4_22884.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ki4_22884/07_2026/7ki4_22884.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ki4_22884/07_2026/7ki4_22884.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ki4_22884/07_2026/7ki4_22884.map" model { file = "/net/cci-nas-00/data/ceres_data/7ki4_22884/07_2026/7ki4_22884.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ki4_22884/07_2026/7ki4_22884.cif" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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 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 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 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 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 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 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 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 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 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 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 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 chiralities: 6 Time building chain proxies: 4.00, per 1000 atoms: 0.25 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: 1.56 Conformation dependent library (CDL) restraints added in 692.1 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: 0.70 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: 3.23 Time building geometry restraints manager: 2.06 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 - 15.64: 8946 15.64 - 31.28: 243 31.28 - 46.92: 63 46.92 - 62.56: 54 62.56 - 78.20: 21 Dihedral angle restraints: 9327 sinusoidal: 3510 harmonic: 5817 Sorted by residual: dihedral pdb=" CB CYS B 71 " pdb=" SG CYS B 71 " pdb=" SG CYS B 192 " pdb=" CB CYS B 192 " ideal model delta sinusoidal sigma weight residual -86.00 -115.92 29.92 1 1.00e+01 1.00e-02 1.28e+01 dihedral pdb=" CB CYS E 71 " pdb=" SG CYS E 71 " pdb=" SG CYS E 192 " pdb=" CB CYS E 192 " ideal model delta sinusoidal sigma weight residual -86.00 -115.90 29.90 1 1.00e+01 1.00e-02 1.28e+01 dihedral pdb=" CB CYS A 71 " pdb=" SG CYS A 71 " pdb=" SG CYS A 192 " pdb=" CB CYS A 192 " ideal model delta sinusoidal sigma weight residual -86.00 -115.90 29.90 1 1.00e+01 1.00e-02 1.28e+01 ... (remaining 9324 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: 0.03 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: 4.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 16.870 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 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:10.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 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 : 10.475 78.198 5544 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/Z covalent geometry : bond 0.01296 / 0.69 (16014) covalent geometry : angle 1.37184 / 0.91 (21780) SS BOND : bond 0.00684 / 0.44 ( 21) SS BOND : angle 2.72722 / 1.94 ( 42) hydrogen bonds : bond 0.15980 / 11.04 ( 691) hydrogen bonds : angle 8.38176 / 5.94 ( 2001) link_ALPHA1-3 : bond 0.05089 / 2.36 ( 3) link_ALPHA1-3 : angle 2.51005 / 1.25 ( 9) link_ALPHA1-6 : bond 0.04443 / 2.05 ( 3) link_ALPHA1-6 : angle 1.73180 / 0.88 ( 9) link_BETA1-4 : bond 0.05668 / 3.41 ( 18) link_BETA1-4 : angle 3.92254 / 2.49 ( 54) link_BETA1-6 : bond 0.04660 / 2.15 ( 3) link_BETA1-6 : angle 1.66898 / 0.84 ( 9) link_NAG-ASN : bond 0.05467 / 3.19 ( 12) link_NAG-ASN : angle 2.80219 / 1.90 ( 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 : 0.598 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: 0.4916 time to fit residues: 209.8060 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 : 0.673 ------------------------------------------------------------------------------- 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... A 64 ASN 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: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.145005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.122157 restraints weight = 19949.607| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 2.12 r_work: 0.3385 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3258 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.2221 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= 0.170 Angle : 0.658 8.966 21939 Z= 0.338 Chirality : 0.050 0.429 2685 Planarity : 0.004 0.034 2703 Dihedral : 4.592 21.158 2145 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.15 % Allowed : 1.46 % Favored : 98.39 % Rotamer: Outliers : 3.44 % Allowed : 10.43 % Favored : 86.14 % 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: 0.87 (0.19), residues: 1986 helix: 1.36 (0.24), residues: 471 sheet: 0.89 (0.20), residues: 594 loop : 0.06 (0.21), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 399 TYR 0.040 0.002 TYR F 32 PHE 0.016 0.002 PHE E 253 TRP 0.013 0.002 TRP D 47 HIS 0.005 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.17 (16014) covalent geometry : angle 0.62892 / 0.33 (21780) SS BOND : bond 0.00194 / 0.13 ( 21) SS BOND : angle 0.78292 / 0.50 ( 42) hydrogen bonds : bond 0.04794 / 3.30 ( 691) hydrogen bonds : angle 5.86480 / 4.14 ( 2001) link_ALPHA1-3 : bond 0.00845 / 0.39 ( 3) link_ALPHA1-3 : angle 1.91199 / 1.02 ( 9) link_ALPHA1-6 : bond 0.00846 / 0.39 ( 3) link_ALPHA1-6 : angle 1.44856 / 0.78 ( 9) link_BETA1-4 : bond 0.00469 / 0.24 ( 18) link_BETA1-4 : angle 2.69759 / 1.74 ( 54) link_BETA1-6 : bond 0.00457 / 0.21 ( 3) link_BETA1-6 : angle 1.34270 / 0.72 ( 9) link_NAG-ASN : bond 0.00399 / 0.23 ( 12) link_NAG-ASN : angle 3.28001 / 1.95 ( 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 293 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 236 time to evaluate : 0.624 Fit side-chains revert: symmetry clash REVERT: A 136 GLU cc_start: 0.7502 (mt-10) cc_final: 0.7206 (mm-30) REVERT: A 167 LYS cc_start: 0.8185 (mtmt) cc_final: 0.7607 (mttt) REVERT: A 240 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.7347 (tm-30) REVERT: A 395 GLN cc_start: 0.7514 (tp40) cc_final: 0.6969 (tm-30) REVERT: L 52 LYS cc_start: 0.8059 (ptpp) cc_final: 0.7448 (mtpp) REVERT: H 11 LEU cc_start: 0.7015 (tp) cc_final: 0.6709 (tm) REVERT: B 138 MET cc_start: 0.6393 (mmm) cc_final: 0.5879 (mmm) REVERT: B 240 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.7418 (tm-30) REVERT: E 138 MET cc_start: 0.6344 (mmm) cc_final: 0.5915 (mmm) REVERT: E 240 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.7601 (tm-30) REVERT: E 244 ARG cc_start: 0.7646 (ttp-110) cc_final: 0.7030 (ttp-110) REVERT: E 395 GLN cc_start: 0.7458 (tp40) cc_final: 0.7158 (tm-30) REVERT: F 11 LEU cc_start: 0.7257 (OUTLIER) cc_final: 0.6670 (tp) REVERT: F 22 THR cc_start: 0.7984 (m) cc_final: 0.7615 (p) REVERT: F 52 LYS cc_start: 0.8112 (ptpp) cc_final: 0.7815 (ptmt) outliers start: 57 outliers final: 19 residues processed: 264 average time/residue: 0.5264 time to fit residues: 153.9930 Evaluate side-chains 220 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 197 time to evaluate : 0.605 ------------------------------------------------------------------------------- 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 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: 0.9980 chunk 71 optimal weight: 0.9990 chunk 96 optimal weight: 0.9980 chunk 182 optimal weight: 0.8980 chunk 136 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 chunk 9 optimal weight: 0.6980 chunk 132 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3712 r_free = 0.3712 target = 0.141091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.118122 restraints weight = 20142.348| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 2.11 r_work: 0.3325 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3196 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.2898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16074 Z= 0.164 Angle : 0.603 8.382 21939 Z= 0.305 Chirality : 0.047 0.304 2685 Planarity : 0.005 0.046 2703 Dihedral : 4.372 20.728 2145 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.77 % Favored : 97.13 % Rotamer: Outliers : 4.16 % Allowed : 11.69 % Favored : 84.15 % 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: 0.72 (0.19), residues: 1986 helix: 1.61 (0.24), residues: 486 sheet: 0.69 (0.20), residues: 585 loop : -0.22 (0.20), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 399 TYR 0.014 0.002 TYR F 32 PHE 0.015 0.002 PHE A 376 TRP 0.016 0.002 TRP H 47 HIS 0.008 0.001 HIS C 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.16 (16014) covalent geometry : angle 0.57580 / 0.30 (21780) SS BOND : bond 0.00183 / 0.12 ( 21) SS BOND : angle 0.69174 / 0.46 ( 42) hydrogen bonds : bond 0.03962 / 2.69 ( 691) hydrogen bonds : angle 5.17113 / 3.63 ( 2001) link_ALPHA1-3 : bond 0.00774 / 0.36 ( 3) link_ALPHA1-3 : angle 1.53859 / 0.83 ( 9) link_ALPHA1-6 : bond 0.00738 / 0.34 ( 3) link_ALPHA1-6 : angle 1.36398 / 0.74 ( 9) link_BETA1-4 : bond 0.00681 / 0.39 ( 18) link_BETA1-4 : angle 2.43025 / 1.52 ( 54) link_BETA1-6 : bond 0.00506 / 0.23 ( 3) link_BETA1-6 : angle 1.00644 / 0.55 ( 9) link_NAG-ASN : bond 0.00351 / 0.20 ( 12) link_NAG-ASN : angle 3.19023 / 1.75 ( 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 297 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 228 time to evaluate : 0.605 Fit side-chains REVERT: A 82 ARG cc_start: 0.8669 (tpt90) cc_final: 0.8319 (tmt-80) REVERT: A 115 MET cc_start: 0.8661 (OUTLIER) cc_final: 0.8252 (mtp) REVERT: A 136 GLU cc_start: 0.7553 (mt-10) cc_final: 0.7342 (mm-30) REVERT: A 167 LYS cc_start: 0.8025 (mtmt) cc_final: 0.7617 (mttt) REVERT: A 240 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.7452 (tm-30) REVERT: A 244 ARG cc_start: 0.7833 (ttp-110) cc_final: 0.7561 (ttp-110) REVERT: A 395 GLN cc_start: 0.7239 (tp40) cc_final: 0.7003 (tm-30) REVERT: L 52 LYS cc_start: 0.8087 (ptpp) cc_final: 0.7494 (mtpp) REVERT: H 11 LEU cc_start: 0.7039 (tp) cc_final: 0.6763 (tm) REVERT: H 46 GLU cc_start: 0.8330 (tt0) cc_final: 0.8116 (pt0) REVERT: H 70 ASN cc_start: 0.7976 (t0) cc_final: 0.7531 (m-40) REVERT: B 138 MET cc_start: 0.6189 (mmm) cc_final: 0.5667 (mmm) REVERT: B 413 ASP cc_start: 0.8351 (p0) cc_final: 0.8089 (p0) REVERT: D 72 ASP cc_start: 0.8676 (OUTLIER) cc_final: 0.8283 (t70) REVERT: E 138 MET cc_start: 0.6347 (mmm) cc_final: 0.5885 (mmm) REVERT: E 240 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.7602 (tm-30) REVERT: E 395 GLN cc_start: 0.7469 (tp40) cc_final: 0.7162 (tm-30) REVERT: E 399 ARG cc_start: 0.6735 (ptp-110) cc_final: 0.6143 (ptp-170) REVERT: F 52 LYS cc_start: 0.8160 (ptpp) cc_final: 0.7856 (ptmm) outliers start: 69 outliers final: 38 residues processed: 265 average time/residue: 0.4438 time to fit residues: 131.6836 Evaluate side-chains 238 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 196 time to evaluate : 0.534 ------------------------------------------------------------------------------- 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 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 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 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 72 ASP Chi-restraints excluded: chain D residue 84 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 415 THR Chi-restraints excluded: chain E residue 416 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 12 optimal weight: 2.9990 chunk 183 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 179 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 135 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 140 ASN A 224 ASN A 393 GLN H 1 GLN B 194 GLN B 380 ASN B 393 GLN B 459 GLN B 469 GLN D 1 GLN E 194 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: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.136614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.113761 restraints weight = 20061.401| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 2.03 r_work: 0.3274 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.3323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 16074 Z= 0.216 Angle : 0.646 9.408 21939 Z= 0.320 Chirality : 0.049 0.324 2685 Planarity : 0.005 0.045 2703 Dihedral : 4.517 21.116 2145 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 4.64 % Allowed : 13.14 % Favored : 82.22 % 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: 0.53 (0.19), residues: 1986 helix: 1.63 (0.24), residues: 486 sheet: 0.50 (0.21), residues: 579 loop : -0.37 (0.20), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 24 TYR 0.020 0.002 TYR L 32 PHE 0.014 0.002 PHE A 376 TRP 0.019 0.002 TRP D 47 HIS 0.010 0.002 HIS F 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00523 / 0.22 (16014) covalent geometry : angle 0.61655 / 0.31 (21780) SS BOND : bond 0.00340 / 0.21 ( 21) SS BOND : angle 1.16714 / 0.70 ( 42) hydrogen bonds : bond 0.03979 / 2.72 ( 691) hydrogen bonds : angle 5.16988 / 3.63 ( 2001) link_ALPHA1-3 : bond 0.00516 / 0.24 ( 3) link_ALPHA1-3 : angle 1.88754 / 1.02 ( 9) link_ALPHA1-6 : bond 0.00479 / 0.22 ( 3) link_ALPHA1-6 : angle 1.65366 / 0.89 ( 9) link_BETA1-4 : bond 0.00551 / 0.28 ( 18) link_BETA1-4 : angle 2.55308 / 1.61 ( 54) link_BETA1-6 : bond 0.00390 / 0.18 ( 3) link_BETA1-6 : angle 1.10022 / 0.60 ( 9) link_NAG-ASN : bond 0.00320 / 0.21 ( 12) link_NAG-ASN : angle 3.33359 / 1.83 ( 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 284 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 207 time to evaluate : 0.606 Fit side-chains REVERT: A 82 ARG cc_start: 0.8715 (tpt90) cc_final: 0.8449 (tmt-80) REVERT: A 115 MET cc_start: 0.8647 (OUTLIER) cc_final: 0.8244 (mtp) REVERT: A 167 LYS cc_start: 0.7900 (mtmt) cc_final: 0.7559 (mttt) REVERT: A 240 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.7373 (tm-30) REVERT: A 260 ASP cc_start: 0.8676 (m-30) cc_final: 0.8468 (m-30) REVERT: A 395 GLN cc_start: 0.7257 (tp40) cc_final: 0.7025 (tm-30) REVERT: H 11 LEU cc_start: 0.7053 (tp) cc_final: 0.6741 (tm) REVERT: H 46 GLU cc_start: 0.8323 (tt0) cc_final: 0.8122 (pt0) REVERT: H 70 ASN cc_start: 0.8036 (t0) cc_final: 0.7564 (m-40) REVERT: B 138 MET cc_start: 0.6434 (mmm) cc_final: 0.5927 (mmm) REVERT: B 167 LYS cc_start: 0.7939 (mtmm) cc_final: 0.7552 (mttt) REVERT: B 399 ARG cc_start: 0.6611 (ptp-110) cc_final: 0.6227 (ptp-170) REVERT: C 52 LYS cc_start: 0.8137 (ptpp) cc_final: 0.7827 (ptmt) REVERT: D 72 ASP cc_start: 0.8651 (OUTLIER) cc_final: 0.8268 (t70) REVERT: E 115 MET cc_start: 0.8892 (OUTLIER) cc_final: 0.8569 (mtm) REVERT: E 138 MET cc_start: 0.6460 (mmm) cc_final: 0.6043 (mmm) REVERT: E 240 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.7651 (tm-30) REVERT: E 399 ARG cc_start: 0.6957 (ptp-110) cc_final: 0.6348 (ptp-170) REVERT: F 52 LYS cc_start: 0.8239 (ptpp) cc_final: 0.7935 (ptmm) REVERT: G 46 GLU cc_start: 0.8485 (tt0) cc_final: 0.8194 (pt0) outliers start: 77 outliers final: 45 residues processed: 255 average time/residue: 0.4873 time to fit residues: 139.3114 Evaluate side-chains 236 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 186 time to evaluate : 0.551 ------------------------------------------------------------------------------- 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 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 392 CYS Chi-restraints excluded: chain A residue 397 THR 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 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 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 397 THR 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 20 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 115 MET 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 11 LEU 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 7 SER Chi-restraints excluded: chain G residue 53 THR 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: 0.2980 chunk 44 optimal weight: 0.8980 chunk 130 optimal weight: 1.9990 chunk 190 optimal weight: 0.0770 chunk 37 optimal weight: 0.6980 chunk 186 optimal weight: 1.9990 chunk 161 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 156 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 120 optimal weight: 4.9990 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 224 ASN A 393 GLN A 469 GLN H 1 GLN B 393 GLN B 469 GLN D 1 GLN E 224 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.139110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.116244 restraints weight = 19965.765| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 2.07 r_work: 0.3309 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.3454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16074 Z= 0.128 Angle : 0.566 7.388 21939 Z= 0.283 Chirality : 0.046 0.301 2685 Planarity : 0.004 0.045 2703 Dihedral : 4.326 20.484 2145 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.56 % Allowed : 14.53 % Favored : 81.92 % 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: 1.82 (0.24), residues: 486 sheet: 0.46 (0.21), residues: 579 loop : -0.43 (0.20), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 24 TYR 0.013 0.001 TYR A 239 PHE 0.016 0.001 PHE E 330 TRP 0.014 0.001 TRP G 47 HIS 0.005 0.001 HIS C 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (16014) covalent geometry : angle 0.53736 / 0.28 (21780) SS BOND : bond 0.00348 / 0.23 ( 21) SS BOND : angle 1.02088 / 0.71 ( 42) hydrogen bonds : bond 0.03404 / 2.33 ( 691) hydrogen bonds : angle 4.90609 / 3.44 ( 2001) link_ALPHA1-3 : bond 0.00666 / 0.31 ( 3) link_ALPHA1-3 : angle 1.51459 / 0.82 ( 9) link_ALPHA1-6 : bond 0.00630 / 0.29 ( 3) link_ALPHA1-6 : angle 1.44017 / 0.78 ( 9) link_BETA1-4 : bond 0.00544 / 0.30 ( 18) link_BETA1-4 : angle 2.31592 / 1.43 ( 54) link_BETA1-6 : bond 0.00510 / 0.23 ( 3) link_BETA1-6 : angle 1.03790 / 0.56 ( 9) link_NAG-ASN : bond 0.00319 / 0.19 ( 12) link_NAG-ASN : angle 3.11380 / 1.70 ( 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 268 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 209 time to evaluate : 0.611 Fit side-chains REVERT: A 82 ARG cc_start: 0.8686 (tpt90) cc_final: 0.8435 (tmt-80) REVERT: A 167 LYS cc_start: 0.7886 (mtmt) cc_final: 0.7536 (mttt) REVERT: A 240 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7348 (tm-30) REVERT: A 260 ASP cc_start: 0.8682 (m-30) cc_final: 0.8474 (m-30) REVERT: A 307 GLU cc_start: 0.8499 (mt-10) cc_final: 0.8287 (mt-10) REVERT: A 395 GLN cc_start: 0.7244 (tp40) cc_final: 0.7023 (tm-30) REVERT: A 399 ARG cc_start: 0.6640 (ptp-110) cc_final: 0.6236 (ptp-110) REVERT: A 406 GLU cc_start: 0.7803 (pm20) cc_final: 0.7479 (pm20) REVERT: L 52 LYS cc_start: 0.8124 (ptpp) cc_final: 0.7832 (ptmt) REVERT: H 11 LEU cc_start: 0.7074 (tp) cc_final: 0.6767 (tm) REVERT: H 38 ARG cc_start: 0.8872 (OUTLIER) cc_final: 0.8549 (ptt180) REVERT: H 70 ASN cc_start: 0.8042 (t0) cc_final: 0.7550 (m-40) REVERT: B 138 MET cc_start: 0.6357 (mmm) cc_final: 0.5856 (mmm) REVERT: B 399 ARG cc_start: 0.6595 (ptp-110) cc_final: 0.6170 (ptp-170) REVERT: C 52 LYS cc_start: 0.8132 (ptpp) cc_final: 0.7852 (ptmt) REVERT: C 86 TYR cc_start: 0.7930 (m-80) cc_final: 0.7729 (m-80) REVERT: D 66 ARG cc_start: 0.8128 (mtp180) cc_final: 0.7884 (mtp180) REVERT: D 72 ASP cc_start: 0.8651 (OUTLIER) cc_final: 0.8282 (t70) REVERT: E 115 MET cc_start: 0.8889 (OUTLIER) cc_final: 0.8513 (mtm) REVERT: E 142 ASP cc_start: 0.7946 (OUTLIER) cc_final: 0.7340 (t0) REVERT: E 240 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.7624 (tm-30) REVERT: E 399 ARG cc_start: 0.6836 (ptp-110) cc_final: 0.6213 (ptp-170) REVERT: F 52 LYS cc_start: 0.8152 (ptpp) cc_final: 0.7871 (ptmm) REVERT: G 46 GLU cc_start: 0.8460 (tt0) cc_final: 0.8217 (pt0) outliers start: 59 outliers final: 30 residues processed: 245 average time/residue: 0.4653 time to fit residues: 128.6630 Evaluate side-chains 226 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 190 time to evaluate : 0.663 ------------------------------------------------------------------------------- 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 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 300 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 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 115 MET 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 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 53 SER Chi-restraints excluded: chain G residue 7 SER 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: 1.9990 chunk 174 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 191 optimal weight: 0.9980 chunk 45 optimal weight: 9.9990 chunk 172 optimal weight: 2.9990 chunk 167 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 100 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 224 ASN H 1 GLN B 393 GLN D 1 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 = 0.3650 r_free = 0.3650 target = 0.135724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.112982 restraints weight = 20020.377| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 2.04 r_work: 0.3261 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.3671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 16074 Z= 0.219 Angle : 0.647 9.642 21939 Z= 0.320 Chirality : 0.048 0.305 2685 Planarity : 0.005 0.046 2703 Dihedral : 4.487 20.060 2145 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 3.86 % Allowed : 14.83 % Favored : 81.31 % 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: 0.35 (0.19), residues: 1986 helix: 1.68 (0.24), residues: 486 sheet: 0.28 (0.21), residues: 579 loop : -0.55 (0.20), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 24 TYR 0.017 0.002 TYR A 239 PHE 0.016 0.002 PHE E 330 TRP 0.018 0.002 TRP D 47 HIS 0.009 0.002 HIS L 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00532 / 0.22 (16014) covalent geometry : angle 0.61910 / 0.31 (21780) SS BOND : bond 0.00419 / 0.28 ( 21) SS BOND : angle 1.13706 / 0.74 ( 42) hydrogen bonds : bond 0.03879 / 2.65 ( 691) hydrogen bonds : angle 5.05894 / 3.55 ( 2001) link_ALPHA1-3 : bond 0.00461 / 0.22 ( 3) link_ALPHA1-3 : angle 1.74797 / 0.95 ( 9) link_ALPHA1-6 : bond 0.00482 / 0.22 ( 3) link_ALPHA1-6 : angle 1.65920 / 0.90 ( 9) link_BETA1-4 : bond 0.00574 / 0.29 ( 18) link_BETA1-4 : angle 2.46408 / 1.55 ( 54) link_BETA1-6 : bond 0.00381 / 0.18 ( 3) link_BETA1-6 : angle 1.12875 / 0.62 ( 9) link_NAG-ASN : bond 0.00279 / 0.19 ( 12) link_NAG-ASN : angle 3.33373 / 1.82 ( 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 256 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 192 time to evaluate : 0.614 Fit side-chains REVERT: A 82 ARG cc_start: 0.8718 (tpt90) cc_final: 0.8445 (tmt-80) REVERT: A 115 MET cc_start: 0.8744 (mtm) cc_final: 0.8218 (mtp) REVERT: A 167 LYS cc_start: 0.7916 (mtmt) cc_final: 0.7552 (mttt) REVERT: A 240 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.7380 (tm-30) REVERT: A 260 ASP cc_start: 0.8698 (m-30) cc_final: 0.8490 (m-30) REVERT: A 406 GLU cc_start: 0.7787 (pm20) cc_final: 0.7548 (pm20) REVERT: L 52 LYS cc_start: 0.8169 (ptpp) cc_final: 0.7899 (ptmt) REVERT: H 11 LEU cc_start: 0.7092 (tp) cc_final: 0.6765 (tm) REVERT: H 38 ARG cc_start: 0.8970 (OUTLIER) cc_final: 0.8710 (ptt180) REVERT: H 70 ASN cc_start: 0.7982 (t0) cc_final: 0.7569 (m-40) REVERT: B 138 MET cc_start: 0.6449 (mmm) cc_final: 0.5952 (mmm) REVERT: B 399 ARG cc_start: 0.6631 (ptp-110) cc_final: 0.6180 (ptp-170) REVERT: D 72 ASP cc_start: 0.8669 (OUTLIER) cc_final: 0.8307 (t70) REVERT: E 115 MET cc_start: 0.8904 (OUTLIER) cc_final: 0.8529 (mtm) REVERT: E 138 MET cc_start: 0.6492 (mmm) cc_final: 0.6097 (mmm) REVERT: E 240 GLU cc_start: 0.8304 (OUTLIER) cc_final: 0.7622 (tm-30) REVERT: E 399 ARG cc_start: 0.6819 (ptp-110) cc_final: 0.6274 (ptp-170) REVERT: F 52 LYS cc_start: 0.8225 (ptpp) cc_final: 0.7884 (ptmt) REVERT: G 43 LYS cc_start: 0.8045 (mmtt) cc_final: 0.7780 (mptt) REVERT: G 46 GLU cc_start: 0.8473 (tt0) cc_final: 0.8247 (pt0) outliers start: 64 outliers final: 41 residues processed: 231 average time/residue: 0.4307 time to fit residues: 112.8635 Evaluate side-chains 222 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 176 time to evaluate : 0.442 ------------------------------------------------------------------------------- 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 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 H residue 72 ASP 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 85 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 115 MET 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 11 LEU 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 7 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: 0.3980 chunk 178 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 158 optimal weight: 0.0870 chunk 110 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 chunk 177 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 194 optimal weight: 0.5980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 224 ASN H 1 GLN D 1 GLN E 224 ASN ** F 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3673 r_free = 0.3673 target = 0.137643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.114978 restraints weight = 19873.309| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 2.04 r_work: 0.3290 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.3739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16074 Z= 0.135 Angle : 0.579 7.726 21939 Z= 0.289 Chirality : 0.046 0.300 2685 Planarity : 0.004 0.045 2703 Dihedral : 4.335 19.699 2145 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 3.32 % Allowed : 16.03 % 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: 0.40 (0.19), residues: 1986 helix: 1.83 (0.24), residues: 486 sheet: 0.34 (0.21), residues: 591 loop : -0.61 (0.20), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 24 TYR 0.014 0.001 TYR A 239 PHE 0.014 0.001 PHE E 330 TRP 0.015 0.001 TRP H 47 HIS 0.005 0.001 HIS C 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.13 (16014) covalent geometry : angle 0.55148 / 0.28 (21780) SS BOND : bond 0.00336 / 0.23 ( 21) SS BOND : angle 0.85828 / 0.55 ( 42) hydrogen bonds : bond 0.03411 / 2.33 ( 691) hydrogen bonds : angle 4.88828 / 3.43 ( 2001) link_ALPHA1-3 : bond 0.00582 / 0.27 ( 3) link_ALPHA1-3 : angle 1.50489 / 0.82 ( 9) link_ALPHA1-6 : bond 0.00587 / 0.27 ( 3) link_ALPHA1-6 : angle 1.52591 / 0.83 ( 9) link_BETA1-4 : bond 0.00529 / 0.29 ( 18) link_BETA1-4 : angle 2.29390 / 1.42 ( 54) link_BETA1-6 : bond 0.00484 / 0.22 ( 3) link_BETA1-6 : angle 1.04031 / 0.57 ( 9) link_NAG-ASN : bond 0.00288 / 0.18 ( 12) link_NAG-ASN : angle 3.18967 / 1.74 ( 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 247 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 192 time to evaluate : 0.615 Fit side-chains REVERT: A 82 ARG cc_start: 0.8686 (tpt90) cc_final: 0.8427 (tmt-80) REVERT: A 167 LYS cc_start: 0.7911 (mtmt) cc_final: 0.7540 (mttt) REVERT: A 240 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.7362 (tm-30) REVERT: A 260 ASP cc_start: 0.8694 (m-30) cc_final: 0.8484 (m-30) REVERT: A 307 GLU cc_start: 0.8513 (mt-10) cc_final: 0.8240 (mt-10) REVERT: A 406 GLU cc_start: 0.7825 (pm20) cc_final: 0.7417 (pm20) REVERT: L 52 LYS cc_start: 0.8132 (ptpp) cc_final: 0.7879 (ptmt) REVERT: H 11 LEU cc_start: 0.6900 (tp) cc_final: 0.6662 (tm) REVERT: H 38 ARG cc_start: 0.8901 (OUTLIER) cc_final: 0.8608 (ptt180) REVERT: H 43 LYS cc_start: 0.8007 (mppt) cc_final: 0.7783 (mppt) REVERT: B 138 MET cc_start: 0.6390 (mmm) cc_final: 0.5879 (mmm) REVERT: B 399 ARG cc_start: 0.6606 (ptp-110) cc_final: 0.6271 (ptp-170) REVERT: C 52 LYS cc_start: 0.8157 (ptmm) cc_final: 0.7726 (ptmt) REVERT: D 1 GLN cc_start: 0.7362 (pt0) cc_final: 0.6985 (pt0) REVERT: D 72 ASP cc_start: 0.8653 (OUTLIER) cc_final: 0.8290 (t70) REVERT: E 115 MET cc_start: 0.8886 (mtm) cc_final: 0.8550 (mtm) REVERT: E 138 MET cc_start: 0.6445 (mmm) cc_final: 0.6022 (mmm) REVERT: E 240 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7575 (tm-30) REVERT: E 399 ARG cc_start: 0.6779 (ptp-110) cc_final: 0.6233 (ptp-170) REVERT: F 52 LYS cc_start: 0.8201 (ptpp) cc_final: 0.7916 (ptmt) REVERT: G 46 GLU cc_start: 0.8469 (tt0) cc_final: 0.8247 (pt0) outliers start: 55 outliers final: 33 residues processed: 226 average time/residue: 0.4459 time to fit residues: 114.6029 Evaluate side-chains 221 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 184 time to evaluate : 0.603 ------------------------------------------------------------------------------- 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 H residue 72 ASP 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 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 53 SER Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 53 THR 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: 0.5980 chunk 27 optimal weight: 1.9990 chunk 144 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 36 optimal weight: 0.0010 chunk 85 optimal weight: 0.6980 chunk 96 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 chunk 37 optimal weight: 0.1980 overall best weight: 0.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 182 ASN A 224 ASN H 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 = 0.3687 r_free = 0.3687 target = 0.138597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.116218 restraints weight = 20110.051| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 2.02 r_work: 0.3317 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.3815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16074 Z= 0.127 Angle : 0.562 7.718 21939 Z= 0.280 Chirality : 0.045 0.287 2685 Planarity : 0.004 0.045 2703 Dihedral : 4.192 19.622 2145 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 3.25 % Allowed : 16.46 % Favored : 80.29 % 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: 1.92 (0.24), residues: 486 sheet: 0.38 (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 0.013 0.001 TYR B 239 PHE 0.015 0.001 PHE E 330 TRP 0.016 0.001 TRP H 47 HIS 0.004 0.001 HIS C 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (16014) covalent geometry : angle 0.53555 / 0.27 (21780) SS BOND : bond 0.00301 / 0.20 ( 21) SS BOND : angle 0.75395 / 0.48 ( 42) hydrogen bonds : bond 0.03227 / 2.22 ( 691) hydrogen bonds : angle 4.72671 / 3.31 ( 2001) link_ALPHA1-3 : bond 0.00568 / 0.26 ( 3) link_ALPHA1-3 : angle 1.43619 / 0.78 ( 9) link_ALPHA1-6 : bond 0.00614 / 0.28 ( 3) link_ALPHA1-6 : angle 1.48031 / 0.80 ( 9) link_BETA1-4 : bond 0.00511 / 0.28 ( 18) link_BETA1-4 : angle 2.19114 / 1.35 ( 54) link_BETA1-6 : bond 0.00458 / 0.21 ( 3) link_BETA1-6 : angle 1.05313 / 0.58 ( 9) link_NAG-ASN : bond 0.00314 / 0.19 ( 12) link_NAG-ASN : angle 3.09327 / 1.69 ( 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 256 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 202 time to evaluate : 0.587 Fit side-chains REVERT: A 82 ARG cc_start: 0.8693 (tpt90) cc_final: 0.8431 (tmt-80) REVERT: A 167 LYS cc_start: 0.7912 (mtmt) cc_final: 0.7511 (mttt) REVERT: A 240 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7284 (tm-30) REVERT: A 260 ASP cc_start: 0.8701 (m-30) cc_final: 0.8497 (m-30) REVERT: A 307 GLU cc_start: 0.8439 (mt-10) cc_final: 0.8163 (tt0) REVERT: A 406 GLU cc_start: 0.7855 (pm20) cc_final: 0.7500 (pm20) REVERT: L 52 LYS cc_start: 0.8064 (ptpp) cc_final: 0.7785 (ptmt) REVERT: H 38 ARG cc_start: 0.8907 (OUTLIER) cc_final: 0.8578 (ptt180) REVERT: H 43 LYS cc_start: 0.8039 (mppt) cc_final: 0.7615 (mptt) REVERT: H 46 GLU cc_start: 0.8510 (tt0) cc_final: 0.8306 (pt0) REVERT: B 138 MET cc_start: 0.6494 (mmm) cc_final: 0.6042 (mmm) REVERT: B 167 LYS cc_start: 0.7843 (mtmm) cc_final: 0.7615 (mttt) REVERT: B 399 ARG cc_start: 0.6555 (ptp-110) cc_final: 0.6230 (ptp-170) REVERT: C 52 LYS cc_start: 0.8218 (ptmm) cc_final: 0.7819 (ptmt) REVERT: E 115 MET cc_start: 0.8877 (OUTLIER) cc_final: 0.8521 (mtm) REVERT: E 142 ASP cc_start: 0.7963 (OUTLIER) cc_final: 0.7370 (t0) REVERT: E 240 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7462 (tm-30) REVERT: E 399 ARG cc_start: 0.6793 (ptp-110) cc_final: 0.6257 (ptp-170) REVERT: F 52 LYS cc_start: 0.8117 (ptpp) cc_final: 0.7877 (ptmt) REVERT: G 43 LYS cc_start: 0.8094 (mmtt) cc_final: 0.7839 (mptt) REVERT: G 46 GLU cc_start: 0.8460 (tt0) cc_final: 0.8236 (pt0) outliers start: 54 outliers final: 34 residues processed: 238 average time/residue: 0.4517 time to fit residues: 122.3768 Evaluate side-chains 235 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 196 time to evaluate : 0.729 ------------------------------------------------------------------------------- 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 H residue 72 ASP 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 422 LEU Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 48 VAL 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 E residue 69 SER Chi-restraints excluded: chain E residue 115 MET Chi-restraints excluded: chain E residue 142 ASP 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 392 CYS Chi-restraints excluded: chain E residue 415 THR Chi-restraints excluded: chain F residue 53 SER Chi-restraints excluded: chain G residue 7 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: 4.9990 chunk 91 optimal weight: 0.9980 chunk 75 optimal weight: 0.7980 chunk 142 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 51 optimal weight: 4.9990 chunk 137 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 127 optimal weight: 4.9990 chunk 90 optimal weight: 1.9990 chunk 189 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 224 ASN H 1 GLN D 1 GLN E 224 ASN ** F 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3672 r_free = 0.3672 target = 0.137512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.114854 restraints weight = 20149.940| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 2.04 r_work: 0.3286 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.3871 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= 0.165 Angle : 0.595 9.098 21939 Z= 0.294 Chirality : 0.047 0.289 2685 Planarity : 0.004 0.045 2703 Dihedral : 4.243 19.955 2145 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.89 % Allowed : 17.12 % Favored : 79.99 % 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: 0.47 (0.19), residues: 1986 helix: 1.88 (0.24), residues: 486 sheet: 0.37 (0.21), residues: 576 loop : -0.54 (0.20), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 24 TYR 0.015 0.001 TYR A 239 PHE 0.016 0.001 PHE E 330 TRP 0.015 0.002 TRP D 47 HIS 0.006 0.001 HIS F 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.17 (16014) covalent geometry : angle 0.56952 / 0.29 (21780) SS BOND : bond 0.00335 / 0.22 ( 21) SS BOND : angle 0.84940 / 0.54 ( 42) hydrogen bonds : bond 0.03404 / 2.34 ( 691) hydrogen bonds : angle 4.79906 / 3.36 ( 2001) link_ALPHA1-3 : bond 0.00511 / 0.24 ( 3) link_ALPHA1-3 : angle 1.44997 / 0.79 ( 9) link_ALPHA1-6 : bond 0.00568 / 0.26 ( 3) link_ALPHA1-6 : angle 1.54122 / 0.83 ( 9) link_BETA1-4 : bond 0.00523 / 0.28 ( 18) link_BETA1-4 : angle 2.23372 / 1.39 ( 54) link_BETA1-6 : bond 0.00392 / 0.18 ( 3) link_BETA1-6 : angle 1.07606 / 0.59 ( 9) link_NAG-ASN : bond 0.00270 / 0.17 ( 12) link_NAG-ASN : angle 3.15857 / 1.72 ( 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 245 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 197 time to evaluate : 0.387 Fit side-chains REVERT: A 82 ARG cc_start: 0.8737 (tpt90) cc_final: 0.8456 (tmt-80) REVERT: A 240 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7327 (tm-30) REVERT: A 260 ASP cc_start: 0.8686 (m-30) cc_final: 0.8471 (m-30) REVERT: A 307 GLU cc_start: 0.8411 (mt-10) cc_final: 0.8189 (tt0) REVERT: A 406 GLU cc_start: 0.7843 (pm20) cc_final: 0.7544 (pm20) REVERT: L 52 LYS cc_start: 0.8133 (ptpp) cc_final: 0.7885 (ptmt) REVERT: H 38 ARG cc_start: 0.8912 (OUTLIER) cc_final: 0.8627 (ptt180) REVERT: H 43 LYS cc_start: 0.8069 (mppt) cc_final: 0.7632 (mptt) REVERT: B 138 MET cc_start: 0.6455 (mmm) cc_final: 0.5989 (mmm) REVERT: B 399 ARG cc_start: 0.6669 (ptp-110) cc_final: 0.6342 (ptp-170) REVERT: C 52 LYS cc_start: 0.8206 (ptmm) cc_final: 0.7793 (ptmt) REVERT: D 1 GLN cc_start: 0.7426 (pt0) cc_final: 0.7083 (pt0) REVERT: E 115 MET cc_start: 0.8862 (mtm) cc_final: 0.8505 (mtm) REVERT: E 138 MET cc_start: 0.6588 (mmm) cc_final: 0.6189 (mmm) REVERT: E 240 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.7562 (tm-30) REVERT: E 399 ARG cc_start: 0.6747 (ptp-110) cc_final: 0.6211 (ptp-170) REVERT: F 52 LYS cc_start: 0.8151 (ptpp) cc_final: 0.7871 (ptmt) REVERT: G 43 LYS cc_start: 0.8110 (mmtt) cc_final: 0.7799 (mptt) REVERT: G 46 GLU cc_start: 0.8445 (tt0) cc_final: 0.8239 (pt0) REVERT: G 70 ASN cc_start: 0.7931 (OUTLIER) cc_final: 0.7697 (m-40) outliers start: 48 outliers final: 34 residues processed: 226 average time/residue: 0.4221 time to fit residues: 108.4533 Evaluate side-chains 225 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 187 time to evaluate : 0.375 ------------------------------------------------------------------------------- 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 H residue 72 ASP 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 440 SER Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 90 HIS Chi-restraints excluded: chain D residue 70 ASN Chi-restraints excluded: chain E residue 69 SER 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 22 THR 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 Chi-restraints excluded: chain G residue 70 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 107 optimal weight: 0.6980 chunk 141 optimal weight: 0.6980 chunk 48 optimal weight: 0.8980 chunk 125 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 90 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 chunk 83 optimal weight: 0.8980 chunk 114 optimal weight: 4.9990 chunk 36 optimal weight: 0.0010 chunk 150 optimal weight: 0.9990 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 224 ASN H 1 GLN E 224 ASN ** 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 = 0.3636 r_free = 0.3636 target = 0.136664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.116361 restraints weight = 20341.882| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 1.75 r_work: 0.3321 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.3906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16074 Z= 0.135 Angle : 0.570 7.033 21939 Z= 0.283 Chirality : 0.046 0.286 2685 Planarity : 0.004 0.045 2703 Dihedral : 4.199 19.771 2145 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.22 % Favored : 96.73 % Rotamer: Outliers : 2.77 % Allowed : 17.24 % Favored : 79.99 % 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: 0.51 (0.19), residues: 1986 helix: 1.95 (0.24), residues: 486 sheet: 0.39 (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 F 24 TYR 0.013 0.001 TYR A 239 PHE 0.016 0.001 PHE E 330 TRP 0.015 0.001 TRP D 47 HIS 0.005 0.001 HIS C 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.13 (16014) covalent geometry : angle 0.54430 / 0.28 (21780) SS BOND : bond 0.00309 / 0.21 ( 21) SS BOND : angle 0.76731 / 0.49 ( 42) hydrogen bonds : bond 0.03267 / 2.24 ( 691) hydrogen bonds : angle 4.73000 / 3.31 ( 2001) link_ALPHA1-3 : bond 0.00533 / 0.25 ( 3) link_ALPHA1-3 : angle 1.41239 / 0.77 ( 9) link_ALPHA1-6 : bond 0.00600 / 0.28 ( 3) link_ALPHA1-6 : angle 1.50215 / 0.81 ( 9) link_BETA1-4 : bond 0.00497 / 0.27 ( 18) link_BETA1-4 : angle 2.17858 / 1.34 ( 54) link_BETA1-6 : bond 0.00449 / 0.20 ( 3) link_BETA1-6 : angle 1.03532 / 0.57 ( 9) link_NAG-ASN : bond 0.00337 / 0.21 ( 12) link_NAG-ASN : angle 3.10673 / 1.68 ( 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 238 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 192 time to evaluate : 0.603 Fit side-chains REVERT: A 82 ARG cc_start: 0.8642 (tpt90) cc_final: 0.8368 (tmt-80) REVERT: A 240 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7233 (tm-30) REVERT: A 260 ASP cc_start: 0.8649 (m-30) cc_final: 0.8442 (m-30) REVERT: A 307 GLU cc_start: 0.8398 (mt-10) cc_final: 0.8183 (tt0) REVERT: A 406 GLU cc_start: 0.7890 (pm20) cc_final: 0.7589 (pm20) REVERT: A 416 THR cc_start: 0.7720 (p) cc_final: 0.7266 (t) REVERT: L 52 LYS cc_start: 0.8008 (ptpp) cc_final: 0.7767 (ptmt) REVERT: H 38 ARG cc_start: 0.8840 (OUTLIER) cc_final: 0.8543 (ptt180) REVERT: H 43 LYS cc_start: 0.7987 (mppt) cc_final: 0.7582 (mptt) REVERT: B 138 MET cc_start: 0.6307 (mmm) cc_final: 0.5847 (mmm) REVERT: B 399 ARG cc_start: 0.6629 (ptp-110) cc_final: 0.6305 (ptp-170) REVERT: C 52 LYS cc_start: 0.8194 (ptmm) cc_final: 0.7803 (ptmt) REVERT: E 115 MET cc_start: 0.8789 (OUTLIER) cc_final: 0.8424 (mtm) REVERT: E 138 MET cc_start: 0.6371 (mmm) cc_final: 0.6019 (mmm) REVERT: E 142 ASP cc_start: 0.7935 (OUTLIER) cc_final: 0.7344 (t0) REVERT: E 240 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7477 (tm-30) REVERT: E 399 ARG cc_start: 0.6740 (ptp-110) cc_final: 0.6201 (ptp-170) REVERT: F 52 LYS cc_start: 0.8090 (ptpp) cc_final: 0.7852 (ptmt) REVERT: G 46 GLU cc_start: 0.8398 (tt0) cc_final: 0.8118 (pt0) REVERT: G 70 ASN cc_start: 0.7890 (OUTLIER) cc_final: 0.7390 (m-40) outliers start: 46 outliers final: 33 residues processed: 222 average time/residue: 0.4479 time to fit residues: 113.5475 Evaluate side-chains 225 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 186 time to evaluate : 0.539 ------------------------------------------------------------------------------- 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 H residue 72 ASP 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 48 VAL Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 90 HIS Chi-restraints excluded: chain D residue 70 ASN Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain E residue 115 MET 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 392 CYS Chi-restraints excluded: chain E residue 415 THR Chi-restraints excluded: chain F residue 22 THR 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 Chi-restraints excluded: chain G residue 70 ASN 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: 0.0770 chunk 27 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 136 optimal weight: 0.9980 chunk 100 optimal weight: 0.9990 chunk 85 optimal weight: 0.7980 chunk 64 optimal weight: 0.5980 chunk 76 optimal weight: 0.4980 chunk 143 optimal weight: 0.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 224 ASN H 1 GLN D 1 GLN E 224 ASN ** F 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3642 r_free = 0.3642 target = 0.137694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.117929 restraints weight = 20383.855| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 1.65 r_work: 0.3320 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3205 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.3957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16074 Z= 0.137 Angle : 0.570 6.957 21939 Z= 0.283 Chirality : 0.046 0.283 2685 Planarity : 0.004 0.044 2703 Dihedral : 4.188 20.152 2145 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.95 % Allowed : 17.36 % Favored : 79.69 % 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: 0.54 (0.19), residues: 1986 helix: 1.96 (0.24), residues: 486 sheet: 0.40 (0.21), residues: 576 loop : -0.50 (0.20), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 24 TYR 0.013 0.001 TYR A 239 PHE 0.016 0.001 PHE E 330 TRP 0.015 0.001 TRP D 47 HIS 0.005 0.001 HIS C 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (16014) covalent geometry : angle 0.54486 / 0.28 (21780) SS BOND : bond 0.00304 / 0.20 ( 21) SS BOND : angle 0.76361 / 0.49 ( 42) hydrogen bonds : bond 0.03254 / 2.24 ( 691) hydrogen bonds : angle 4.70875 / 3.29 ( 2001) link_ALPHA1-3 : bond 0.00510 / 0.24 ( 3) link_ALPHA1-3 : angle 1.39860 / 0.76 ( 9) link_ALPHA1-6 : bond 0.00610 / 0.28 ( 3) link_ALPHA1-6 : angle 1.50474 / 0.81 ( 9) link_BETA1-4 : bond 0.00505 / 0.27 ( 18) link_BETA1-4 : angle 2.14847 / 1.33 ( 54) link_BETA1-6 : bond 0.00406 / 0.19 ( 3) link_BETA1-6 : angle 1.07037 / 0.58 ( 9) link_NAG-ASN : bond 0.00298 / 0.18 ( 12) link_NAG-ASN : angle 3.07034 / 1.67 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4940.09 seconds wall clock time: 85 minutes 8.05 seconds (5108.05 seconds total)