Starting phenix.real_space_refine on Sun Feb 8 11:10:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9iyi_60997/02_2026/9iyi_60997_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9iyi_60997/02_2026/9iyi_60997.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9iyi_60997/02_2026/9iyi_60997.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9iyi_60997/02_2026/9iyi_60997.map" model { file = "/net/cci-nas-00/data/ceres_data/9iyi_60997/02_2026/9iyi_60997_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9iyi_60997/02_2026/9iyi_60997_neut.cif" } resolution = 3.73 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= 0.005 sd= 0.042 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 288 5.16 5 C 28101 2.51 5 N 7623 2.21 5 O 8577 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 210 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 44589 Number of models: 1 Model: "" Number of chains: 29 Chain: "S" Number of atoms: 1671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1671 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 11, 'TRANS': 212} Chain: "T" Number of atoms: 1631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1631 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 10, 'TRANS': 200} Chain: "A" Number of atoms: 3325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3325 Classifications: {'peptide': 439} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 411} Chain: "B" Number of atoms: 3325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3325 Classifications: {'peptide': 439} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 411} Chain: "C" Number of atoms: 3325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3325 Classifications: {'peptide': 439} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 411} Chain: "D" Number of atoms: 3325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3325 Classifications: {'peptide': 439} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 411} Chain: "E" Number of atoms: 3282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3282 Classifications: {'peptide': 419} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 31, 'TRANS': 387} Chain: "F" Number of atoms: 3282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3282 Classifications: {'peptide': 419} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 31, 'TRANS': 387} Chain: "G" Number of atoms: 3282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3282 Classifications: {'peptide': 419} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 31, 'TRANS': 387} Chain: "H" Number of atoms: 3263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3263 Classifications: {'peptide': 417} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 31, 'TRANS': 385} Chain: "I" Number of atoms: 1156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1156 Classifications: {'peptide': 151} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 143} Chain: "J" Number of atoms: 1156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1156 Classifications: {'peptide': 151} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 143} Chain: "K" Number of atoms: 1156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1156 Classifications: {'peptide': 151} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 143} Chain: "L" Number of atoms: 1156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1156 Classifications: {'peptide': 151} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 143} Chain: "Q" Number of atoms: 1671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1671 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 11, 'TRANS': 212} Chain: "R" Number of atoms: 1631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1631 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 10, 'TRANS': 200} Chain: "O" Number of atoms: 1671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1671 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 11, 'TRANS': 212} Chain: "P" Number of atoms: 1631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1631 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 10, 'TRANS': 200} Chain: "M" Number of atoms: 1671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1671 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 11, 'TRANS': 212} Chain: "N" Number of atoms: 1631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1631 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 10, 'TRANS': 200} Chain: "U" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "V" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'FUC': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "W" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "X" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "Y" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 29 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 10.54, per 1000 atoms: 0.24 Number of scatterers: 44589 At special positions: 0 Unit cell: (210.38, 210.38, 234.5, 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 288 16.00 O 8577 8.00 N 7623 7.00 C 28101 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=73, symmetry=0 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.05 Simple disulfide: pdb=" SG CYS S 151 " - pdb=" SG CYS S 207 " distance=2.16 Simple disulfide: pdb=" SG CYS T 23 " - pdb=" SG CYS T 88 " distance=2.05 Simple disulfide: pdb=" SG CYS T 135 " - pdb=" SG CYS T 195 " distance=2.24 Simple disulfide: pdb=" SG CYS A 49 " - pdb=" SG CYS A 114 " distance=2.02 Simple disulfide: pdb=" SG CYS A 62 " - pdb=" SG CYS A 94 " distance=2.10 Simple disulfide: pdb=" SG CYS A 63 " - pdb=" SG CYS A 96 " distance=2.02 Simple disulfide: pdb=" SG CYS A 68 " - pdb=" SG CYS A 78 " distance=2.14 Simple disulfide: pdb=" SG CYS A 259 " - pdb=" SG CYS A 271 " distance=2.03 Simple disulfide: pdb=" SG CYS A 301 " - pdb=" SG CYS A 376 " distance=2.02 Simple disulfide: pdb=" SG CYS A 306 " - pdb=" SG CYS A 380 " distance=2.01 Simple disulfide: pdb=" SG CYS A 328 " - pdb=" SG CYS A 370 " distance=2.01 Simple disulfide: pdb=" SG CYS B 49 " - pdb=" SG CYS B 114 " distance=2.03 Simple disulfide: pdb=" SG CYS B 62 " - pdb=" SG CYS B 94 " distance=2.11 Simple disulfide: pdb=" SG CYS B 63 " - pdb=" SG CYS B 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 68 " - pdb=" SG CYS B 78 " distance=2.09 Simple disulfide: pdb=" SG CYS B 259 " - pdb=" SG CYS B 271 " distance=2.03 Simple disulfide: pdb=" SG CYS B 301 " - pdb=" SG CYS B 376 " distance=2.09 Simple disulfide: pdb=" SG CYS B 306 " - pdb=" SG CYS B 380 " distance=2.04 Simple disulfide: pdb=" SG CYS B 328 " - pdb=" SG CYS B 370 " distance=2.01 Simple disulfide: pdb=" SG CYS C 49 " - pdb=" SG CYS C 114 " distance=2.02 Simple disulfide: pdb=" SG CYS C 62 " - pdb=" SG CYS C 94 " distance=2.03 Simple disulfide: pdb=" SG CYS C 63 " - pdb=" SG CYS C 96 " distance=2.20 Simple disulfide: pdb=" SG CYS C 68 " - pdb=" SG CYS C 78 " distance=2.03 Simple disulfide: pdb=" SG CYS C 259 " - pdb=" SG CYS C 271 " distance=2.03 Simple disulfide: pdb=" SG CYS C 301 " - pdb=" SG CYS C 376 " distance=2.03 Simple disulfide: pdb=" SG CYS C 306 " - pdb=" SG CYS C 380 " distance=2.03 Simple disulfide: pdb=" SG CYS C 328 " - pdb=" SG CYS C 370 " distance=2.02 Simple disulfide: pdb=" SG CYS D 49 " - pdb=" SG CYS D 114 " distance=2.02 Simple disulfide: pdb=" SG CYS D 62 " - pdb=" SG CYS D 94 " distance=2.04 Simple disulfide: pdb=" SG CYS D 63 " - pdb=" SG CYS D 96 " distance=2.07 Simple disulfide: pdb=" SG CYS D 68 " - pdb=" SG CYS D 78 " distance=2.07 Simple disulfide: pdb=" SG CYS D 259 " - pdb=" SG CYS D 271 " distance=2.03 Simple disulfide: pdb=" SG CYS D 301 " - pdb=" SG CYS D 376 " distance=2.03 Simple disulfide: pdb=" SG CYS D 306 " - pdb=" SG CYS D 380 " distance=2.03 Simple disulfide: pdb=" SG CYS D 328 " - pdb=" SG CYS D 370 " distance=2.03 Simple disulfide: pdb=" SG CYS E 19 " - pdb=" SG CYS E 125 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 28 " distance=2.03 Simple disulfide: pdb=" SG CYS E 91 " - pdb=" SG CYS E 105 " distance=2.04 Simple disulfide: pdb=" SG CYS E 153 " - pdb=" SG CYS E 266 " distance=2.03 Simple disulfide: pdb=" SG CYS E 201 " - pdb=" SG CYS E 225 " distance=2.02 Simple disulfide: pdb=" SG CYS E 203 " - pdb=" SG CYS E 220 " distance=2.04 Simple disulfide: pdb=" SG CYS F 19 " - pdb=" SG CYS F 125 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 28 " distance=2.02 Simple disulfide: pdb=" SG CYS F 91 " - pdb=" SG CYS F 105 " distance=2.03 Simple disulfide: pdb=" SG CYS F 153 " - pdb=" SG CYS F 266 " distance=2.04 Simple disulfide: pdb=" SG CYS F 201 " - pdb=" SG CYS F 225 " distance=2.15 Simple disulfide: pdb=" SG CYS F 203 " - pdb=" SG CYS F 220 " distance=2.04 Simple disulfide: pdb=" SG CYS G 19 " - pdb=" SG CYS G 125 " distance=2.02 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 28 " distance=2.03 Simple disulfide: pdb=" SG CYS G 91 " - pdb=" SG CYS G 105 " distance=2.03 Simple disulfide: pdb=" SG CYS G 153 " - pdb=" SG CYS G 266 " distance=2.03 Simple disulfide: pdb=" SG CYS G 201 " - pdb=" SG CYS G 225 " distance=2.22 Simple disulfide: pdb=" SG CYS G 203 " - pdb=" SG CYS G 220 " distance=2.02 Simple disulfide: pdb=" SG CYS H 19 " - pdb=" SG CYS H 125 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 28 " distance=2.03 Simple disulfide: pdb=" SG CYS H 91 " - pdb=" SG CYS H 105 " distance=2.03 Simple disulfide: pdb=" SG CYS H 153 " - pdb=" SG CYS H 266 " distance=2.03 Simple disulfide: pdb=" SG CYS H 201 " - pdb=" SG CYS H 225 " distance=2.19 Simple disulfide: pdb=" SG CYS H 203 " - pdb=" SG CYS H 220 " distance=2.04 Simple disulfide: pdb=" SG CYS I 113 " - pdb=" SG CYS I 128 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 22 " - pdb=" SG CYS Q 96 " distance=2.02 Simple disulfide: pdb=" SG CYS Q 151 " - pdb=" SG CYS Q 207 " distance=2.03 Simple disulfide: pdb=" SG CYS R 23 " - pdb=" SG CYS R 88 " distance=2.05 Simple disulfide: pdb=" SG CYS R 135 " - pdb=" SG CYS R 195 " distance=2.14 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 96 " distance=1.78 Simple disulfide: pdb=" SG CYS O 151 " - pdb=" SG CYS O 207 " distance=2.11 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 88 " distance=2.02 Simple disulfide: pdb=" SG CYS P 135 " - pdb=" SG CYS P 195 " distance=2.14 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 96 " distance=2.05 Simple disulfide: pdb=" SG CYS M 151 " - pdb=" SG CYS M 207 " distance=2.04 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.02 Simple disulfide: pdb=" SG CYS N 135 " - pdb=" SG CYS N 195 " distance=2.02 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=7, symmetry=0 Links applied ALPHA1-3 " MAN U 3 " - " MAN U 4 " ALPHA1-4 " NAG U 2 " - " MAN U 3 " " NAG V 2 " - " MAN V 3 " BETA1-4 " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " BETA1-6 " NAG U 1 " - " FUC U 6 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " MAN U 3 " - " BMA U 5 " " NAG V 1 " - " FUC V 4 " " NAG W 1 " - " FUC W 3 " " NAG X 1 " - " FUC X 4 " NAG-ASN " NAG U 1 " - " ASN A 141 " " NAG V 1 " - " ASN B 141 " " NAG W 1 " - " ASN C 141 " " NAG X 1 " - " ASN D 141 " " NAG Y 1 " - " ASN E 263 " Number of additional bonds: simple=7, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.00 Conformation dependent library (CDL) restraints added in 2.2 seconds 11468 Ramachandran restraints generated. 5734 Oldfield, 0 Emsley, 5734 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10692 Finding SS restraints... Secondary structure from input PDB file: 87 helices and 110 sheets defined 12.5% alpha, 31.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.02 Creating SS restraints... Processing helix chain 'S' and resid 53 through 56 Processing helix chain 'S' and resid 62 through 65 Processing helix chain 'S' and resid 87 through 91 Processing helix chain 'S' and resid 167 through 169 No H-bonds generated for 'chain 'S' and resid 167 through 169' Processing helix chain 'S' and resid 196 through 200 Processing helix chain 'S' and resid 212 through 215 Processing helix chain 'T' and resid 79 through 83 removed outlier: 4.095A pdb=" N PHE T 83 " --> pdb=" O PRO T 80 " (cutoff:3.500A) Processing helix chain 'T' and resid 122 through 127 Processing helix chain 'T' and resid 184 through 188 Processing helix chain 'A' and resid 112 through 116 removed outlier: 3.542A pdb=" N LYS A 115 " --> pdb=" O GLU A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 246 Processing helix chain 'A' and resid 250 through 255 Processing helix chain 'A' and resid 403 through 438 removed outlier: 3.666A pdb=" N TRP A 409 " --> pdb=" O THR A 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 116 Processing helix chain 'B' and resid 238 through 246 Processing helix chain 'B' and resid 250 through 255 Processing helix chain 'B' and resid 283 through 287 Processing helix chain 'B' and resid 399 through 403 Processing helix chain 'B' and resid 407 through 438 removed outlier: 3.591A pdb=" N GLN B 411 " --> pdb=" O MET B 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'C' and resid 238 through 246 removed outlier: 3.527A pdb=" N TYR C 242 " --> pdb=" O SER C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 255 Processing helix chain 'C' and resid 283 through 287 Processing helix chain 'C' and resid 407 through 436 removed outlier: 3.615A pdb=" N GLN C 411 " --> pdb=" O MET C 407 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 116 Processing helix chain 'D' and resid 238 through 246 removed outlier: 3.550A pdb=" N TYR D 242 " --> pdb=" O SER D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 255 Processing helix chain 'D' and resid 256 through 259 Processing helix chain 'D' and resid 283 through 287 Processing helix chain 'D' and resid 404 through 406 No H-bonds generated for 'chain 'D' and resid 404 through 406' Processing helix chain 'D' and resid 407 through 436 Processing helix chain 'E' and resid 5 through 10 removed outlier: 4.017A pdb=" N VAL E 8 " --> pdb=" O ASN E 5 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 83 No H-bonds generated for 'chain 'E' and resid 81 through 83' Processing helix chain 'E' and resid 221 through 223 No H-bonds generated for 'chain 'E' and resid 221 through 223' Processing helix chain 'E' and resid 351 through 363 removed outlier: 4.005A pdb=" N LEU E 357 " --> pdb=" O HIS E 353 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 402 Proline residue: E 399 - end of helix Processing helix chain 'E' and resid 409 through 417 Processing helix chain 'F' and resid 8 through 12 removed outlier: 4.145A pdb=" N ALA F 11 " --> pdb=" O VAL F 8 " (cutoff:3.500A) Processing helix chain 'F' and resid 81 through 83 No H-bonds generated for 'chain 'F' and resid 81 through 83' Processing helix chain 'F' and resid 221 through 223 No H-bonds generated for 'chain 'F' and resid 221 through 223' Processing helix chain 'F' and resid 351 through 363 Processing helix chain 'F' and resid 363 through 396 Processing helix chain 'F' and resid 397 through 403 Processing helix chain 'F' and resid 409 through 417 Processing helix chain 'G' and resid 6 through 10 Processing helix chain 'G' and resid 81 through 83 No H-bonds generated for 'chain 'G' and resid 81 through 83' Processing helix chain 'G' and resid 351 through 363 Processing helix chain 'G' and resid 363 through 403 Proline residue: G 399 - end of helix Processing helix chain 'G' and resid 409 through 416 Processing helix chain 'H' and resid 81 through 83 No H-bonds generated for 'chain 'H' and resid 81 through 83' Processing helix chain 'H' and resid 178 through 181 Processing helix chain 'H' and resid 351 through 363 Processing helix chain 'H' and resid 365 through 402 Proline residue: H 399 - end of helix Processing helix chain 'H' and resid 409 through 417 Processing helix chain 'I' and resid 146 through 151 Processing helix chain 'I' and resid 168 through 175 removed outlier: 4.889A pdb=" N SER I 173 " --> pdb=" O HIS I 170 " (cutoff:3.500A) Processing helix chain 'J' and resid 168 through 175 removed outlier: 5.170A pdb=" N SER J 173 " --> pdb=" O HIS J 170 " (cutoff:3.500A) Processing helix chain 'K' and resid 146 through 151 Processing helix chain 'L' and resid 146 through 151 Processing helix chain 'Q' and resid 28 through 32 Processing helix chain 'Q' and resid 53 through 56 Processing helix chain 'Q' and resid 62 through 65 Processing helix chain 'Q' and resid 87 through 91 Processing helix chain 'Q' and resid 167 through 169 No H-bonds generated for 'chain 'Q' and resid 167 through 169' Processing helix chain 'Q' and resid 196 through 200 Processing helix chain 'Q' and resid 213 through 215 No H-bonds generated for 'chain 'Q' and resid 213 through 215' Processing helix chain 'R' and resid 79 through 83 removed outlier: 3.995A pdb=" N PHE R 83 " --> pdb=" O PRO R 80 " (cutoff:3.500A) Processing helix chain 'R' and resid 122 through 127 Processing helix chain 'R' and resid 184 through 188 Processing helix chain 'O' and resid 28 through 32 removed outlier: 4.021A pdb=" N TYR O 32 " --> pdb=" O PHE O 29 " (cutoff:3.500A) Processing helix chain 'O' and resid 53 through 56 Processing helix chain 'O' and resid 87 through 91 Processing helix chain 'O' and resid 167 through 169 No H-bonds generated for 'chain 'O' and resid 167 through 169' Processing helix chain 'O' and resid 196 through 200 Processing helix chain 'P' and resid 122 through 127 Processing helix chain 'P' and resid 184 through 188 Processing helix chain 'M' and resid 28 through 32 removed outlier: 3.849A pdb=" N TYR M 32 " --> pdb=" O PHE M 29 " (cutoff:3.500A) Processing helix chain 'M' and resid 53 through 56 Processing helix chain 'M' and resid 62 through 65 Processing helix chain 'M' and resid 87 through 91 Processing helix chain 'M' and resid 138 through 143 removed outlier: 3.657A pdb=" N SER M 143 " --> pdb=" O SER M 139 " (cutoff:3.500A) Processing helix chain 'M' and resid 167 through 169 No H-bonds generated for 'chain 'M' and resid 167 through 169' Processing helix chain 'M' and resid 196 through 200 Processing helix chain 'M' and resid 212 through 215 Processing helix chain 'N' and resid 79 through 83 removed outlier: 4.068A pdb=" N PHE N 83 " --> pdb=" O PRO N 80 " (cutoff:3.500A) Processing helix chain 'N' and resid 122 through 127 Processing helix chain 'N' and resid 184 through 189 Processing sheet with id=AA1, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'S' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'S' and resid 10 through 12 current: chain 'S' and resid 46 through 51 WARNING: can't find start of bonding for strands! previous: chain 'S' and resid 58 through 60 current: chain 'S' and resid 111 through 114 Processing sheet with id=AA3, first strand: chain 'S' and resid 131 through 135 WARNING: can't find start of bonding for strands! previous: chain 'S' and resid 147 through 156 current: chain 'S' and resid 187 through 195 Processing sheet with id=AA4, first strand: chain 'S' and resid 162 through 165 removed outlier: 4.579A pdb=" N TYR S 205 " --> pdb=" O VAL S 222 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'T' and resid 4 through 6 Processing sheet with id=AA6, first strand: chain 'T' and resid 10 through 13 removed outlier: 6.395A pdb=" N LEU T 11 " --> pdb=" O GLU T 106 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'T' and resid 53 through 54 removed outlier: 6.593A pdb=" N TRP T 35 " --> pdb=" O LEU T 47 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'T' and resid 115 through 119 removed outlier: 5.780A pdb=" N TYR T 174 " --> pdb=" O ASN T 139 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'T' and resid 154 through 156 removed outlier: 4.594A pdb=" N TRP T 149 " --> pdb=" O GLN T 156 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 2 through 8 removed outlier: 3.574A pdb=" N SER A 279 " --> pdb=" O ILE A 162 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 14 through 19 removed outlier: 3.611A pdb=" N GLU A 30 " --> pdb=" O LEU A 136 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N LYS A 132 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N VAL A 36 " --> pdb=" O SER A 130 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N SER A 130 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N LEU A 38 " --> pdb=" O SER A 128 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N SER A 128 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N THR A 126 " --> pdb=" O PRO A 40 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N LEU A 42 " --> pdb=" O ALA A 124 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N ALA A 124 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N LEU A 44 " --> pdb=" O TYR A 122 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N TYR A 122 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N TYR A 46 " --> pdb=" O SER A 120 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N SER A 120 " --> pdb=" O TYR A 46 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 140 through 147 current: chain 'A' and resid 184 through 186 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 184 through 186 current: chain 'A' and resid 213 through 215 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 213 through 215 current: chain 'A' and resid 267 through 269 Processing sheet with id=AB3, first strand: chain 'A' and resid 51 through 54 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 51 through 54 current: chain 'A' and resid 101 through 110 No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 87 through 88 Processing sheet with id=AB5, first strand: chain 'A' and resid 220 through 221 Processing sheet with id=AB6, first strand: chain 'A' and resid 296 through 305 removed outlier: 4.117A pdb=" N MET A 299 " --> pdb=" O LYS A 319 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N LYS A 319 " --> pdb=" O MET A 299 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N CYS A 301 " --> pdb=" O VAL A 317 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N VAL A 317 " --> pdb=" O CYS A 301 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N VAL A 303 " --> pdb=" O VAL A 315 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N VAL A 315 " --> pdb=" O VAL A 303 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 343 through 346 removed outlier: 3.531A pdb=" N VAL A 346 " --> pdb=" O GLY A 326 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLY A 326 " --> pdb=" O VAL A 346 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 387 through 388 Processing sheet with id=AB9, first strand: chain 'B' and resid 2 through 8 Processing sheet with id=AC1, first strand: chain 'B' and resid 14 through 19 removed outlier: 3.637A pdb=" N GLU B 30 " --> pdb=" O LEU B 136 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N LYS B 132 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N VAL B 36 " --> pdb=" O SER B 130 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N SER B 130 " --> pdb=" O VAL B 36 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 140 through 147 current: chain 'B' and resid 267 through 269 Processing sheet with id=AC2, first strand: chain 'B' and resid 184 through 186 removed outlier: 6.578A pdb=" N ALA B 119 " --> pdb=" O ILE B 47 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N ILE B 47 " --> pdb=" O ALA B 119 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ALA B 121 " --> pdb=" O ASP B 45 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N THR B 41 " --> pdb=" O HIS B 125 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 51 through 54 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 51 through 54 current: chain 'B' and resid 101 through 110 No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'B' and resid 87 through 88 Processing sheet with id=AC5, first strand: chain 'B' and resid 220 through 221 Processing sheet with id=AC6, first strand: chain 'B' and resid 296 through 306 removed outlier: 5.494A pdb=" N ASP B 298 " --> pdb=" O ALA B 321 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N ALA B 321 " --> pdb=" O ASP B 298 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N VAL B 315 " --> pdb=" O PRO B 304 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 326 through 329 Processing sheet with id=AC8, first strand: chain 'B' and resid 331 through 332 Processing sheet with id=AC9, first strand: chain 'B' and resid 387 through 388 Processing sheet with id=AD1, first strand: chain 'C' and resid 2 through 8 Processing sheet with id=AD2, first strand: chain 'C' and resid 14 through 19 removed outlier: 4.622A pdb=" N GLU C 30 " --> pdb=" O LEU C 136 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LYS C 132 " --> pdb=" O LEU C 34 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N VAL C 36 " --> pdb=" O SER C 130 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N SER C 130 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N LEU C 38 " --> pdb=" O SER C 128 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N SER C 128 " --> pdb=" O LEU C 38 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N THR C 126 " --> pdb=" O PRO C 40 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N LEU C 42 " --> pdb=" O ALA C 124 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N ALA C 124 " --> pdb=" O LEU C 42 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N LEU C 44 " --> pdb=" O TYR C 122 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N TYR C 122 " --> pdb=" O LEU C 44 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N TYR C 46 " --> pdb=" O SER C 120 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N SER C 120 " --> pdb=" O TYR C 46 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 140 through 147 current: chain 'C' and resid 184 through 185 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 184 through 185 current: chain 'C' and resid 267 through 269 Processing sheet with id=AD3, first strand: chain 'C' and resid 51 through 54 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 51 through 54 current: chain 'C' and resid 101 through 110 No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'C' and resid 87 through 88 Processing sheet with id=AD5, first strand: chain 'C' and resid 203 through 205 Processing sheet with id=AD6, first strand: chain 'C' and resid 220 through 221 Processing sheet with id=AD7, first strand: chain 'C' and resid 297 through 305 removed outlier: 6.101A pdb=" N ASP C 298 " --> pdb=" O ALA C 321 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N ALA C 321 " --> pdb=" O ASP C 298 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N VAL C 315 " --> pdb=" O PRO C 304 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 343 through 346 Processing sheet with id=AD9, first strand: chain 'C' and resid 387 through 388 Processing sheet with id=AE1, first strand: chain 'D' and resid 2 through 8 Processing sheet with id=AE2, first strand: chain 'D' and resid 15 through 19 removed outlier: 9.112A pdb=" N LEU D 29 " --> pdb=" O TYR D 137 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N TYR D 137 " --> pdb=" O LEU D 29 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N MET D 31 " --> pdb=" O VAL D 135 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N VAL D 135 " --> pdb=" O MET D 31 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N LEU D 33 " --> pdb=" O LEU D 133 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N LEU D 133 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N SER D 35 " --> pdb=" O ALA D 131 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ALA D 131 " --> pdb=" O SER D 35 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N THR D 37 " --> pdb=" O ALA D 129 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ALA D 129 " --> pdb=" O THR D 37 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N GLU D 39 " --> pdb=" O ALA D 127 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N ALA D 127 " --> pdb=" O GLU D 39 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N THR D 41 " --> pdb=" O HIS D 125 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N ALA D 121 " --> pdb=" O ASP D 45 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N ILE D 47 " --> pdb=" O ALA D 119 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ALA D 119 " --> pdb=" O ILE D 47 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 140 through 147 current: chain 'D' and resid 183 through 185 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 183 through 185 current: chain 'D' and resid 267 through 269 Processing sheet with id=AE3, first strand: chain 'D' and resid 51 through 54 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 51 through 54 current: chain 'D' and resid 101 through 110 No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'D' and resid 87 through 88 Processing sheet with id=AE5, first strand: chain 'D' and resid 203 through 205 Processing sheet with id=AE6, first strand: chain 'D' and resid 220 through 221 Processing sheet with id=AE7, first strand: chain 'D' and resid 296 through 305 removed outlier: 5.474A pdb=" N ASP D 298 " --> pdb=" O ALA D 321 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ALA D 321 " --> pdb=" O ASP D 298 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N VAL D 315 " --> pdb=" O PRO D 304 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 326 through 329 Processing sheet with id=AE9, first strand: chain 'D' and resid 331 through 332 Processing sheet with id=AF1, first strand: chain 'D' and resid 387 through 388 Processing sheet with id=AF2, first strand: chain 'E' and resid 17 through 19 Processing sheet with id=AF3, first strand: chain 'E' and resid 34 through 38 removed outlier: 8.685A pdb=" N LEU E 34 " --> pdb=" O SER E 51 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N SER E 51 " --> pdb=" O LEU E 34 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG E 36 " --> pdb=" O GLN E 49 " (cutoff:3.500A) removed outlier: 10.502A pdb=" N SER E 51 " --> pdb=" O MET E 70 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N MET E 70 " --> pdb=" O SER E 51 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N LYS E 66 " --> pdb=" O GLY E 55 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 84 through 86 removed outlier: 4.153A pdb=" N GLU E 109 " --> pdb=" O PHE E 129 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'E' and resid 149 through 156 Processing sheet with id=AF6, first strand: chain 'E' and resid 236 through 237 Processing sheet with id=AF7, first strand: chain 'E' and resid 175 through 176 Processing sheet with id=AF8, first strand: chain 'E' and resid 183 through 184 Processing sheet with id=AF9, first strand: chain 'E' and resid 275 through 279 Processing sheet with id=AG1, first strand: chain 'F' and resid 17 through 19 Processing sheet with id=AG2, first strand: chain 'F' and resid 34 through 38 removed outlier: 8.797A pdb=" N LEU F 34 " --> pdb=" O SER F 51 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N SER F 51 " --> pdb=" O LEU F 34 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG F 36 " --> pdb=" O GLN F 49 " (cutoff:3.500A) removed outlier: 17.172A pdb=" N GLN F 49 " --> pdb=" O TYR F 69 " (cutoff:3.500A) removed outlier: 13.976A pdb=" N TYR F 69 " --> pdb=" O GLN F 49 " (cutoff:3.500A) removed outlier: 12.162A pdb=" N SER F 51 " --> pdb=" O LEU F 67 " (cutoff:3.500A) removed outlier: 10.814A pdb=" N LEU F 67 " --> pdb=" O SER F 51 " (cutoff:3.500A) removed outlier: 11.706A pdb=" N GLN F 53 " --> pdb=" O THR F 65 " (cutoff:3.500A) removed outlier: 9.298A pdb=" N THR F 65 " --> pdb=" O GLN F 53 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N GLY F 55 " --> pdb=" O ASP F 63 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER F 61 " --> pdb=" O LYS F 57 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'F' and resid 84 through 86 removed outlier: 4.104A pdb=" N GLU F 109 " --> pdb=" O PHE F 129 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'F' and resid 149 through 156 Processing sheet with id=AG5, first strand: chain 'F' and resid 236 through 237 Processing sheet with id=AG6, first strand: chain 'F' and resid 175 through 176 Processing sheet with id=AG7, first strand: chain 'F' and resid 181 through 184 Processing sheet with id=AG8, first strand: chain 'F' and resid 275 through 279 Processing sheet with id=AG9, first strand: chain 'G' and resid 17 through 19 Processing sheet with id=AH1, first strand: chain 'G' and resid 34 through 38 removed outlier: 8.681A pdb=" N LEU G 34 " --> pdb=" O SER G 51 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N SER G 51 " --> pdb=" O LEU G 34 " (cutoff:3.500A) removed outlier: 10.440A pdb=" N SER G 51 " --> pdb=" O MET G 70 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N MET G 70 " --> pdb=" O SER G 51 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N LYS G 66 " --> pdb=" O GLY G 55 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'G' and resid 84 through 86 removed outlier: 4.105A pdb=" N GLU G 109 " --> pdb=" O PHE G 129 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'G' and resid 149 through 156 Processing sheet with id=AH4, first strand: chain 'G' and resid 236 through 237 Processing sheet with id=AH5, first strand: chain 'G' and resid 175 through 176 Processing sheet with id=AH6, first strand: chain 'G' and resid 183 through 184 Processing sheet with id=AH7, first strand: chain 'G' and resid 275 through 279 removed outlier: 3.792A pdb=" N GLN G 282 " --> pdb=" O GLY G 279 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'H' and resid 17 through 19 Processing sheet with id=AH9, first strand: chain 'H' and resid 34 through 38 removed outlier: 8.747A pdb=" N LEU H 34 " --> pdb=" O SER H 51 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N SER H 51 " --> pdb=" O LEU H 34 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG H 36 " --> pdb=" O GLN H 49 " (cutoff:3.500A) removed outlier: 10.582A pdb=" N SER H 51 " --> pdb=" O MET H 70 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N MET H 70 " --> pdb=" O SER H 51 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N LYS H 66 " --> pdb=" O GLY H 55 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'H' and resid 84 through 86 removed outlier: 4.145A pdb=" N GLU H 109 " --> pdb=" O PHE H 129 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'H' and resid 149 through 156 Processing sheet with id=AI3, first strand: chain 'H' and resid 236 through 237 Processing sheet with id=AI4, first strand: chain 'H' and resid 175 through 176 Processing sheet with id=AI5, first strand: chain 'H' and resid 183 through 184 Processing sheet with id=AI6, first strand: chain 'H' and resid 275 through 279 removed outlier: 3.777A pdb=" N GLN H 282 " --> pdb=" O GLY H 279 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'I' and resid 143 through 144 removed outlier: 6.457A pdb=" N PHE I 115 " --> pdb=" O TYR I 126 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N TYR I 126 " --> pdb=" O PHE I 115 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N VAL I 117 " --> pdb=" O THR I 124 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N TYR I 126 " --> pdb=" O PRO I 137 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'I' and resid 177 through 178 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 177 through 178 current: chain 'I' and resid 193 through 197 removed outlier: 9.954A pdb=" N ALA I 193 " --> pdb=" O PRO I 204 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 200 through 204 current: chain 'I' and resid 223 through 234 removed outlier: 8.373A pdb=" N VAL I 225 " --> pdb=" O TRP I 245 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N TRP I 245 " --> pdb=" O VAL I 225 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N SER I 241 " --> pdb=" O LEU I 229 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N GLY I 231 " --> pdb=" O ALA I 239 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ALA I 239 " --> pdb=" O GLY I 231 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N ASN I 233 " --> pdb=" O ARG I 237 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N ARG I 237 " --> pdb=" O ASN I 233 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'J' and resid 128 through 130 removed outlier: 3.510A pdb=" N LEU J 162 " --> pdb=" O SER J 157 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'J' and resid 185 through 189 removed outlier: 8.568A pdb=" N ALA J 193 " --> pdb=" O PRO J 204 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 200 through 204 current: chain 'J' and resid 224 through 234 removed outlier: 7.975A pdb=" N VAL J 225 " --> pdb=" O TRP J 245 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N TRP J 245 " --> pdb=" O VAL J 225 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N SER J 241 " --> pdb=" O LEU J 229 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N GLY J 231 " --> pdb=" O ALA J 239 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ALA J 239 " --> pdb=" O GLY J 231 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N ASN J 233 " --> pdb=" O ARG J 237 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N ARG J 237 " --> pdb=" O ASN J 233 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'K' and resid 114 through 119 removed outlier: 6.942A pdb=" N PHE K 115 " --> pdb=" O TYR K 126 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N TYR K 126 " --> pdb=" O PHE K 115 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N VAL K 117 " --> pdb=" O THR K 124 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'K' and resid 185 through 189 removed outlier: 3.656A pdb=" N GLY K 185 " --> pdb=" O TYR K 196 " (cutoff:3.500A) removed outlier: 9.156A pdb=" N ALA K 193 " --> pdb=" O PRO K 204 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 201 through 204 current: chain 'K' and resid 224 through 234 removed outlier: 8.290A pdb=" N VAL K 225 " --> pdb=" O TRP K 245 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N TRP K 245 " --> pdb=" O VAL K 225 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N SER K 241 " --> pdb=" O LEU K 229 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N GLY K 231 " --> pdb=" O ALA K 239 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ALA K 239 " --> pdb=" O GLY K 231 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N ASN K 233 " --> pdb=" O ARG K 237 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ARG K 237 " --> pdb=" O ASN K 233 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'L' and resid 143 through 144 removed outlier: 7.544A pdb=" N TYR L 126 " --> pdb=" O PRO L 137 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'L' and resid 185 through 188 removed outlier: 9.378A pdb=" N ALA L 193 " --> pdb=" O PRO L 204 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 200 through 204 current: chain 'L' and resid 224 through 233 removed outlier: 8.368A pdb=" N VAL L 225 " --> pdb=" O TRP L 245 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N TRP L 245 " --> pdb=" O VAL L 225 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N SER L 241 " --> pdb=" O LEU L 229 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N GLY L 231 " --> pdb=" O ALA L 239 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N ALA L 239 " --> pdb=" O GLY L 231 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N ASN L 233 " --> pdb=" O ARG L 237 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N ARG L 237 " --> pdb=" O ASN L 233 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'Q' and resid 3 through 7 Processing sheet with id=AJ7, first strand: chain 'Q' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 10 through 12 current: chain 'Q' and resid 46 through 51 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 58 through 60 current: chain 'Q' and resid 113 through 114 Processing sheet with id=AJ8, first strand: chain 'Q' and resid 131 through 135 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 147 through 156 current: chain 'Q' and resid 187 through 195 Processing sheet with id=AJ9, first strand: chain 'Q' and resid 161 through 165 removed outlier: 4.249A pdb=" N TYR Q 205 " --> pdb=" O VAL Q 222 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'R' and resid 4 through 6 Processing sheet with id=AK2, first strand: chain 'R' and resid 10 through 13 WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 10 through 13 current: chain 'R' and resid 45 through 49 WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 53 through 54 current: chain 'R' and resid 98 through 99 Processing sheet with id=AK3, first strand: chain 'R' and resid 115 through 119 removed outlier: 4.977A pdb=" N SER R 132 " --> pdb=" O LEU R 182 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N LEU R 182 " --> pdb=" O SER R 132 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N VAL R 134 " --> pdb=" O LEU R 180 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N LEU R 180 " --> pdb=" O VAL R 134 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N LEU R 136 " --> pdb=" O SER R 178 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N SER R 178 " --> pdb=" O LEU R 136 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N ASN R 138 " --> pdb=" O LEU R 176 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N LEU R 176 " --> pdb=" O ASN R 138 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'R' and resid 155 through 156 removed outlier: 4.517A pdb=" N TRP R 149 " --> pdb=" O GLN R 156 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'O' and resid 3 through 8 Processing sheet with id=AK6, first strand: chain 'O' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 10 through 12 current: chain 'O' and resid 45 through 51 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 58 through 60 current: chain 'O' and resid 111 through 114 Processing sheet with id=AK7, first strand: chain 'O' and resid 131 through 135 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 147 through 156 current: chain 'O' and resid 187 through 195 Processing sheet with id=AK8, first strand: chain 'O' and resid 161 through 165 Processing sheet with id=AK9, first strand: chain 'P' and resid 4 through 5 Processing sheet with id=AL1, first strand: chain 'P' and resid 10 through 13 WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 10 through 13 current: chain 'P' and resid 45 through 49 WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 53 through 54 current: chain 'P' and resid 98 through 99 Processing sheet with id=AL2, first strand: chain 'P' and resid 115 through 119 removed outlier: 5.794A pdb=" N TYR P 174 " --> pdb=" O ASN P 139 " (cutoff:3.500A) Processing sheet with id=AL3, first strand: chain 'P' and resid 154 through 156 removed outlier: 4.191A pdb=" N TRP P 149 " --> pdb=" O GLN P 156 " (cutoff:3.500A) Processing sheet with id=AL4, first strand: chain 'M' and resid 3 through 7 Processing sheet with id=AL5, first strand: chain 'M' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 10 through 12 current: chain 'M' and resid 46 through 51 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 58 through 60 current: chain 'M' and resid 111 through 114 Processing sheet with id=AL6, first strand: chain 'M' and resid 131 through 135 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 147 through 156 current: chain 'M' and resid 187 through 195 Processing sheet with id=AL7, first strand: chain 'M' and resid 162 through 165 removed outlier: 4.206A pdb=" N TYR M 205 " --> pdb=" O VAL M 222 " (cutoff:3.500A) Processing sheet with id=AL8, first strand: chain 'N' and resid 4 through 5 Processing sheet with id=AL9, first strand: chain 'N' and resid 10 through 13 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 10 through 13 current: chain 'N' and resid 45 through 49 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 53 through 54 current: chain 'N' and resid 98 through 99 Processing sheet with id=AM1, first strand: chain 'N' and resid 115 through 119 removed outlier: 4.908A pdb=" N SER N 132 " --> pdb=" O LEU N 182 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N LEU N 182 " --> pdb=" O SER N 132 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N VAL N 134 " --> pdb=" O LEU N 180 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N LEU N 180 " --> pdb=" O VAL N 134 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N LEU N 136 " --> pdb=" O SER N 178 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N SER N 178 " --> pdb=" O LEU N 136 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N ASN N 138 " --> pdb=" O LEU N 176 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N LEU N 176 " --> pdb=" O ASN N 138 " (cutoff:3.500A) Processing sheet with id=AM2, first strand: chain 'N' and resid 154 through 156 removed outlier: 4.258A pdb=" N TRP N 149 " --> pdb=" O GLN N 156 " (cutoff:3.500A) 1445 hydrogen bonds defined for protein. 3576 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.18 Time building geometry restraints manager: 5.24 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: 10258 1.33 - 1.46: 13089 1.46 - 1.59: 21941 1.59 - 1.72: 0 1.72 - 1.85: 396 Bond restraints: 45684 Sorted by residual: bond pdb=" C VAL A 13 " pdb=" N PRO A 14 " ideal model delta sigma weight residual 1.331 1.392 -0.061 1.28e-02 6.10e+03 2.26e+01 bond pdb=" CA THR A 358 " pdb=" C THR A 358 " ideal model delta sigma weight residual 1.522 1.465 0.057 1.24e-02 6.50e+03 2.12e+01 bond pdb=" CA HIS A 308 " pdb=" C HIS A 308 " ideal model delta sigma weight residual 1.526 1.472 0.055 1.21e-02 6.83e+03 2.03e+01 bond pdb=" CA HIS A 152 " pdb=" C HIS A 152 " ideal model delta sigma weight residual 1.522 1.470 0.052 1.22e-02 6.72e+03 1.79e+01 bond pdb=" CA GLN A 235 " pdb=" C GLN A 235 " ideal model delta sigma weight residual 1.521 1.469 0.052 1.24e-02 6.50e+03 1.74e+01 ... (remaining 45679 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.23: 60333 3.23 - 6.47: 1544 6.47 - 9.70: 327 9.70 - 12.94: 7 12.94 - 16.17: 1 Bond angle restraints: 62212 Sorted by residual: angle pdb=" N GLY A 313 " pdb=" CA GLY A 313 " pdb=" C GLY A 313 " ideal model delta sigma weight residual 112.77 128.94 -16.17 1.28e+00 6.10e-01 1.60e+02 angle pdb=" N LYS G 189 " pdb=" CA LYS G 189 " pdb=" C LYS G 189 " ideal model delta sigma weight residual 111.36 123.67 -12.31 1.09e+00 8.42e-01 1.28e+02 angle pdb=" N HIS A 386 " pdb=" CA HIS A 386 " pdb=" C HIS A 386 " ideal model delta sigma weight residual 111.36 122.33 -10.97 1.09e+00 8.42e-01 1.01e+02 angle pdb=" C ASP F 132 " pdb=" N PRO F 133 " pdb=" CA PRO F 133 " ideal model delta sigma weight residual 119.66 126.71 -7.05 7.30e-01 1.88e+00 9.34e+01 angle pdb=" C ASP G 132 " pdb=" N PRO G 133 " pdb=" CA PRO G 133 " ideal model delta sigma weight residual 119.66 126.70 -7.04 7.30e-01 1.88e+00 9.31e+01 ... (remaining 62207 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.94: 27204 26.94 - 53.88: 481 53.88 - 80.82: 149 80.82 - 107.76: 57 107.76 - 134.71: 26 Dihedral angle restraints: 27917 sinusoidal: 11219 harmonic: 16698 Sorted by residual: dihedral pdb=" CB CYS C 62 " pdb=" SG CYS C 62 " pdb=" SG CYS C 94 " pdb=" CB CYS C 94 " ideal model delta sinusoidal sigma weight residual -86.00 -175.30 89.30 1 1.00e+01 1.00e-02 9.48e+01 dihedral pdb=" CB CYS B 63 " pdb=" SG CYS B 63 " pdb=" SG CYS B 96 " pdb=" CB CYS B 96 " ideal model delta sinusoidal sigma weight residual 93.00 178.53 -85.53 1 1.00e+01 1.00e-02 8.85e+01 dihedral pdb=" C THR G 191 " pdb=" N THR G 191 " pdb=" CA THR G 191 " pdb=" CB THR G 191 " ideal model delta harmonic sigma weight residual -122.00 -145.12 23.12 0 2.50e+00 1.60e-01 8.56e+01 ... (remaining 27914 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.937: 7048 0.937 - 1.874: 1 1.874 - 2.811: 1 2.811 - 3.748: 0 3.748 - 4.685: 8 Chirality restraints: 7058 Sorted by residual: chirality pdb=" C1 FUC V 4 " pdb=" O6 NAG V 1 " pdb=" C2 FUC V 4 " pdb=" O5 FUC V 4 " both_signs ideal model delta sigma weight residual False -2.40 2.29 -4.69 2.00e-02 2.50e+03 5.49e+04 chirality pdb=" C1 BMA X 3 " pdb=" O4 NAG X 2 " pdb=" C2 BMA X 3 " pdb=" O5 BMA X 3 " both_signs ideal model delta sigma weight residual False -2.40 2.12 -4.52 2.00e-02 2.50e+03 5.11e+04 chirality pdb=" C1 NAG W 2 " pdb=" O4 NAG W 1 " pdb=" C2 NAG W 2 " pdb=" O5 NAG W 2 " both_signs ideal model delta sigma weight residual False -2.40 2.12 -4.52 2.00e-02 2.50e+03 5.11e+04 ... (remaining 7055 not shown) Planarity restraints: 7971 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG V 1 " 0.342 2.00e-02 2.50e+03 2.95e-01 1.09e+03 pdb=" C7 NAG V 1 " -0.079 2.00e-02 2.50e+03 pdb=" C8 NAG V 1 " 0.055 2.00e-02 2.50e+03 pdb=" N2 NAG V 1 " -0.519 2.00e-02 2.50e+03 pdb=" O7 NAG V 1 " 0.200 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG Y 2 " -0.333 2.00e-02 2.50e+03 2.82e-01 9.96e+02 pdb=" C7 NAG Y 2 " 0.085 2.00e-02 2.50e+03 pdb=" C8 NAG Y 2 " -0.186 2.00e-02 2.50e+03 pdb=" N2 NAG Y 2 " 0.492 2.00e-02 2.50e+03 pdb=" O7 NAG Y 2 " -0.059 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG W 1 " -0.333 2.00e-02 2.50e+03 2.74e-01 9.40e+02 pdb=" C7 NAG W 1 " 0.093 2.00e-02 2.50e+03 pdb=" C8 NAG W 1 " -0.210 2.00e-02 2.50e+03 pdb=" N2 NAG W 1 " 0.461 2.00e-02 2.50e+03 pdb=" O7 NAG W 1 " -0.011 2.00e-02 2.50e+03 ... (remaining 7968 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 56 2.49 - 3.09: 30844 3.09 - 3.70: 65055 3.70 - 4.30: 97641 4.30 - 4.90: 159341 Nonbonded interactions: 352937 Sorted by model distance: nonbonded pdb=" OE1 GLN C 400 " pdb=" C6 CLR C 501 " model vdw 1.889 3.340 nonbonded pdb=" CG TYR H 359 " pdb=" C16 CLR D 501 " model vdw 2.121 2.928 nonbonded pdb=" CD2 TYR F 359 " pdb=" C16 CLR F 501 " model vdw 2.213 2.992 nonbonded pdb=" OH TYR G 69 " pdb=" OD1 ASP G 117 " model vdw 2.217 3.040 nonbonded pdb=" CE MET H 366 " pdb=" O1 CLR D 501 " model vdw 2.281 3.460 ... (remaining 352932 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = (chain 'C' and resid 1 through 439) selection = (chain 'D' and resid 1 through 439) } ncs_group { reference = (chain 'E' and resid 7 through 423) selection = (chain 'F' and resid 7 through 423) selection = (chain 'G' and resid 7 through 423) selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'O' selection = chain 'Q' selection = chain 'S' } ncs_group { reference = chain 'N' selection = chain 'P' selection = chain 'R' selection = chain 'T' } ncs_group { reference = (chain 'V' and (resid 1 through 2 or resid 4)) selection = (chain 'X' and (resid 1 through 2 or resid 4)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.650 Check model and map are aligned: 0.130 Set scattering table: 0.120 Process input model: 43.690 Find NCS groups from input model: 1.140 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 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 : 0.011 0.486 45783 Z= 0.722 Angle : 1.335 21.440 62415 Z= 0.914 Chirality : 0.162 4.685 7058 Planarity : 0.009 0.295 7966 Dihedral : 12.704 134.706 17006 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.50 % Favored : 98.47 % Rotamer: Outliers : 0.77 % Allowed : 1.28 % Favored : 97.94 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 2.33 % 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: 1.85 (0.11), residues: 5734 helix: 0.27 (0.21), residues: 520 sheet: 1.63 (0.11), residues: 1913 loop : 1.33 (0.11), residues: 3301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 196 TYR 0.024 0.003 TYR A 189 PHE 0.026 0.002 PHE A 365 TRP 0.023 0.003 TRP K 189 HIS 0.012 0.001 HIS A 308 Details of bonding type rmsd covalent geometry : bond 0.01035 (45684) covalent geometry : angle 1.30848 (62212) SS BOND : bond 0.06356 ( 73) SS BOND : angle 4.28781 ( 146) hydrogen bonds : bond 0.19156 ( 1445) hydrogen bonds : angle 8.22305 ( 3576) Misc. bond : bond 0.29899 ( 7) link_ALPHA1-3 : bond 0.00082 ( 1) link_ALPHA1-3 : angle 1.13098 ( 3) link_ALPHA1-4 : bond 0.03409 ( 2) link_ALPHA1-4 : angle 10.58500 ( 6) link_BETA1-4 : bond 0.01254 ( 6) link_BETA1-4 : angle 5.52135 ( 18) link_BETA1-6 : bond 0.00501 ( 5) link_BETA1-6 : angle 1.82453 ( 15) link_NAG-ASN : bond 0.02368 ( 5) link_NAG-ASN : angle 7.49534 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11468 Ramachandran restraints generated. 5734 Oldfield, 0 Emsley, 5734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11468 Ramachandran restraints generated. 5734 Oldfield, 0 Emsley, 5734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1346 residues out of total 4906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 1308 time to evaluate : 1.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: S 34 MET cc_start: 0.9172 (mmm) cc_final: 0.8901 (mmm) REVERT: S 156 TYR cc_start: 0.7033 (p90) cc_final: 0.6713 (p90) REVERT: S 165 TRP cc_start: 0.7019 (m100) cc_final: 0.6751 (m100) REVERT: T 135 CYS cc_start: 0.6001 (t) cc_final: 0.5364 (t) REVERT: T 149 TRP cc_start: 0.7081 (m100) cc_final: 0.6799 (m100) REVERT: T 163 SER cc_start: 0.7275 (t) cc_final: 0.6849 (p) REVERT: T 168 ASP cc_start: 0.7829 (t70) cc_final: 0.7577 (t0) REVERT: A 69 LYS cc_start: 0.7164 (mmtt) cc_final: 0.6805 (mttm) REVERT: A 75 ASP cc_start: 0.7850 (t0) cc_final: 0.7520 (t0) REVERT: A 135 VAL cc_start: 0.9368 (t) cc_final: 0.9033 (p) REVERT: A 341 GLU cc_start: 0.8234 (mt-10) cc_final: 0.7805 (mm-30) REVERT: A 343 GLU cc_start: 0.8639 (pt0) cc_final: 0.8412 (pp20) REVERT: A 349 ASN cc_start: 0.8333 (OUTLIER) cc_final: 0.8114 (t0) REVERT: A 364 GLU cc_start: 0.8515 (OUTLIER) cc_final: 0.8270 (mt-10) REVERT: B 186 ASN cc_start: 0.8886 (m-40) cc_final: 0.8611 (m-40) REVERT: B 187 MET cc_start: 0.8497 (ttp) cc_final: 0.8263 (ttm) REVERT: B 212 ASP cc_start: 0.8526 (t0) cc_final: 0.7747 (p0) REVERT: B 252 GLN cc_start: 0.8570 (tt0) cc_final: 0.8355 (tp-100) REVERT: B 364 GLU cc_start: 0.8198 (mt-10) cc_final: 0.7763 (mp0) REVERT: C 31 MET cc_start: 0.8577 (mtt) cc_final: 0.8376 (mtp) REVERT: C 47 ILE cc_start: 0.9225 (mm) cc_final: 0.8951 (tt) REVERT: C 51 TYR cc_start: 0.8801 (p90) cc_final: 0.8353 (p90) REVERT: C 158 ASP cc_start: 0.8667 (m-30) cc_final: 0.8139 (t0) REVERT: C 209 GLU cc_start: 0.7807 (pm20) cc_final: 0.7517 (pm20) REVERT: C 212 ASP cc_start: 0.8813 (t0) cc_final: 0.8410 (t0) REVERT: C 311 ASP cc_start: 0.7828 (t0) cc_final: 0.7452 (t0) REVERT: C 337 VAL cc_start: 0.9398 (t) cc_final: 0.9023 (m) REVERT: C 364 GLU cc_start: 0.8380 (tt0) cc_final: 0.7841 (pt0) REVERT: D 51 TYR cc_start: 0.9259 (p90) cc_final: 0.8902 (p90) REVERT: D 158 ASP cc_start: 0.9111 (m-30) cc_final: 0.8122 (t0) REVERT: D 188 ASP cc_start: 0.9112 (t0) cc_final: 0.8822 (t0) REVERT: D 212 ASP cc_start: 0.8584 (t0) cc_final: 0.7460 (p0) REVERT: D 368 GLN cc_start: 0.9131 (tt0) cc_final: 0.8483 (tt0) REVERT: D 372 THR cc_start: 0.9145 (OUTLIER) cc_final: 0.8894 (p) REVERT: E 245 ASN cc_start: 0.8564 (m-40) cc_final: 0.8231 (m-40) REVERT: E 366 MET cc_start: 0.8687 (mmm) cc_final: 0.8246 (mmm) REVERT: F 126 THR cc_start: 0.8839 (m) cc_final: 0.8191 (p) REVERT: F 221 LYS cc_start: 0.8724 (mttt) cc_final: 0.8474 (pttm) REVERT: F 330 TRP cc_start: 0.8140 (t60) cc_final: 0.6734 (t60) REVERT: F 366 MET cc_start: 0.8908 (mmt) cc_final: 0.8666 (mmm) REVERT: F 410 PHE cc_start: 0.8341 (t80) cc_final: 0.8084 (t80) REVERT: F 411 LEU cc_start: 0.8776 (mt) cc_final: 0.8548 (pt) REVERT: G 167 ILE cc_start: 0.8301 (mt) cc_final: 0.7970 (pt) REVERT: G 192 VAL cc_start: 0.9359 (t) cc_final: 0.9106 (m) REVERT: G 195 GLN cc_start: 0.7452 (mt0) cc_final: 0.7246 (mp10) REVERT: G 224 GLN cc_start: 0.7262 (mt0) cc_final: 0.6955 (mt0) REVERT: G 347 THR cc_start: 0.8204 (m) cc_final: 0.7965 (m) REVERT: G 360 TYR cc_start: 0.8740 (t80) cc_final: 0.8313 (t80) REVERT: G 390 MET cc_start: 0.7797 (mmm) cc_final: 0.7502 (tmm) REVERT: H 117 ASP cc_start: 0.8142 (t70) cc_final: 0.7940 (t0) REVERT: H 121 ILE cc_start: 0.8610 (mt) cc_final: 0.8399 (tp) REVERT: H 191 THR cc_start: 0.8291 (OUTLIER) cc_final: 0.8022 (t) REVERT: H 195 GLN cc_start: 0.7709 (OUTLIER) cc_final: 0.6786 (mp10) REVERT: H 208 GLU cc_start: 0.7044 (pt0) cc_final: 0.6251 (pp20) REVERT: H 314 LYS cc_start: 0.6447 (mttt) cc_final: 0.5945 (ttmt) REVERT: J 134 VAL cc_start: 0.8362 (t) cc_final: 0.8064 (t) REVERT: J 136 LYS cc_start: 0.8762 (pttp) cc_final: 0.8535 (pttm) REVERT: J 163 GLU cc_start: 0.8032 (mt-10) cc_final: 0.7825 (mp0) REVERT: J 182 LYS cc_start: 0.8655 (mtmm) cc_final: 0.8258 (mttt) REVERT: J 228 VAL cc_start: 0.9516 (t) cc_final: 0.9139 (p) REVERT: L 123 VAL cc_start: 0.8364 (t) cc_final: 0.8157 (p) REVERT: L 172 LYS cc_start: 0.9024 (mmtm) cc_final: 0.7966 (mmtm) REVERT: L 204 PRO cc_start: 0.8029 (Cg_exo) cc_final: 0.7673 (Cg_endo) REVERT: Q 90 ASP cc_start: 0.9046 (m-30) cc_final: 0.8842 (m-30) REVERT: Q 122 VAL cc_start: 0.9033 (t) cc_final: 0.8723 (t) REVERT: Q 128 LYS cc_start: 0.7092 (tttp) cc_final: 0.6785 (tptm) REVERT: Q 155 ASP cc_start: 0.7271 (m-30) cc_final: 0.6159 (t70) REVERT: R 35 TRP cc_start: 0.8503 (m100) cc_final: 0.8072 (m100) REVERT: R 103 THR cc_start: 0.8618 (m) cc_final: 0.8380 (p) REVERT: O 108 TYR cc_start: 0.7282 (t80) cc_final: 0.6859 (t80) REVERT: M 32 TYR cc_start: 0.8091 (m-80) cc_final: 0.7316 (m-80) REVERT: M 106 ASP cc_start: 0.6657 (t0) cc_final: 0.6137 (t0) REVERT: M 114 TRP cc_start: 0.8523 (m100) cc_final: 0.8222 (m100) REVERT: M 165 TRP cc_start: 0.4262 (m100) cc_final: 0.4062 (m100) REVERT: M 186 LEU cc_start: 0.7930 (mt) cc_final: 0.6742 (mt) REVERT: M 187 TYR cc_start: 0.8667 (m-80) cc_final: 0.8281 (m-80) REVERT: N 118 ILE cc_start: 0.4906 (mm) cc_final: 0.3783 (mt) REVERT: N 132 SER cc_start: 0.7937 (t) cc_final: 0.7585 (m) outliers start: 38 outliers final: 13 residues processed: 1336 average time/residue: 0.2668 time to fit residues: 577.0241 Evaluate side-chains 734 residues out of total 4906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 716 time to evaluate : 1.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 183 ASP Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 349 ASN Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain D residue 372 THR Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain G residue 220 CYS Chi-restraints excluded: chain H residue 191 THR Chi-restraints excluded: chain H residue 195 GLN Chi-restraints excluded: chain H residue 201 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 568 random chunks: chunk 394 optimal weight: 8.9990 chunk 430 optimal weight: 0.9980 chunk 41 optimal weight: 8.9990 chunk 265 optimal weight: 9.9990 chunk 523 optimal weight: 6.9990 chunk 497 optimal weight: 30.0000 chunk 414 optimal weight: 8.9990 chunk 310 optimal weight: 6.9990 chunk 488 optimal weight: 20.0000 chunk 366 optimal weight: 5.9990 chunk 223 optimal weight: 5.9990 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** T 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 138 GLN A 331 HIS B 140 ASN B 152 HIS C 138 GLN ** C 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 235 GLN ** D 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 127 HIS F 142 HIS F 170 HIS F 218 ASN ** F 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 183 GLN H 170 HIS ** I 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 190 HIS J 195 GLN J 220 ASN ** K 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 190 HIS R 79 GLN P 79 GLN M 182 GLN N 161 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.166147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.114450 restraints weight = 81842.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.118152 restraints weight = 37959.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.120428 restraints weight = 22495.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.121803 restraints weight = 16068.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.122711 restraints weight = 13158.311| |-----------------------------------------------------------------------------| r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.3068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 45783 Z= 0.269 Angle : 0.784 29.177 62415 Z= 0.395 Chirality : 0.052 0.867 7058 Planarity : 0.005 0.060 7966 Dihedral : 10.366 103.478 6894 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.83 % Favored : 98.10 % Rotamer: Outliers : 3.04 % Allowed : 8.60 % Favored : 88.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 1.44 (0.11), residues: 5734 helix: 1.53 (0.23), residues: 526 sheet: 1.48 (0.11), residues: 2069 loop : 0.60 (0.11), residues: 3139 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG Q 72 TYR 0.043 0.002 TYR F 359 PHE 0.031 0.002 PHE B 161 TRP 0.042 0.002 TRP I 189 HIS 0.011 0.002 HIS F 18 Details of bonding type rmsd covalent geometry : bond 0.00623 (45684) covalent geometry : angle 0.75482 (62212) SS BOND : bond 0.00604 ( 73) SS BOND : angle 1.58940 ( 146) hydrogen bonds : bond 0.04761 ( 1445) hydrogen bonds : angle 6.38471 ( 3576) Misc. bond : bond 0.00723 ( 7) link_ALPHA1-3 : bond 0.01538 ( 1) link_ALPHA1-3 : angle 2.88082 ( 3) link_ALPHA1-4 : bond 0.02769 ( 2) link_ALPHA1-4 : angle 3.14607 ( 6) link_BETA1-4 : bond 0.01669 ( 6) link_BETA1-4 : angle 5.70425 ( 18) link_BETA1-6 : bond 0.00582 ( 5) link_BETA1-6 : angle 2.97243 ( 15) link_NAG-ASN : bond 0.01569 ( 5) link_NAG-ASN : angle 10.81064 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11468 Ramachandran restraints generated. 5734 Oldfield, 0 Emsley, 5734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11468 Ramachandran restraints generated. 5734 Oldfield, 0 Emsley, 5734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 909 residues out of total 4906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 760 time to evaluate : 1.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: S 83 MET cc_start: 0.8159 (mtm) cc_final: 0.7740 (mtm) REVERT: S 111 MET cc_start: 0.8922 (mtm) cc_final: 0.8645 (mtt) REVERT: S 217 LYS cc_start: 0.7324 (ttmm) cc_final: 0.6862 (ttmm) REVERT: T 156 GLN cc_start: 0.5173 (mp10) cc_final: 0.4857 (mp10) REVERT: T 168 ASP cc_start: 0.7980 (t70) cc_final: 0.7504 (t0) REVERT: A 69 LYS cc_start: 0.8110 (mmtt) cc_final: 0.7475 (mttm) REVERT: A 75 ASP cc_start: 0.8763 (t0) cc_final: 0.8546 (t0) REVERT: A 189 TYR cc_start: 0.8304 (p90) cc_final: 0.7902 (p90) REVERT: B 88 MET cc_start: 0.8598 (mmm) cc_final: 0.8150 (mmm) REVERT: B 212 ASP cc_start: 0.8124 (t0) cc_final: 0.7384 (p0) REVERT: B 252 GLN cc_start: 0.8472 (tt0) cc_final: 0.8212 (tp-100) REVERT: B 364 GLU cc_start: 0.7971 (mt-10) cc_final: 0.7730 (mp0) REVERT: C 302 GLU cc_start: 0.7975 (pm20) cc_final: 0.7583 (pm20) REVERT: C 311 ASP cc_start: 0.7659 (t0) cc_final: 0.7363 (t0) REVERT: D 158 ASP cc_start: 0.8498 (m-30) cc_final: 0.8152 (t0) REVERT: D 160 LYS cc_start: 0.8676 (OUTLIER) cc_final: 0.8409 (ttmm) REVERT: D 212 ASP cc_start: 0.8114 (t0) cc_final: 0.7344 (p0) REVERT: E 117 ASP cc_start: 0.8648 (p0) cc_final: 0.8313 (p0) REVERT: E 158 GLN cc_start: 0.8194 (OUTLIER) cc_final: 0.7955 (mm110) REVERT: F 126 THR cc_start: 0.9078 (m) cc_final: 0.8862 (p) REVERT: F 221 LYS cc_start: 0.8861 (mttt) cc_final: 0.8623 (pttm) REVERT: F 330 TRP cc_start: 0.8484 (t60) cc_final: 0.7162 (t60) REVERT: F 400 TYR cc_start: 0.8337 (m-80) cc_final: 0.8118 (m-80) REVERT: G 195 GLN cc_start: 0.7853 (mt0) cc_final: 0.7610 (mp10) REVERT: G 224 GLN cc_start: 0.7895 (mt0) cc_final: 0.7502 (mt0) REVERT: G 390 MET cc_start: 0.8030 (mmm) cc_final: 0.7418 (tmm) REVERT: H 97 MET cc_start: 0.8605 (tmm) cc_final: 0.8379 (tmm) REVERT: H 181 MET cc_start: 0.8656 (mmt) cc_final: 0.8261 (mmm) REVERT: H 184 GLN cc_start: 0.8341 (tm-30) cc_final: 0.8064 (pp30) REVERT: H 191 THR cc_start: 0.8874 (OUTLIER) cc_final: 0.8476 (t) REVERT: H 201 CYS cc_start: 0.5878 (OUTLIER) cc_final: 0.4900 (m) REVERT: H 314 LYS cc_start: 0.6717 (mttt) cc_final: 0.6352 (mttt) REVERT: H 324 GLU cc_start: 0.8262 (mp0) cc_final: 0.8023 (mp0) REVERT: H 365 THR cc_start: 0.9303 (p) cc_final: 0.9101 (t) REVERT: H 381 MET cc_start: 0.8347 (mmp) cc_final: 0.7952 (mtm) REVERT: H 394 ARG cc_start: 0.7605 (ttm-80) cc_final: 0.7163 (ttm170) REVERT: H 400 TYR cc_start: 0.8685 (m-80) cc_final: 0.8430 (m-80) REVERT: I 134 VAL cc_start: 0.7537 (t) cc_final: 0.6989 (m) REVERT: I 164 CYS cc_start: 0.7961 (m) cc_final: 0.7315 (t) REVERT: I 195 GLN cc_start: 0.7909 (tm-30) cc_final: 0.7294 (tm-30) REVERT: J 136 LYS cc_start: 0.7933 (pttp) cc_final: 0.7411 (pttm) REVERT: J 163 GLU cc_start: 0.7730 (mt-10) cc_final: 0.7144 (mp0) REVERT: J 172 LYS cc_start: 0.8918 (ttmm) cc_final: 0.8684 (ttpp) REVERT: J 186 TYR cc_start: 0.8080 (m-10) cc_final: 0.7760 (m-10) REVERT: J 188 ASN cc_start: 0.8571 (m-40) cc_final: 0.8334 (p0) REVERT: J 218 PHE cc_start: 0.8685 (m-80) cc_final: 0.8376 (m-80) REVERT: K 178 PHE cc_start: 0.7570 (p90) cc_final: 0.7142 (p90) REVERT: L 139 HIS cc_start: 0.8252 (p90) cc_final: 0.8012 (p-80) REVERT: L 156 ARG cc_start: 0.8262 (OUTLIER) cc_final: 0.7939 (ttt-90) REVERT: L 161 ASP cc_start: 0.8720 (t0) cc_final: 0.8519 (t0) REVERT: L 215 ARG cc_start: 0.8681 (mtt-85) cc_final: 0.8363 (mtt-85) REVERT: L 246 ASN cc_start: 0.8936 (t0) cc_final: 0.8577 (t0) REVERT: Q 73 ASP cc_start: 0.8120 (t0) cc_final: 0.7866 (t0) REVERT: Q 83 MET cc_start: 0.7789 (mtm) cc_final: 0.7530 (mtm) REVERT: Q 111 MET cc_start: 0.8837 (OUTLIER) cc_final: 0.7386 (mmm) REVERT: Q 116 GLN cc_start: 0.8405 (OUTLIER) cc_final: 0.8165 (mm-40) REVERT: R 35 TRP cc_start: 0.8916 (m100) cc_final: 0.7917 (m100) REVERT: R 82 ASP cc_start: 0.8345 (m-30) cc_final: 0.7559 (m-30) REVERT: R 103 THR cc_start: 0.8661 (m) cc_final: 0.8190 (p) REVERT: R 168 ASP cc_start: 0.7506 (t0) cc_final: 0.7159 (t0) REVERT: R 173 THR cc_start: 0.8223 (p) cc_final: 0.7912 (t) REVERT: R 196 GLU cc_start: 0.7460 (mm-30) cc_final: 0.7120 (mm-30) REVERT: R 200 GLN cc_start: 0.9050 (tm-30) cc_final: 0.8836 (tm-30) REVERT: M 31 ASP cc_start: 0.8169 (t70) cc_final: 0.7893 (t70) REVERT: M 46 GLU cc_start: 0.7870 (tt0) cc_final: 0.7566 (tt0) REVERT: M 58 ILE cc_start: 0.8990 (mm) cc_final: 0.8788 (mm) REVERT: M 73 ASP cc_start: 0.6017 (t0) cc_final: 0.5726 (t70) REVERT: M 99 ASP cc_start: 0.8612 (t70) cc_final: 0.8175 (t0) REVERT: M 111 MET cc_start: 0.7566 (OUTLIER) cc_final: 0.6665 (mtt) REVERT: M 112 ASP cc_start: 0.6955 (t0) cc_final: 0.6616 (m-30) REVERT: M 114 TRP cc_start: 0.8752 (m100) cc_final: 0.8177 (m100) REVERT: M 165 TRP cc_start: 0.4511 (m100) cc_final: 0.4289 (m100) REVERT: M 186 LEU cc_start: 0.7874 (mt) cc_final: 0.7426 (pp) REVERT: M 187 TYR cc_start: 0.8708 (m-80) cc_final: 0.8437 (m-80) REVERT: N 18 ARG cc_start: 0.7315 (tpp80) cc_final: 0.6630 (ttm-80) REVERT: N 24 ARG cc_start: 0.8165 (ptp-170) cc_final: 0.7208 (ptm160) REVERT: N 132 SER cc_start: 0.7943 (t) cc_final: 0.7667 (p) outliers start: 149 outliers final: 89 residues processed: 856 average time/residue: 0.2548 time to fit residues: 362.5999 Evaluate side-chains 712 residues out of total 4906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 615 time to evaluate : 1.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 53 TRP Chi-restraints excluded: chain S residue 58 ILE Chi-restraints excluded: chain S residue 107 ASP Chi-restraints excluded: chain S residue 188 SER Chi-restraints excluded: chain S residue 190 SER Chi-restraints excluded: chain S residue 209 VAL Chi-restraints excluded: chain T residue 172 SER Chi-restraints excluded: chain A residue 31 MET Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 183 ASP Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 339 ILE Chi-restraints excluded: chain B residue 347 GLU Chi-restraints excluded: chain B residue 414 THR Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain B residue 437 SER Chi-restraints excluded: chain C residue 78 CYS Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 327 LYS Chi-restraints excluded: chain C residue 393 SER Chi-restraints excluded: chain C residue 436 PHE Chi-restraints excluded: chain D residue 160 LYS Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain D residue 344 ILE Chi-restraints excluded: chain D residue 410 VAL Chi-restraints excluded: chain D residue 423 VAL Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain E residue 147 HIS Chi-restraints excluded: chain E residue 158 GLN Chi-restraints excluded: chain E residue 170 HIS Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 347 THR Chi-restraints excluded: chain E residue 355 ILE Chi-restraints excluded: chain E residue 396 CYS Chi-restraints excluded: chain F residue 88 SER Chi-restraints excluded: chain F residue 136 ILE Chi-restraints excluded: chain F residue 218 ASN Chi-restraints excluded: chain F residue 362 LEU Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain G residue 183 GLN Chi-restraints excluded: chain H residue 107 LYS Chi-restraints excluded: chain H residue 191 THR Chi-restraints excluded: chain H residue 201 CYS Chi-restraints excluded: chain H residue 226 HIS Chi-restraints excluded: chain H residue 368 VAL Chi-restraints excluded: chain H residue 398 THR Chi-restraints excluded: chain I residue 249 ILE Chi-restraints excluded: chain J residue 123 VAL Chi-restraints excluded: chain J residue 169 VAL Chi-restraints excluded: chain J residue 170 HIS Chi-restraints excluded: chain J residue 190 HIS Chi-restraints excluded: chain K residue 129 LEU Chi-restraints excluded: chain K residue 139 HIS Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 140 VAL Chi-restraints excluded: chain L residue 156 ARG Chi-restraints excluded: chain L residue 179 THR Chi-restraints excluded: chain L residue 189 TRP Chi-restraints excluded: chain L residue 197 SER Chi-restraints excluded: chain Q residue 2 VAL Chi-restraints excluded: chain Q residue 53 TRP Chi-restraints excluded: chain Q residue 57 SER Chi-restraints excluded: chain Q residue 96 CYS Chi-restraints excluded: chain Q residue 111 MET Chi-restraints excluded: chain Q residue 116 GLN Chi-restraints excluded: chain Q residue 180 VAL Chi-restraints excluded: chain Q residue 192 VAL Chi-restraints excluded: chain R residue 198 THR Chi-restraints excluded: chain O residue 119 THR Chi-restraints excluded: chain O residue 122 VAL Chi-restraints excluded: chain O residue 163 VAL Chi-restraints excluded: chain P residue 53 SER Chi-restraints excluded: chain M residue 57 SER Chi-restraints excluded: chain M residue 87 ARG Chi-restraints excluded: chain M residue 96 CYS Chi-restraints excluded: chain M residue 111 MET Chi-restraints excluded: chain M residue 131 SER Chi-restraints excluded: chain M residue 163 VAL Chi-restraints excluded: chain N residue 134 VAL Chi-restraints excluded: chain N residue 198 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 568 random chunks: chunk 272 optimal weight: 8.9990 chunk 6 optimal weight: 3.9990 chunk 310 optimal weight: 7.9990 chunk 194 optimal weight: 4.9990 chunk 261 optimal weight: 6.9990 chunk 425 optimal weight: 10.0000 chunk 76 optimal weight: 4.9990 chunk 428 optimal weight: 6.9990 chunk 304 optimal weight: 4.9990 chunk 23 optimal weight: 20.0000 chunk 286 optimal weight: 3.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** T 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 79 GLN ** T 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 100 ASN C 107 HIS ** C 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 230 HIS D 439 HIS F 218 ASN F 256 HIS F 349 HIS G 127 HIS G 170 HIS G 183 GLN H 18 HIS H 53 GLN H 184 GLN H 263 ASN ** I 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 190 HIS K 146 ASN Q 54 ASN Q 175 HIS M 13 GLN ** M 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 175 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.161191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.116464 restraints weight = 80520.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.114469 restraints weight = 44656.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.115185 restraints weight = 36997.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.116020 restraints weight = 30205.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.116632 restraints weight = 24719.430| |-----------------------------------------------------------------------------| r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.3709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.096 45783 Z= 0.220 Angle : 0.678 17.845 62415 Z= 0.345 Chirality : 0.048 0.643 7058 Planarity : 0.005 0.048 7966 Dihedral : 9.298 93.408 6880 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.55 % Favored : 97.42 % Rotamer: Outliers : 3.61 % Allowed : 10.42 % Favored : 85.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 1.18 (0.11), residues: 5734 helix: 1.69 (0.24), residues: 526 sheet: 1.34 (0.11), residues: 2106 loop : 0.31 (0.11), residues: 3102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 366 TYR 0.042 0.002 TYR F 359 PHE 0.022 0.002 PHE A 95 TRP 0.026 0.002 TRP M 53 HIS 0.007 0.001 HIS R 190 Details of bonding type rmsd covalent geometry : bond 0.00510 (45684) covalent geometry : angle 0.65857 (62212) SS BOND : bond 0.00407 ( 73) SS BOND : angle 1.36606 ( 146) hydrogen bonds : bond 0.04423 ( 1445) hydrogen bonds : angle 5.92883 ( 3576) Misc. bond : bond 0.00445 ( 7) link_ALPHA1-3 : bond 0.01854 ( 1) link_ALPHA1-3 : angle 2.86903 ( 3) link_ALPHA1-4 : bond 0.02043 ( 2) link_ALPHA1-4 : angle 3.28292 ( 6) link_BETA1-4 : bond 0.01534 ( 6) link_BETA1-4 : angle 5.44441 ( 18) link_BETA1-6 : bond 0.00464 ( 5) link_BETA1-6 : angle 1.98265 ( 15) link_NAG-ASN : bond 0.00877 ( 5) link_NAG-ASN : angle 7.26725 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11468 Ramachandran restraints generated. 5734 Oldfield, 0 Emsley, 5734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11468 Ramachandran restraints generated. 5734 Oldfield, 0 Emsley, 5734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 820 residues out of total 4906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 177 poor density : 643 time to evaluate : 1.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: S 13 GLN cc_start: 0.8632 (mm-40) cc_final: 0.8370 (mm110) REVERT: S 83 MET cc_start: 0.8331 (mtm) cc_final: 0.7852 (mtm) REVERT: S 205 TYR cc_start: 0.7609 (m-10) cc_final: 0.7403 (m-10) REVERT: S 212 LYS cc_start: 0.8641 (tppt) cc_final: 0.8152 (tppt) REVERT: S 217 LYS cc_start: 0.7179 (ttmm) cc_final: 0.6701 (ttmm) REVERT: T 168 ASP cc_start: 0.7808 (t70) cc_final: 0.7360 (t0) REVERT: A 30 GLU cc_start: 0.7630 (tt0) cc_final: 0.7401 (tt0) REVERT: A 69 LYS cc_start: 0.8079 (mmtt) cc_final: 0.6947 (mmtt) REVERT: A 189 TYR cc_start: 0.8366 (p90) cc_final: 0.7955 (p90) REVERT: B 69 LYS cc_start: 0.8636 (pttp) cc_final: 0.7949 (ptmt) REVERT: B 364 GLU cc_start: 0.8001 (mt-10) cc_final: 0.7533 (mp0) REVERT: C 158 ASP cc_start: 0.7880 (t0) cc_final: 0.7439 (t0) REVERT: C 302 GLU cc_start: 0.7907 (pm20) cc_final: 0.7239 (pm20) REVERT: D 88 MET cc_start: 0.8791 (mmm) cc_final: 0.8442 (mtp) REVERT: D 158 ASP cc_start: 0.8358 (m-30) cc_final: 0.8117 (t0) REVERT: D 160 LYS cc_start: 0.8793 (OUTLIER) cc_final: 0.8469 (ttmm) REVERT: D 211 LYS cc_start: 0.9324 (mmtt) cc_final: 0.8924 (tppt) REVERT: D 212 ASP cc_start: 0.8166 (t0) cc_final: 0.7961 (t0) REVERT: D 284 GLU cc_start: 0.7209 (tm-30) cc_final: 0.6998 (tm-30) REVERT: E 158 GLN cc_start: 0.8275 (OUTLIER) cc_final: 0.7921 (mm-40) REVERT: F 97 MET cc_start: 0.8926 (ttp) cc_final: 0.7978 (ppp) REVERT: F 126 THR cc_start: 0.9110 (m) cc_final: 0.8819 (p) REVERT: F 150 GLU cc_start: 0.7564 (OUTLIER) cc_final: 0.7117 (mt-10) REVERT: F 221 LYS cc_start: 0.8800 (mttt) cc_final: 0.8533 (pttm) REVERT: F 330 TRP cc_start: 0.8554 (t60) cc_final: 0.7532 (t60) REVERT: F 400 TYR cc_start: 0.8319 (m-80) cc_final: 0.7819 (m-80) REVERT: F 411 LEU cc_start: 0.8930 (mm) cc_final: 0.8694 (pt) REVERT: G 195 GLN cc_start: 0.8045 (mt0) cc_final: 0.7679 (mp10) REVERT: G 224 GLN cc_start: 0.7923 (mt0) cc_final: 0.7210 (mt0) REVERT: G 285 MET cc_start: 0.8883 (OUTLIER) cc_final: 0.8603 (ptm) REVERT: G 390 MET cc_start: 0.8116 (mmm) cc_final: 0.7435 (tmm) REVERT: H 97 MET cc_start: 0.8666 (tmm) cc_final: 0.8113 (ttp) REVERT: H 181 MET cc_start: 0.8832 (mmt) cc_final: 0.8523 (mmm) REVERT: H 184 GLN cc_start: 0.8340 (OUTLIER) cc_final: 0.8097 (pp30) REVERT: H 195 GLN cc_start: 0.8773 (OUTLIER) cc_final: 0.7938 (mp10) REVERT: H 201 CYS cc_start: 0.5262 (OUTLIER) cc_final: 0.4354 (m) REVERT: H 208 GLU cc_start: 0.7138 (mp0) cc_final: 0.6637 (pm20) REVERT: H 314 LYS cc_start: 0.6886 (mttt) cc_final: 0.6313 (mttp) REVERT: H 324 GLU cc_start: 0.8366 (mp0) cc_final: 0.8031 (mp0) REVERT: I 164 CYS cc_start: 0.7875 (m) cc_final: 0.7170 (t) REVERT: I 195 GLN cc_start: 0.7958 (tm-30) cc_final: 0.7370 (tm-30) REVERT: J 135 MET cc_start: 0.8207 (mtp) cc_final: 0.7739 (tpp) REVERT: J 136 LYS cc_start: 0.7887 (pttp) cc_final: 0.7471 (pttm) REVERT: J 163 GLU cc_start: 0.7750 (mt-10) cc_final: 0.7055 (mp0) REVERT: J 180 HIS cc_start: 0.8422 (p-80) cc_final: 0.7537 (p90) REVERT: J 188 ASN cc_start: 0.8680 (m-40) cc_final: 0.8323 (p0) REVERT: J 215 ARG cc_start: 0.8712 (mtt-85) cc_final: 0.8276 (mmt180) REVERT: J 218 PHE cc_start: 0.8927 (m-80) cc_final: 0.8441 (m-80) REVERT: J 219 ASP cc_start: 0.7653 (p0) cc_final: 0.6935 (p0) REVERT: J 223 ARG cc_start: 0.8394 (mtm180) cc_final: 0.7850 (mtm180) REVERT: K 178 PHE cc_start: 0.7249 (p90) cc_final: 0.6617 (p90) REVERT: L 139 HIS cc_start: 0.8454 (p90) cc_final: 0.8121 (p-80) REVERT: L 156 ARG cc_start: 0.8276 (OUTLIER) cc_final: 0.7920 (ttt-90) REVERT: L 215 ARG cc_start: 0.8801 (mtt-85) cc_final: 0.8352 (mtt-85) REVERT: L 246 ASN cc_start: 0.9013 (t0) cc_final: 0.8692 (t0) REVERT: Q 73 ASP cc_start: 0.8061 (t0) cc_final: 0.7850 (t0) REVERT: Q 83 MET cc_start: 0.7916 (mtm) cc_final: 0.7704 (mtm) REVERT: Q 111 MET cc_start: 0.8913 (OUTLIER) cc_final: 0.7350 (mmm) REVERT: Q 155 ASP cc_start: 0.7691 (m-30) cc_final: 0.6950 (t70) REVERT: R 35 TRP cc_start: 0.9031 (m100) cc_final: 0.8084 (m100) REVERT: R 103 THR cc_start: 0.8730 (m) cc_final: 0.8332 (p) REVERT: R 124 GLU cc_start: 0.7721 (mp0) cc_final: 0.7272 (mp0) REVERT: R 168 ASP cc_start: 0.7626 (t0) cc_final: 0.7185 (t0) REVERT: M 31 ASP cc_start: 0.8306 (t70) cc_final: 0.7915 (t70) REVERT: M 32 TYR cc_start: 0.7933 (m-80) cc_final: 0.7328 (m-80) REVERT: M 58 ILE cc_start: 0.8931 (mm) cc_final: 0.8692 (mm) REVERT: M 73 ASP cc_start: 0.5845 (t0) cc_final: 0.5449 (t70) REVERT: M 83 MET cc_start: 0.7466 (mtp) cc_final: 0.6926 (mmm) REVERT: M 99 ASP cc_start: 0.8399 (t70) cc_final: 0.7977 (t0) REVERT: M 111 MET cc_start: 0.7617 (OUTLIER) cc_final: 0.6073 (mtt) REVERT: M 112 ASP cc_start: 0.7040 (t0) cc_final: 0.6655 (m-30) REVERT: M 114 TRP cc_start: 0.8741 (m100) cc_final: 0.7967 (m100) REVERT: M 165 TRP cc_start: 0.4854 (m100) cc_final: 0.4528 (m100) REVERT: M 187 TYR cc_start: 0.8722 (m-80) cc_final: 0.8395 (m-80) REVERT: N 18 ARG cc_start: 0.7449 (tpp80) cc_final: 0.6902 (ttm-80) REVERT: N 49 TYR cc_start: 0.8526 (p90) cc_final: 0.8321 (p90) outliers start: 177 outliers final: 112 residues processed: 764 average time/residue: 0.2515 time to fit residues: 322.0456 Evaluate side-chains 697 residues out of total 4906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 575 time to evaluate : 1.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 53 TRP Chi-restraints excluded: chain S residue 58 ILE Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 107 ASP Chi-restraints excluded: chain S residue 188 SER Chi-restraints excluded: chain S residue 190 SER Chi-restraints excluded: chain S residue 192 VAL Chi-restraints excluded: chain S residue 209 VAL Chi-restraints excluded: chain T residue 31 SER Chi-restraints excluded: chain T residue 92 TYR Chi-restraints excluded: chain T residue 172 SER Chi-restraints excluded: chain A residue 31 MET Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 183 ASP Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 351 GLN Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 339 ILE Chi-restraints excluded: chain B residue 414 THR Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 437 SER Chi-restraints excluded: chain C residue 78 CYS Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 393 SER Chi-restraints excluded: chain C residue 436 PHE Chi-restraints excluded: chain D residue 160 LYS Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain D residue 372 THR Chi-restraints excluded: chain D residue 396 THR Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain D residue 402 ILE Chi-restraints excluded: chain D residue 410 VAL Chi-restraints excluded: chain D residue 423 VAL Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 431 VAL Chi-restraints excluded: chain E residue 146 GLN Chi-restraints excluded: chain E residue 147 HIS Chi-restraints excluded: chain E residue 158 GLN Chi-restraints excluded: chain E residue 170 HIS Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 349 HIS Chi-restraints excluded: chain F residue 59 ASP Chi-restraints excluded: chain F residue 136 ILE Chi-restraints excluded: chain F residue 150 GLU Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain F residue 218 ASN Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 362 LEU Chi-restraints excluded: chain F residue 379 LEU Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain F residue 412 LEU Chi-restraints excluded: chain G residue 188 VAL Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain G residue 201 CYS Chi-restraints excluded: chain G residue 285 MET Chi-restraints excluded: chain G residue 363 TYR Chi-restraints excluded: chain G residue 410 PHE Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 170 HIS Chi-restraints excluded: chain H residue 184 GLN Chi-restraints excluded: chain H residue 195 GLN Chi-restraints excluded: chain H residue 201 CYS Chi-restraints excluded: chain H residue 226 HIS Chi-restraints excluded: chain H residue 368 VAL Chi-restraints excluded: chain H residue 372 SER Chi-restraints excluded: chain H residue 398 THR Chi-restraints excluded: chain I residue 155 LYS Chi-restraints excluded: chain I residue 158 SER Chi-restraints excluded: chain I residue 249 ILE Chi-restraints excluded: chain J residue 123 VAL Chi-restraints excluded: chain J residue 159 LYS Chi-restraints excluded: chain J residue 177 LYS Chi-restraints excluded: chain J residue 203 ILE Chi-restraints excluded: chain J residue 242 VAL Chi-restraints excluded: chain J residue 245 TRP Chi-restraints excluded: chain K residue 129 LEU Chi-restraints excluded: chain K residue 179 THR Chi-restraints excluded: chain K residue 194 VAL Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 156 ARG Chi-restraints excluded: chain L residue 176 SER Chi-restraints excluded: chain L residue 179 THR Chi-restraints excluded: chain L residue 189 TRP Chi-restraints excluded: chain L residue 197 SER Chi-restraints excluded: chain L residue 249 ILE Chi-restraints excluded: chain Q residue 2 VAL Chi-restraints excluded: chain Q residue 53 TRP Chi-restraints excluded: chain Q residue 86 LEU Chi-restraints excluded: chain Q residue 96 CYS Chi-restraints excluded: chain Q residue 107 ASP Chi-restraints excluded: chain Q residue 111 MET Chi-restraints excluded: chain Q residue 180 VAL Chi-restraints excluded: chain Q residue 192 VAL Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain R residue 198 THR Chi-restraints excluded: chain O residue 119 THR Chi-restraints excluded: chain O residue 122 VAL Chi-restraints excluded: chain O residue 163 VAL Chi-restraints excluded: chain O residue 187 TYR Chi-restraints excluded: chain P residue 11 LEU Chi-restraints excluded: chain P residue 115 SER Chi-restraints excluded: chain M residue 87 ARG Chi-restraints excluded: chain M residue 111 MET Chi-restraints excluded: chain M residue 163 VAL Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 198 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 568 random chunks: chunk 169 optimal weight: 0.4980 chunk 405 optimal weight: 0.7980 chunk 203 optimal weight: 0.7980 chunk 313 optimal weight: 8.9990 chunk 425 optimal weight: 20.0000 chunk 73 optimal weight: 4.9990 chunk 371 optimal weight: 4.9990 chunk 142 optimal weight: 9.9990 chunk 94 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 526 optimal weight: 8.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** T 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 252 GLN D 230 HIS E 224 GLN F 127 HIS ** F 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 218 ASN G 341 GLN H 263 ASN ** I 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 175 HIS P 6 GLN M 35 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.165026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.113352 restraints weight = 80759.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.117113 restraints weight = 36338.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.119474 restraints weight = 21291.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.120885 restraints weight = 15128.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.121540 restraints weight = 12406.952| |-----------------------------------------------------------------------------| r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.3955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 45783 Z= 0.114 Angle : 0.608 16.182 62415 Z= 0.303 Chirality : 0.046 0.624 7058 Planarity : 0.004 0.071 7966 Dihedral : 8.291 88.797 6876 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.30 % Favored : 97.66 % Rotamer: Outliers : 2.49 % Allowed : 12.29 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 1.24 (0.11), residues: 5734 helix: 1.84 (0.24), residues: 527 sheet: 1.37 (0.11), residues: 2076 loop : 0.34 (0.11), residues: 3131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 366 TYR 0.043 0.001 TYR F 359 PHE 0.032 0.001 PHE D 436 TRP 0.033 0.001 TRP M 53 HIS 0.012 0.001 HIS C 331 Details of bonding type rmsd covalent geometry : bond 0.00247 (45684) covalent geometry : angle 0.58736 (62212) SS BOND : bond 0.00490 ( 73) SS BOND : angle 1.41233 ( 146) hydrogen bonds : bond 0.03577 ( 1445) hydrogen bonds : angle 5.52781 ( 3576) Misc. bond : bond 0.00431 ( 7) link_ALPHA1-3 : bond 0.01942 ( 1) link_ALPHA1-3 : angle 2.85739 ( 3) link_ALPHA1-4 : bond 0.01788 ( 2) link_ALPHA1-4 : angle 3.38502 ( 6) link_BETA1-4 : bond 0.01543 ( 6) link_BETA1-4 : angle 5.17264 ( 18) link_BETA1-6 : bond 0.00534 ( 5) link_BETA1-6 : angle 1.79694 ( 15) link_NAG-ASN : bond 0.01323 ( 5) link_NAG-ASN : angle 6.78928 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11468 Ramachandran restraints generated. 5734 Oldfield, 0 Emsley, 5734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11468 Ramachandran restraints generated. 5734 Oldfield, 0 Emsley, 5734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 758 residues out of total 4906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 636 time to evaluate : 1.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: S 83 MET cc_start: 0.8217 (mtm) cc_final: 0.7768 (mtm) REVERT: S 212 LYS cc_start: 0.8785 (tppt) cc_final: 0.8300 (tppt) REVERT: S 220 LYS cc_start: 0.6511 (tppt) cc_final: 0.5402 (ttpp) REVERT: T 168 ASP cc_start: 0.7608 (t70) cc_final: 0.7234 (t0) REVERT: A 27 MET cc_start: 0.7289 (ttm) cc_final: 0.7050 (ttt) REVERT: A 189 TYR cc_start: 0.8367 (p90) cc_final: 0.7951 (p90) REVERT: B 69 LYS cc_start: 0.8654 (pttp) cc_final: 0.8143 (ptmt) REVERT: B 364 GLU cc_start: 0.7788 (mt-10) cc_final: 0.7486 (mp0) REVERT: C 158 ASP cc_start: 0.8014 (t0) cc_final: 0.7558 (t0) REVERT: C 302 GLU cc_start: 0.7885 (pm20) cc_final: 0.7063 (pm20) REVERT: D 88 MET cc_start: 0.8780 (mmm) cc_final: 0.8415 (mtp) REVERT: D 160 LYS cc_start: 0.8700 (OUTLIER) cc_final: 0.8372 (ttmm) REVERT: D 211 LYS cc_start: 0.9123 (mmtt) cc_final: 0.8903 (tppt) REVERT: D 238 SER cc_start: 0.8327 (t) cc_final: 0.8106 (p) REVERT: E 158 GLN cc_start: 0.8179 (OUTLIER) cc_final: 0.7862 (mm-40) REVERT: E 302 GLU cc_start: 0.8273 (mm-30) cc_final: 0.8031 (tp30) REVERT: F 21 ASP cc_start: 0.8592 (t0) cc_final: 0.8323 (t0) REVERT: F 97 MET cc_start: 0.8921 (ttp) cc_final: 0.8158 (tmm) REVERT: F 166 GLU cc_start: 0.7261 (pt0) cc_final: 0.7056 (pt0) REVERT: F 221 LYS cc_start: 0.8895 (mttt) cc_final: 0.8647 (pttm) REVERT: F 330 TRP cc_start: 0.8420 (t60) cc_final: 0.7581 (t60) REVERT: F 366 MET cc_start: 0.7941 (mtp) cc_final: 0.7575 (mtm) REVERT: F 400 TYR cc_start: 0.8267 (m-80) cc_final: 0.7875 (m-80) REVERT: F 410 PHE cc_start: 0.8543 (t80) cc_final: 0.8298 (t80) REVERT: F 411 LEU cc_start: 0.8937 (mm) cc_final: 0.8707 (pt) REVERT: G 195 GLN cc_start: 0.7994 (mt0) cc_final: 0.7701 (mp10) REVERT: G 224 GLN cc_start: 0.8063 (mt0) cc_final: 0.7464 (mt0) REVERT: G 285 MET cc_start: 0.8633 (OUTLIER) cc_final: 0.8300 (ptm) REVERT: G 390 MET cc_start: 0.8105 (mmm) cc_final: 0.7446 (tmm) REVERT: H 97 MET cc_start: 0.8851 (tmm) cc_final: 0.8627 (ttp) REVERT: H 165 GLU cc_start: 0.7361 (tp30) cc_final: 0.7026 (tp30) REVERT: H 181 MET cc_start: 0.8708 (mmt) cc_final: 0.8496 (mmm) REVERT: H 185 SER cc_start: 0.8556 (m) cc_final: 0.8318 (p) REVERT: H 195 GLN cc_start: 0.8752 (OUTLIER) cc_final: 0.7914 (mp10) REVERT: H 208 GLU cc_start: 0.7283 (mp0) cc_final: 0.6698 (mm-30) REVERT: H 314 LYS cc_start: 0.6797 (mttt) cc_final: 0.6156 (ttmt) REVERT: H 394 ARG cc_start: 0.7797 (ttm-80) cc_final: 0.7414 (ttm170) REVERT: I 164 CYS cc_start: 0.7800 (m) cc_final: 0.7167 (t) REVERT: I 187 TYR cc_start: 0.7418 (m-80) cc_final: 0.6464 (m-80) REVERT: J 135 MET cc_start: 0.8159 (mtp) cc_final: 0.7486 (tpp) REVERT: J 136 LYS cc_start: 0.7995 (pttp) cc_final: 0.7539 (pttm) REVERT: J 163 GLU cc_start: 0.7747 (mt-10) cc_final: 0.7120 (mp0) REVERT: J 180 HIS cc_start: 0.8185 (p-80) cc_final: 0.7872 (p-80) REVERT: J 215 ARG cc_start: 0.8721 (mtt-85) cc_final: 0.8273 (mmt180) REVERT: J 218 PHE cc_start: 0.8951 (m-80) cc_final: 0.8581 (m-80) REVERT: J 219 ASP cc_start: 0.7785 (p0) cc_final: 0.7278 (p0) REVERT: J 223 ARG cc_start: 0.8549 (mtm180) cc_final: 0.8135 (mtm180) REVERT: K 245 TRP cc_start: 0.8161 (p90) cc_final: 0.7721 (p90) REVERT: L 139 HIS cc_start: 0.8364 (p90) cc_final: 0.8074 (p-80) REVERT: L 156 ARG cc_start: 0.8139 (OUTLIER) cc_final: 0.7811 (ttt-90) REVERT: L 215 ARG cc_start: 0.8683 (mtt-85) cc_final: 0.8288 (mtt-85) REVERT: L 246 ASN cc_start: 0.8946 (t0) cc_final: 0.8667 (t0) REVERT: L 260 GLU cc_start: 0.8563 (mt-10) cc_final: 0.8309 (mt-10) REVERT: Q 73 ASP cc_start: 0.7999 (t0) cc_final: 0.7695 (t0) REVERT: Q 116 GLN cc_start: 0.8666 (mm-40) cc_final: 0.8281 (mm-40) REVERT: R 35 TRP cc_start: 0.8975 (m100) cc_final: 0.8095 (m100) REVERT: R 103 THR cc_start: 0.8769 (m) cc_final: 0.8394 (p) REVERT: R 124 GLU cc_start: 0.7678 (mp0) cc_final: 0.7437 (mp0) REVERT: R 168 ASP cc_start: 0.7825 (t0) cc_final: 0.7586 (t0) REVERT: R 172 SER cc_start: 0.9284 (m) cc_final: 0.8971 (p) REVERT: O 107 ASP cc_start: 0.7850 (p0) cc_final: 0.6916 (t0) REVERT: O 135 LEU cc_start: 0.3047 (tp) cc_final: 0.1539 (mt) REVERT: M 31 ASP cc_start: 0.8355 (t70) cc_final: 0.7923 (t70) REVERT: M 32 TYR cc_start: 0.8064 (m-80) cc_final: 0.7431 (m-80) REVERT: M 73 ASP cc_start: 0.6121 (t0) cc_final: 0.5648 (t70) REVERT: M 98 LYS cc_start: 0.8467 (ttpp) cc_final: 0.8237 (ptmm) REVERT: M 99 ASP cc_start: 0.8519 (t70) cc_final: 0.8115 (t0) REVERT: M 111 MET cc_start: 0.6848 (OUTLIER) cc_final: 0.6507 (mmt) REVERT: M 114 TRP cc_start: 0.8526 (m100) cc_final: 0.7945 (m100) REVERT: M 165 TRP cc_start: 0.4678 (m100) cc_final: 0.4319 (m100) REVERT: M 186 LEU cc_start: 0.7538 (mp) cc_final: 0.7278 (mp) REVERT: M 187 TYR cc_start: 0.8708 (m-80) cc_final: 0.8302 (m-80) REVERT: M 208 ASN cc_start: 0.2348 (m110) cc_final: 0.1619 (t0) REVERT: N 18 ARG cc_start: 0.7530 (tpp80) cc_final: 0.7067 (ttm-80) REVERT: N 49 TYR cc_start: 0.8537 (p90) cc_final: 0.8254 (p90) outliers start: 122 outliers final: 79 residues processed: 714 average time/residue: 0.2425 time to fit residues: 288.5295 Evaluate side-chains 669 residues out of total 4906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 584 time to evaluate : 1.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 53 TRP Chi-restraints excluded: chain S residue 58 ILE Chi-restraints excluded: chain S residue 209 VAL Chi-restraints excluded: chain T residue 92 TYR Chi-restraints excluded: chain T residue 172 SER Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 183 ASP Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 351 GLN Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 401 ASP Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 372 THR Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 437 SER Chi-restraints excluded: chain C residue 78 CYS Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 299 MET Chi-restraints excluded: chain D residue 160 LYS Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain D residue 402 ILE Chi-restraints excluded: chain D residue 410 VAL Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain E residue 147 HIS Chi-restraints excluded: chain E residue 158 GLN Chi-restraints excluded: chain E residue 170 HIS Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 362 LEU Chi-restraints excluded: chain F residue 18 HIS Chi-restraints excluded: chain F residue 147 HIS Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain F residue 218 ASN Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain F residue 413 SER Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain G residue 201 CYS Chi-restraints excluded: chain G residue 285 MET Chi-restraints excluded: chain G residue 375 SER Chi-restraints excluded: chain G residue 410 PHE Chi-restraints excluded: chain H residue 195 GLN Chi-restraints excluded: chain H residue 226 HIS Chi-restraints excluded: chain H residue 398 THR Chi-restraints excluded: chain I residue 155 LYS Chi-restraints excluded: chain I residue 249 ILE Chi-restraints excluded: chain J residue 123 VAL Chi-restraints excluded: chain J residue 169 VAL Chi-restraints excluded: chain J residue 177 LYS Chi-restraints excluded: chain J residue 245 TRP Chi-restraints excluded: chain K residue 129 LEU Chi-restraints excluded: chain K residue 179 THR Chi-restraints excluded: chain K residue 243 VAL Chi-restraints excluded: chain K residue 254 THR Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 140 VAL Chi-restraints excluded: chain L residue 156 ARG Chi-restraints excluded: chain L residue 179 THR Chi-restraints excluded: chain L residue 189 TRP Chi-restraints excluded: chain L residue 203 ILE Chi-restraints excluded: chain L residue 249 ILE Chi-restraints excluded: chain Q residue 2 VAL Chi-restraints excluded: chain Q residue 86 LEU Chi-restraints excluded: chain Q residue 96 CYS Chi-restraints excluded: chain Q residue 107 ASP Chi-restraints excluded: chain Q residue 180 VAL Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain R residue 198 THR Chi-restraints excluded: chain O residue 122 VAL Chi-restraints excluded: chain O residue 163 VAL Chi-restraints excluded: chain O residue 187 TYR Chi-restraints excluded: chain M residue 57 SER Chi-restraints excluded: chain M residue 87 ARG Chi-restraints excluded: chain M residue 111 MET Chi-restraints excluded: chain M residue 163 VAL Chi-restraints excluded: chain N residue 198 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 568 random chunks: chunk 72 optimal weight: 5.9990 chunk 344 optimal weight: 9.9990 chunk 335 optimal weight: 30.0000 chunk 307 optimal weight: 0.7980 chunk 461 optimal weight: 8.9990 chunk 337 optimal weight: 30.0000 chunk 39 optimal weight: 1.9990 chunk 274 optimal weight: 5.9990 chunk 462 optimal weight: 30.0000 chunk 434 optimal weight: 9.9990 chunk 257 optimal weight: 9.9990 overall best weight: 4.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** T 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 167 GLN B 235 GLN B 335 ASN D 230 HIS E 170 HIS E 224 GLN F 218 ASN ** I 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 175 HIS N 190 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.160552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.108566 restraints weight = 80850.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.112230 restraints weight = 35464.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.114489 restraints weight = 20729.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.115896 restraints weight = 14762.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.116547 restraints weight = 12115.184| |-----------------------------------------------------------------------------| r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.4353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 45783 Z= 0.225 Angle : 0.664 16.355 62415 Z= 0.334 Chirality : 0.047 0.603 7058 Planarity : 0.005 0.065 7966 Dihedral : 7.705 89.780 6874 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.09 % Favored : 96.86 % Rotamer: Outliers : 3.02 % Allowed : 12.76 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 0.95 (0.11), residues: 5734 helix: 1.64 (0.24), residues: 546 sheet: 1.21 (0.11), residues: 2107 loop : 0.09 (0.11), residues: 3081 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG M 38 TYR 0.041 0.002 TYR F 359 PHE 0.032 0.002 PHE D 436 TRP 0.036 0.002 TRP M 53 HIS 0.008 0.001 HIS H 226 Details of bonding type rmsd covalent geometry : bond 0.00527 (45684) covalent geometry : angle 0.64575 (62212) SS BOND : bond 0.00384 ( 73) SS BOND : angle 1.35070 ( 146) hydrogen bonds : bond 0.03886 ( 1445) hydrogen bonds : angle 5.46106 ( 3576) Misc. bond : bond 0.00420 ( 7) link_ALPHA1-3 : bond 0.01955 ( 1) link_ALPHA1-3 : angle 2.86620 ( 3) link_ALPHA1-4 : bond 0.01843 ( 2) link_ALPHA1-4 : angle 2.96506 ( 6) link_BETA1-4 : bond 0.01533 ( 6) link_BETA1-4 : angle 5.00126 ( 18) link_BETA1-6 : bond 0.00554 ( 5) link_BETA1-6 : angle 1.86659 ( 15) link_NAG-ASN : bond 0.01086 ( 5) link_NAG-ASN : angle 6.77947 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11468 Ramachandran restraints generated. 5734 Oldfield, 0 Emsley, 5734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11468 Ramachandran restraints generated. 5734 Oldfield, 0 Emsley, 5734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 758 residues out of total 4906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 610 time to evaluate : 1.042 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: S 83 MET cc_start: 0.8413 (mtm) cc_final: 0.7928 (mtm) REVERT: S 212 LYS cc_start: 0.8759 (tppt) cc_final: 0.8250 (tppt) REVERT: S 220 LYS cc_start: 0.6942 (tppt) cc_final: 0.5871 (ttpp) REVERT: T 81 GLU cc_start: 0.8526 (mp0) cc_final: 0.8321 (tm-30) REVERT: T 168 ASP cc_start: 0.7772 (t70) cc_final: 0.7314 (t0) REVERT: A 189 TYR cc_start: 0.8568 (p90) cc_final: 0.8161 (p90) REVERT: B 69 LYS cc_start: 0.8621 (pttp) cc_final: 0.8069 (ptmm) REVERT: B 333 MET cc_start: 0.8475 (mmm) cc_final: 0.8106 (tpp) REVERT: B 364 GLU cc_start: 0.7887 (mt-10) cc_final: 0.7526 (mp0) REVERT: C 158 ASP cc_start: 0.8216 (t0) cc_final: 0.7819 (t0) REVERT: C 302 GLU cc_start: 0.7877 (pm20) cc_final: 0.7104 (pm20) REVERT: D 70 ASP cc_start: 0.8234 (t0) cc_final: 0.8015 (t0) REVERT: D 88 MET cc_start: 0.8891 (mmm) cc_final: 0.8662 (mtp) REVERT: D 160 LYS cc_start: 0.8681 (OUTLIER) cc_final: 0.8367 (ttmm) REVERT: D 211 LYS cc_start: 0.9161 (mmtt) cc_final: 0.8920 (tppt) REVERT: D 238 SER cc_start: 0.8763 (t) cc_final: 0.8496 (p) REVERT: D 397 LEU cc_start: 0.8226 (OUTLIER) cc_final: 0.7653 (pp) REVERT: E 158 GLN cc_start: 0.8342 (OUTLIER) cc_final: 0.8004 (mm-40) REVERT: F 97 MET cc_start: 0.8973 (ttp) cc_final: 0.7634 (ppp) REVERT: F 221 LYS cc_start: 0.8879 (mttt) cc_final: 0.8598 (pttm) REVERT: F 330 TRP cc_start: 0.8654 (t60) cc_final: 0.8092 (t60) REVERT: F 400 TYR cc_start: 0.8382 (m-80) cc_final: 0.7825 (m-80) REVERT: F 410 PHE cc_start: 0.8635 (t80) cc_final: 0.8434 (t80) REVERT: G 195 GLN cc_start: 0.7934 (mt0) cc_final: 0.7627 (mp10) REVERT: G 224 GLN cc_start: 0.8029 (mt0) cc_final: 0.7366 (mt0) REVERT: G 285 MET cc_start: 0.8815 (OUTLIER) cc_final: 0.8495 (ptm) REVERT: G 365 THR cc_start: 0.8315 (p) cc_final: 0.7892 (t) REVERT: G 366 MET cc_start: 0.7258 (mtt) cc_final: 0.6949 (mtt) REVERT: G 390 MET cc_start: 0.8196 (mmm) cc_final: 0.7442 (tmm) REVERT: H 97 MET cc_start: 0.8917 (tmm) cc_final: 0.8260 (ttp) REVERT: H 165 GLU cc_start: 0.7436 (tp30) cc_final: 0.7194 (tp30) REVERT: H 195 GLN cc_start: 0.8873 (OUTLIER) cc_final: 0.7966 (mp10) REVERT: I 164 CYS cc_start: 0.7841 (m) cc_final: 0.7195 (t) REVERT: I 179 THR cc_start: 0.8395 (m) cc_final: 0.8110 (m) REVERT: I 195 GLN cc_start: 0.7994 (tm-30) cc_final: 0.7492 (tm-30) REVERT: J 136 LYS cc_start: 0.7967 (pttp) cc_final: 0.7518 (pttm) REVERT: J 163 GLU cc_start: 0.7674 (mt-10) cc_final: 0.7110 (mp0) REVERT: J 180 HIS cc_start: 0.8335 (p-80) cc_final: 0.8037 (p-80) REVERT: J 215 ARG cc_start: 0.8789 (mtt-85) cc_final: 0.7820 (mtt-85) REVERT: J 219 ASP cc_start: 0.7766 (p0) cc_final: 0.6292 (p0) REVERT: J 223 ARG cc_start: 0.8732 (mtm180) cc_final: 0.7989 (mtm180) REVERT: K 245 TRP cc_start: 0.8183 (p90) cc_final: 0.7842 (p90) REVERT: L 155 LYS cc_start: 0.7052 (mmtm) cc_final: 0.6811 (mmtm) REVERT: L 156 ARG cc_start: 0.8018 (OUTLIER) cc_final: 0.7687 (ttt-90) REVERT: L 161 ASP cc_start: 0.8793 (t0) cc_final: 0.8525 (t0) REVERT: L 215 ARG cc_start: 0.8697 (mtt-85) cc_final: 0.8273 (mtt-85) REVERT: L 246 ASN cc_start: 0.9001 (t0) cc_final: 0.8723 (t0) REVERT: Q 1 GLU cc_start: 0.8139 (tp30) cc_final: 0.7646 (tp30) REVERT: Q 73 ASP cc_start: 0.8361 (t0) cc_final: 0.8147 (t0) REVERT: Q 111 MET cc_start: 0.8935 (OUTLIER) cc_final: 0.7423 (mmm) REVERT: Q 159 GLU cc_start: 0.8382 (tp30) cc_final: 0.8103 (mm-30) REVERT: R 35 TRP cc_start: 0.8991 (m100) cc_final: 0.8037 (m100) REVERT: R 92 TYR cc_start: 0.7600 (t80) cc_final: 0.7344 (t80) REVERT: R 103 THR cc_start: 0.8822 (m) cc_final: 0.8390 (p) REVERT: R 124 GLU cc_start: 0.7703 (mp0) cc_final: 0.7424 (mp0) REVERT: R 172 SER cc_start: 0.9302 (m) cc_final: 0.8994 (p) REVERT: O 181 LEU cc_start: 0.7118 (OUTLIER) cc_final: 0.6041 (pt) REVERT: M 30 ASP cc_start: 0.8989 (p0) cc_final: 0.8567 (p0) REVERT: M 31 ASP cc_start: 0.8510 (t70) cc_final: 0.8027 (t70) REVERT: M 32 TYR cc_start: 0.8191 (m-80) cc_final: 0.7587 (m-80) REVERT: M 73 ASP cc_start: 0.6215 (t0) cc_final: 0.5603 (t70) REVERT: M 98 LYS cc_start: 0.8449 (ttpp) cc_final: 0.8245 (ptmm) REVERT: M 99 ASP cc_start: 0.8574 (t70) cc_final: 0.8259 (t0) REVERT: M 111 MET cc_start: 0.7176 (OUTLIER) cc_final: 0.6863 (mmt) REVERT: M 114 TRP cc_start: 0.8555 (m100) cc_final: 0.8146 (m100) REVERT: M 186 LEU cc_start: 0.7278 (mp) cc_final: 0.6807 (mp) REVERT: M 187 TYR cc_start: 0.8720 (m-80) cc_final: 0.8413 (m-80) REVERT: M 208 ASN cc_start: 0.2466 (m110) cc_final: 0.1488 (t0) REVERT: N 18 ARG cc_start: 0.7686 (tpp80) cc_final: 0.7130 (ttm-80) outliers start: 148 outliers final: 108 residues processed: 714 average time/residue: 0.2235 time to fit residues: 266.2484 Evaluate side-chains 689 residues out of total 4906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 572 time to evaluate : 1.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 53 TRP Chi-restraints excluded: chain S residue 58 ILE Chi-restraints excluded: chain S residue 107 ASP Chi-restraints excluded: chain S residue 190 SER Chi-restraints excluded: chain S residue 209 VAL Chi-restraints excluded: chain T residue 31 SER Chi-restraints excluded: chain T residue 33 LEU Chi-restraints excluded: chain T residue 92 TYR Chi-restraints excluded: chain T residue 172 SER Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 183 ASP Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 351 GLN Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 401 ASP Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 347 GLU Chi-restraints excluded: chain B residue 372 THR Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain B residue 437 SER Chi-restraints excluded: chain C residue 78 CYS Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 299 MET Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain D residue 160 LYS Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 338 THR Chi-restraints excluded: chain D residue 397 LEU Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain D residue 402 ILE Chi-restraints excluded: chain D residue 410 VAL Chi-restraints excluded: chain D residue 423 VAL Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 139 GLU Chi-restraints excluded: chain E residue 147 HIS Chi-restraints excluded: chain E residue 158 GLN Chi-restraints excluded: chain E residue 170 HIS Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 291 HIS Chi-restraints excluded: chain E residue 349 HIS Chi-restraints excluded: chain E residue 355 ILE Chi-restraints excluded: chain F residue 59 ASP Chi-restraints excluded: chain F residue 136 ILE Chi-restraints excluded: chain F residue 147 HIS Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 379 LEU Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain F residue 413 SER Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain G residue 201 CYS Chi-restraints excluded: chain G residue 226 HIS Chi-restraints excluded: chain G residue 285 MET Chi-restraints excluded: chain G residue 375 SER Chi-restraints excluded: chain G residue 410 PHE Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 170 HIS Chi-restraints excluded: chain H residue 188 VAL Chi-restraints excluded: chain H residue 195 GLN Chi-restraints excluded: chain H residue 226 HIS Chi-restraints excluded: chain H residue 247 GLU Chi-restraints excluded: chain H residue 382 VAL Chi-restraints excluded: chain H residue 398 THR Chi-restraints excluded: chain I residue 155 LYS Chi-restraints excluded: chain I residue 158 SER Chi-restraints excluded: chain I residue 249 ILE Chi-restraints excluded: chain J residue 123 VAL Chi-restraints excluded: chain J residue 169 VAL Chi-restraints excluded: chain J residue 177 LYS Chi-restraints excluded: chain J residue 245 TRP Chi-restraints excluded: chain K residue 129 LEU Chi-restraints excluded: chain K residue 179 THR Chi-restraints excluded: chain K residue 243 VAL Chi-restraints excluded: chain K residue 254 THR Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 140 VAL Chi-restraints excluded: chain L residue 156 ARG Chi-restraints excluded: chain L residue 176 SER Chi-restraints excluded: chain L residue 179 THR Chi-restraints excluded: chain L residue 189 TRP Chi-restraints excluded: chain L residue 203 ILE Chi-restraints excluded: chain Q residue 2 VAL Chi-restraints excluded: chain Q residue 57 SER Chi-restraints excluded: chain Q residue 96 CYS Chi-restraints excluded: chain Q residue 107 ASP Chi-restraints excluded: chain Q residue 111 MET Chi-restraints excluded: chain Q residue 180 VAL Chi-restraints excluded: chain Q residue 189 LEU Chi-restraints excluded: chain Q residue 207 CYS Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain R residue 198 THR Chi-restraints excluded: chain O residue 122 VAL Chi-restraints excluded: chain O residue 163 VAL Chi-restraints excluded: chain O residue 181 LEU Chi-restraints excluded: chain O residue 187 TYR Chi-restraints excluded: chain P residue 126 LEU Chi-restraints excluded: chain P residue 147 VAL Chi-restraints excluded: chain M residue 111 MET Chi-restraints excluded: chain M residue 163 VAL Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 134 VAL Chi-restraints excluded: chain N residue 198 THR Chi-restraints excluded: chain N residue 206 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 568 random chunks: chunk 414 optimal weight: 20.0000 chunk 234 optimal weight: 6.9990 chunk 478 optimal weight: 20.0000 chunk 173 optimal weight: 0.9980 chunk 46 optimal weight: 4.9990 chunk 270 optimal weight: 10.0000 chunk 398 optimal weight: 0.3980 chunk 160 optimal weight: 9.9990 chunk 274 optimal weight: 6.9990 chunk 293 optimal weight: 9.9990 chunk 120 optimal weight: 5.9990 overall best weight: 3.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** T 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 230 HIS E 224 GLN I 195 GLN J 191 HIS J 195 GLN Q 175 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.163553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.109391 restraints weight = 81848.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.113284 restraints weight = 37196.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.115993 restraints weight = 21039.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.115482 restraints weight = 17502.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.115832 restraints weight = 15991.483| |-----------------------------------------------------------------------------| r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.4580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 45783 Z= 0.184 Angle : 0.630 15.261 62415 Z= 0.317 Chirality : 0.046 0.523 7058 Planarity : 0.004 0.053 7966 Dihedral : 7.232 88.617 6874 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.16 % Favored : 96.79 % Rotamer: Outliers : 3.00 % Allowed : 13.33 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 0.86 (0.11), residues: 5734 helix: 1.69 (0.24), residues: 547 sheet: 1.25 (0.12), residues: 1993 loop : -0.03 (0.11), residues: 3194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG Q 87 TYR 0.041 0.002 TYR F 359 PHE 0.021 0.001 PHE L 154 TRP 0.033 0.002 TRP M 53 HIS 0.023 0.001 HIS E 170 Details of bonding type rmsd covalent geometry : bond 0.00425 (45684) covalent geometry : angle 0.61353 (62212) SS BOND : bond 0.00366 ( 73) SS BOND : angle 1.19569 ( 146) hydrogen bonds : bond 0.03638 ( 1445) hydrogen bonds : angle 5.33146 ( 3576) Misc. bond : bond 0.00416 ( 7) link_ALPHA1-3 : bond 0.01973 ( 1) link_ALPHA1-3 : angle 2.68881 ( 3) link_ALPHA1-4 : bond 0.01854 ( 2) link_ALPHA1-4 : angle 2.68941 ( 6) link_BETA1-4 : bond 0.01292 ( 6) link_BETA1-4 : angle 4.82833 ( 18) link_BETA1-6 : bond 0.00469 ( 5) link_BETA1-6 : angle 1.73860 ( 15) link_NAG-ASN : bond 0.01109 ( 5) link_NAG-ASN : angle 6.59074 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11468 Ramachandran restraints generated. 5734 Oldfield, 0 Emsley, 5734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11468 Ramachandran restraints generated. 5734 Oldfield, 0 Emsley, 5734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 753 residues out of total 4906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 606 time to evaluate : 1.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: S 83 MET cc_start: 0.8475 (mtm) cc_final: 0.7996 (mtm) REVERT: S 212 LYS cc_start: 0.8727 (tppt) cc_final: 0.8217 (tppt) REVERT: T 168 ASP cc_start: 0.7773 (t70) cc_final: 0.7226 (t0) REVERT: A 189 TYR cc_start: 0.8669 (p90) cc_final: 0.8237 (p90) REVERT: B 27 MET cc_start: 0.7275 (OUTLIER) cc_final: 0.6912 (ttm) REVERT: B 145 THR cc_start: 0.9315 (OUTLIER) cc_final: 0.8983 (p) REVERT: B 333 MET cc_start: 0.8481 (mmm) cc_final: 0.8111 (tpp) REVERT: B 364 GLU cc_start: 0.7889 (mt-10) cc_final: 0.7531 (mp0) REVERT: C 158 ASP cc_start: 0.8227 (t0) cc_final: 0.7831 (t0) REVERT: C 302 GLU cc_start: 0.7916 (pm20) cc_final: 0.7132 (pm20) REVERT: D 70 ASP cc_start: 0.8364 (t0) cc_final: 0.8132 (t0) REVERT: D 160 LYS cc_start: 0.8636 (OUTLIER) cc_final: 0.8375 (ttmm) REVERT: D 211 LYS cc_start: 0.9192 (mmtt) cc_final: 0.8946 (tppt) REVERT: D 238 SER cc_start: 0.8733 (t) cc_final: 0.8456 (p) REVERT: E 158 GLN cc_start: 0.8340 (OUTLIER) cc_final: 0.7992 (mm-40) REVERT: F 97 MET cc_start: 0.8922 (ttp) cc_final: 0.8103 (tmm) REVERT: F 221 LYS cc_start: 0.8787 (mttt) cc_final: 0.8464 (pttm) REVERT: F 226 HIS cc_start: 0.6598 (OUTLIER) cc_final: 0.5915 (t-90) REVERT: F 330 TRP cc_start: 0.8620 (t60) cc_final: 0.7516 (t60) REVERT: F 366 MET cc_start: 0.8081 (mtp) cc_final: 0.7687 (mtm) REVERT: F 400 TYR cc_start: 0.8246 (m-80) cc_final: 0.7661 (m-80) REVERT: G 195 GLN cc_start: 0.8014 (mt0) cc_final: 0.7613 (mt0) REVERT: G 224 GLN cc_start: 0.7959 (mt0) cc_final: 0.7567 (mt0) REVERT: G 285 MET cc_start: 0.8814 (OUTLIER) cc_final: 0.8479 (ptm) REVERT: G 365 THR cc_start: 0.8095 (p) cc_final: 0.7710 (t) REVERT: G 390 MET cc_start: 0.8032 (mmm) cc_final: 0.7335 (tmm) REVERT: H 97 MET cc_start: 0.8913 (tmm) cc_final: 0.8276 (ttp) REVERT: H 165 GLU cc_start: 0.7712 (tp30) cc_final: 0.7450 (tp30) REVERT: H 195 GLN cc_start: 0.8902 (OUTLIER) cc_final: 0.8222 (mp10) REVERT: H 394 ARG cc_start: 0.7735 (ttm-80) cc_final: 0.7366 (ttm170) REVERT: I 164 CYS cc_start: 0.7801 (m) cc_final: 0.7255 (t) REVERT: I 179 THR cc_start: 0.8444 (m) cc_final: 0.8169 (m) REVERT: I 195 GLN cc_start: 0.7952 (tm130) cc_final: 0.7473 (tm-30) REVERT: J 136 LYS cc_start: 0.7849 (pttp) cc_final: 0.7421 (pttm) REVERT: J 157 SER cc_start: 0.8516 (t) cc_final: 0.8121 (t) REVERT: J 163 GLU cc_start: 0.7675 (mt-10) cc_final: 0.6943 (mp0) REVERT: J 180 HIS cc_start: 0.8393 (p-80) cc_final: 0.8118 (p-80) REVERT: J 215 ARG cc_start: 0.8773 (mtt-85) cc_final: 0.7755 (mtt-85) REVERT: J 219 ASP cc_start: 0.7737 (p0) cc_final: 0.7406 (p0) REVERT: J 223 ARG cc_start: 0.8736 (mtm180) cc_final: 0.8366 (mtm180) REVERT: K 151 LYS cc_start: 0.9105 (tptp) cc_final: 0.8456 (pttp) REVERT: K 245 TRP cc_start: 0.8159 (p90) cc_final: 0.7838 (p90) REVERT: L 156 ARG cc_start: 0.8019 (OUTLIER) cc_final: 0.7698 (ttt-90) REVERT: L 161 ASP cc_start: 0.8688 (t0) cc_final: 0.8440 (t0) REVERT: L 215 ARG cc_start: 0.8741 (mtt-85) cc_final: 0.8098 (mtt-85) REVERT: L 246 ASN cc_start: 0.8932 (t0) cc_final: 0.8705 (t0) REVERT: Q 1 GLU cc_start: 0.8222 (tp30) cc_final: 0.7808 (tp30) REVERT: Q 111 MET cc_start: 0.8959 (OUTLIER) cc_final: 0.7362 (mmm) REVERT: Q 159 GLU cc_start: 0.8414 (tp30) cc_final: 0.8098 (mm-30) REVERT: R 17 ASP cc_start: 0.8169 (t0) cc_final: 0.7938 (t0) REVERT: R 92 TYR cc_start: 0.7715 (t80) cc_final: 0.7432 (t80) REVERT: R 103 THR cc_start: 0.8757 (m) cc_final: 0.8363 (p) REVERT: R 124 GLU cc_start: 0.7662 (mp0) cc_final: 0.7380 (mp0) REVERT: R 172 SER cc_start: 0.9268 (m) cc_final: 0.8942 (p) REVERT: O 34 MET cc_start: 0.4954 (mtt) cc_final: 0.3076 (mmm) REVERT: O 181 LEU cc_start: 0.7089 (OUTLIER) cc_final: 0.6207 (pt) REVERT: M 30 ASP cc_start: 0.9000 (p0) cc_final: 0.8648 (p0) REVERT: M 31 ASP cc_start: 0.8533 (t70) cc_final: 0.7990 (t70) REVERT: M 32 TYR cc_start: 0.8148 (m-80) cc_final: 0.7491 (m-80) REVERT: M 73 ASP cc_start: 0.6502 (t0) cc_final: 0.5921 (t70) REVERT: M 98 LYS cc_start: 0.8413 (ttpp) cc_final: 0.8150 (ptmm) REVERT: M 99 ASP cc_start: 0.8565 (t70) cc_final: 0.8133 (t0) REVERT: M 114 TRP cc_start: 0.8498 (m100) cc_final: 0.8109 (m-10) REVERT: M 186 LEU cc_start: 0.7198 (mp) cc_final: 0.6750 (mp) REVERT: M 187 TYR cc_start: 0.8644 (m-80) cc_final: 0.8271 (m-80) outliers start: 147 outliers final: 108 residues processed: 711 average time/residue: 0.2140 time to fit residues: 253.9782 Evaluate side-chains 694 residues out of total 4906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 576 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 53 TRP Chi-restraints excluded: chain S residue 58 ILE Chi-restraints excluded: chain S residue 107 ASP Chi-restraints excluded: chain S residue 190 SER Chi-restraints excluded: chain S residue 209 VAL Chi-restraints excluded: chain T residue 31 SER Chi-restraints excluded: chain T residue 33 LEU Chi-restraints excluded: chain T residue 92 TYR Chi-restraints excluded: chain T residue 172 SER Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 183 ASP Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 351 GLN Chi-restraints excluded: chain A residue 401 ASP Chi-restraints excluded: chain B residue 27 MET Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 347 GLU Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 437 SER Chi-restraints excluded: chain C residue 2 GLU Chi-restraints excluded: chain C residue 78 CYS Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 299 MET Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 393 SER Chi-restraints excluded: chain D residue 160 LYS Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 344 ILE Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain D residue 402 ILE Chi-restraints excluded: chain D residue 410 VAL Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain E residue 139 GLU Chi-restraints excluded: chain E residue 147 HIS Chi-restraints excluded: chain E residue 158 GLN Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 291 HIS Chi-restraints excluded: chain E residue 349 HIS Chi-restraints excluded: chain E residue 355 ILE Chi-restraints excluded: chain F residue 59 ASP Chi-restraints excluded: chain F residue 147 HIS Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain F residue 218 ASN Chi-restraints excluded: chain F residue 226 HIS Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 379 LEU Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain F residue 413 SER Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain G residue 201 CYS Chi-restraints excluded: chain G residue 285 MET Chi-restraints excluded: chain G residue 375 SER Chi-restraints excluded: chain G residue 410 PHE Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 170 HIS Chi-restraints excluded: chain H residue 191 THR Chi-restraints excluded: chain H residue 195 GLN Chi-restraints excluded: chain H residue 226 HIS Chi-restraints excluded: chain H residue 291 HIS Chi-restraints excluded: chain I residue 155 LYS Chi-restraints excluded: chain I residue 158 SER Chi-restraints excluded: chain I residue 249 ILE Chi-restraints excluded: chain J residue 123 VAL Chi-restraints excluded: chain J residue 169 VAL Chi-restraints excluded: chain J residue 177 LYS Chi-restraints excluded: chain J residue 242 VAL Chi-restraints excluded: chain J residue 245 TRP Chi-restraints excluded: chain K residue 129 LEU Chi-restraints excluded: chain K residue 130 VAL Chi-restraints excluded: chain K residue 179 THR Chi-restraints excluded: chain K residue 243 VAL Chi-restraints excluded: chain K residue 254 THR Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 140 VAL Chi-restraints excluded: chain L residue 156 ARG Chi-restraints excluded: chain L residue 179 THR Chi-restraints excluded: chain L residue 189 TRP Chi-restraints excluded: chain Q residue 2 VAL Chi-restraints excluded: chain Q residue 57 SER Chi-restraints excluded: chain Q residue 96 CYS Chi-restraints excluded: chain Q residue 107 ASP Chi-restraints excluded: chain Q residue 111 MET Chi-restraints excluded: chain Q residue 180 VAL Chi-restraints excluded: chain Q residue 189 LEU Chi-restraints excluded: chain Q residue 207 CYS Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain R residue 198 THR Chi-restraints excluded: chain O residue 53 TRP Chi-restraints excluded: chain O residue 122 VAL Chi-restraints excluded: chain O residue 163 VAL Chi-restraints excluded: chain O residue 181 LEU Chi-restraints excluded: chain O residue 187 TYR Chi-restraints excluded: chain P residue 115 SER Chi-restraints excluded: chain P residue 126 LEU Chi-restraints excluded: chain M residue 87 ARG Chi-restraints excluded: chain M residue 163 VAL Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 134 VAL Chi-restraints excluded: chain N residue 189 LYS Chi-restraints excluded: chain N residue 198 THR Chi-restraints excluded: chain N residue 206 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 568 random chunks: chunk 385 optimal weight: 1.9990 chunk 547 optimal weight: 30.0000 chunk 434 optimal weight: 10.0000 chunk 343 optimal weight: 0.0040 chunk 198 optimal weight: 3.9990 chunk 115 optimal weight: 10.0000 chunk 82 optimal weight: 6.9990 chunk 453 optimal weight: 50.0000 chunk 511 optimal weight: 30.0000 chunk 107 optimal weight: 9.9990 chunk 154 optimal weight: 0.8980 overall best weight: 2.7798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** T 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 186 ASN D 230 HIS E 224 GLN J 195 GLN L 119 HIS Q 175 HIS R 38 GLN M 35 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.160157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.115517 restraints weight = 79370.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.113272 restraints weight = 43928.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.113740 restraints weight = 38566.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.114615 restraints weight = 31380.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.115199 restraints weight = 25616.670| |-----------------------------------------------------------------------------| r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.4746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 45783 Z= 0.148 Angle : 0.615 13.669 62415 Z= 0.308 Chirality : 0.045 0.507 7058 Planarity : 0.004 0.050 7966 Dihedral : 6.931 86.054 6873 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.07 % Favored : 96.84 % Rotamer: Outliers : 2.55 % Allowed : 14.13 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.11), residues: 5734 helix: 1.80 (0.24), residues: 546 sheet: 1.25 (0.12), residues: 2000 loop : -0.03 (0.11), residues: 3188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG Q 87 TYR 0.041 0.001 TYR F 359 PHE 0.029 0.001 PHE C 95 TRP 0.035 0.001 TRP M 53 HIS 0.013 0.001 HIS I 170 Details of bonding type rmsd covalent geometry : bond 0.00341 (45684) covalent geometry : angle 0.59895 (62212) SS BOND : bond 0.00326 ( 73) SS BOND : angle 1.29647 ( 146) hydrogen bonds : bond 0.03409 ( 1445) hydrogen bonds : angle 5.20443 ( 3576) Misc. bond : bond 0.00429 ( 7) link_ALPHA1-3 : bond 0.02158 ( 1) link_ALPHA1-3 : angle 2.56289 ( 3) link_ALPHA1-4 : bond 0.01916 ( 2) link_ALPHA1-4 : angle 2.68684 ( 6) link_BETA1-4 : bond 0.01340 ( 6) link_BETA1-4 : angle 4.69205 ( 18) link_BETA1-6 : bond 0.00496 ( 5) link_BETA1-6 : angle 1.58162 ( 15) link_NAG-ASN : bond 0.01085 ( 5) link_NAG-ASN : angle 6.20255 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11468 Ramachandran restraints generated. 5734 Oldfield, 0 Emsley, 5734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11468 Ramachandran restraints generated. 5734 Oldfield, 0 Emsley, 5734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 728 residues out of total 4906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 603 time to evaluate : 1.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: S 83 MET cc_start: 0.8531 (mtm) cc_final: 0.8031 (mtm) REVERT: S 111 MET cc_start: 0.8060 (mtt) cc_final: 0.7664 (mtt) REVERT: S 212 LYS cc_start: 0.8780 (tppt) cc_final: 0.8299 (tppt) REVERT: T 168 ASP cc_start: 0.7864 (t70) cc_final: 0.7242 (t0) REVERT: B 333 MET cc_start: 0.8513 (mmm) cc_final: 0.8129 (tpp) REVERT: B 364 GLU cc_start: 0.7952 (mt-10) cc_final: 0.7530 (mp0) REVERT: B 419 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.8106 (tp) REVERT: C 158 ASP cc_start: 0.8277 (t0) cc_final: 0.7871 (t0) REVERT: C 302 GLU cc_start: 0.7976 (pm20) cc_final: 0.7160 (pm20) REVERT: D 70 ASP cc_start: 0.8499 (t0) cc_final: 0.8173 (t0) REVERT: D 160 LYS cc_start: 0.8623 (OUTLIER) cc_final: 0.8398 (ttmm) REVERT: D 211 LYS cc_start: 0.9293 (mmtt) cc_final: 0.8954 (tppt) REVERT: D 238 SER cc_start: 0.8797 (t) cc_final: 0.8577 (p) REVERT: E 158 GLN cc_start: 0.8356 (OUTLIER) cc_final: 0.7999 (mm-40) REVERT: E 302 GLU cc_start: 0.8384 (mm-30) cc_final: 0.8168 (tp30) REVERT: F 97 MET cc_start: 0.8876 (ttp) cc_final: 0.8068 (tmm) REVERT: F 330 TRP cc_start: 0.8511 (t60) cc_final: 0.7428 (t60) REVERT: F 366 MET cc_start: 0.8069 (mtp) cc_final: 0.7683 (mtm) REVERT: F 388 MET cc_start: 0.7732 (mtp) cc_final: 0.7164 (ttm) REVERT: F 400 TYR cc_start: 0.8200 (m-80) cc_final: 0.7641 (m-80) REVERT: G 195 GLN cc_start: 0.8097 (mt0) cc_final: 0.7676 (mt0) REVERT: G 224 GLN cc_start: 0.7862 (mt0) cc_final: 0.7495 (mt0) REVERT: G 285 MET cc_start: 0.8724 (OUTLIER) cc_final: 0.8377 (ptm) REVERT: G 390 MET cc_start: 0.8096 (mmm) cc_final: 0.7407 (tmm) REVERT: H 165 GLU cc_start: 0.7822 (tp30) cc_final: 0.7545 (tp30) REVERT: H 181 MET cc_start: 0.8958 (OUTLIER) cc_final: 0.8440 (mmp) REVERT: H 195 GLN cc_start: 0.8858 (OUTLIER) cc_final: 0.8240 (mp10) REVERT: H 394 ARG cc_start: 0.7758 (ttm-80) cc_final: 0.7406 (ttm170) REVERT: I 135 MET cc_start: 0.8212 (tpt) cc_final: 0.7639 (mmm) REVERT: I 164 CYS cc_start: 0.7906 (m) cc_final: 0.7251 (t) REVERT: I 179 THR cc_start: 0.8483 (m) cc_final: 0.8181 (m) REVERT: I 195 GLN cc_start: 0.7964 (tm130) cc_final: 0.7703 (tm-30) REVERT: J 135 MET cc_start: 0.7947 (tpp) cc_final: 0.7530 (tpp) REVERT: J 136 LYS cc_start: 0.7846 (pttp) cc_final: 0.7390 (pttm) REVERT: J 157 SER cc_start: 0.8517 (t) cc_final: 0.8135 (t) REVERT: J 163 GLU cc_start: 0.7682 (mt-10) cc_final: 0.7020 (mp0) REVERT: J 180 HIS cc_start: 0.8415 (p-80) cc_final: 0.8166 (p-80) REVERT: J 184 GLU cc_start: 0.8598 (tt0) cc_final: 0.8217 (mm-30) REVERT: J 215 ARG cc_start: 0.8833 (mtt-85) cc_final: 0.7835 (mtt-85) REVERT: J 219 ASP cc_start: 0.7824 (p0) cc_final: 0.6795 (p0) REVERT: J 223 ARG cc_start: 0.8782 (mtm180) cc_final: 0.8109 (mtm180) REVERT: K 151 LYS cc_start: 0.9077 (tptp) cc_final: 0.8452 (pttp) REVERT: K 245 TRP cc_start: 0.8124 (p90) cc_final: 0.7799 (p90) REVERT: L 156 ARG cc_start: 0.7936 (OUTLIER) cc_final: 0.7631 (ttt-90) REVERT: L 161 ASP cc_start: 0.8721 (t0) cc_final: 0.8497 (t0) REVERT: L 166 GLN cc_start: 0.7282 (mm110) cc_final: 0.6477 (tp40) REVERT: L 171 MET cc_start: 0.8237 (ppp) cc_final: 0.7707 (ppp) REVERT: L 215 ARG cc_start: 0.8811 (mtt-85) cc_final: 0.8141 (mtt-85) REVERT: L 223 ARG cc_start: 0.8132 (mtm180) cc_final: 0.7656 (mtm180) REVERT: L 246 ASN cc_start: 0.8913 (t0) cc_final: 0.8659 (t0) REVERT: Q 1 GLU cc_start: 0.8118 (tp30) cc_final: 0.7811 (tp30) REVERT: Q 111 MET cc_start: 0.8909 (OUTLIER) cc_final: 0.7167 (mmm) REVERT: R 17 ASP cc_start: 0.8077 (t0) cc_final: 0.7819 (t0) REVERT: R 92 TYR cc_start: 0.7769 (t80) cc_final: 0.7506 (t80) REVERT: R 103 THR cc_start: 0.8753 (m) cc_final: 0.8425 (p) REVERT: R 124 GLU cc_start: 0.7581 (mp0) cc_final: 0.7296 (mp0) REVERT: R 172 SER cc_start: 0.9167 (m) cc_final: 0.8898 (p) REVERT: O 34 MET cc_start: 0.4946 (mtt) cc_final: 0.3027 (mmm) REVERT: O 107 ASP cc_start: 0.8054 (p0) cc_final: 0.6939 (t0) REVERT: O 181 LEU cc_start: 0.7116 (OUTLIER) cc_final: 0.6195 (pt) REVERT: M 30 ASP cc_start: 0.8971 (p0) cc_final: 0.8603 (p0) REVERT: M 31 ASP cc_start: 0.8580 (t70) cc_final: 0.8078 (t70) REVERT: M 32 TYR cc_start: 0.8137 (m-80) cc_final: 0.7520 (m-80) REVERT: M 73 ASP cc_start: 0.6612 (t0) cc_final: 0.6019 (t70) REVERT: M 99 ASP cc_start: 0.8616 (t70) cc_final: 0.8263 (t0) REVERT: M 114 TRP cc_start: 0.8577 (m100) cc_final: 0.8117 (m100) REVERT: M 186 LEU cc_start: 0.7142 (mp) cc_final: 0.6673 (mp) REVERT: M 219 ASP cc_start: 0.5972 (m-30) cc_final: 0.5648 (t0) REVERT: N 18 ARG cc_start: 0.8028 (mmm-85) cc_final: 0.7505 (ttm-80) outliers start: 125 outliers final: 91 residues processed: 693 average time/residue: 0.2021 time to fit residues: 234.6982 Evaluate side-chains 675 residues out of total 4906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 575 time to evaluate : 1.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 53 TRP Chi-restraints excluded: chain S residue 58 ILE Chi-restraints excluded: chain S residue 146 THR Chi-restraints excluded: chain S residue 192 VAL Chi-restraints excluded: chain S residue 209 VAL Chi-restraints excluded: chain T residue 33 LEU Chi-restraints excluded: chain T residue 92 TYR Chi-restraints excluded: chain T residue 172 SER Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 183 ASP Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 351 GLN Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 401 ASP Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 437 SER Chi-restraints excluded: chain C residue 2 GLU Chi-restraints excluded: chain C residue 78 CYS Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 393 SER Chi-restraints excluded: chain D residue 160 LYS Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 299 MET Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain D residue 410 VAL Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 139 GLU Chi-restraints excluded: chain E residue 147 HIS Chi-restraints excluded: chain E residue 158 GLN Chi-restraints excluded: chain E residue 170 HIS Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 291 HIS Chi-restraints excluded: chain E residue 349 HIS Chi-restraints excluded: chain E residue 355 ILE Chi-restraints excluded: chain F residue 147 HIS Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain G residue 107 LYS Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain G residue 201 CYS Chi-restraints excluded: chain G residue 285 MET Chi-restraints excluded: chain G residue 375 SER Chi-restraints excluded: chain G residue 410 PHE Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 181 MET Chi-restraints excluded: chain H residue 191 THR Chi-restraints excluded: chain H residue 195 GLN Chi-restraints excluded: chain H residue 226 HIS Chi-restraints excluded: chain H residue 412 LEU Chi-restraints excluded: chain I residue 155 LYS Chi-restraints excluded: chain I residue 249 ILE Chi-restraints excluded: chain J residue 123 VAL Chi-restraints excluded: chain J residue 245 TRP Chi-restraints excluded: chain K residue 129 LEU Chi-restraints excluded: chain K residue 130 VAL Chi-restraints excluded: chain K residue 179 THR Chi-restraints excluded: chain K residue 243 VAL Chi-restraints excluded: chain K residue 254 THR Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 140 VAL Chi-restraints excluded: chain L residue 156 ARG Chi-restraints excluded: chain L residue 176 SER Chi-restraints excluded: chain L residue 189 TRP Chi-restraints excluded: chain Q residue 2 VAL Chi-restraints excluded: chain Q residue 57 SER Chi-restraints excluded: chain Q residue 96 CYS Chi-restraints excluded: chain Q residue 107 ASP Chi-restraints excluded: chain Q residue 111 MET Chi-restraints excluded: chain Q residue 180 VAL Chi-restraints excluded: chain Q residue 189 LEU Chi-restraints excluded: chain Q residue 207 CYS Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain R residue 198 THR Chi-restraints excluded: chain O residue 53 TRP Chi-restraints excluded: chain O residue 122 VAL Chi-restraints excluded: chain O residue 163 VAL Chi-restraints excluded: chain O residue 181 LEU Chi-restraints excluded: chain O residue 187 TYR Chi-restraints excluded: chain P residue 126 LEU Chi-restraints excluded: chain M residue 87 ARG Chi-restraints excluded: chain M residue 163 VAL Chi-restraints excluded: chain M residue 208 ASN Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 198 THR Chi-restraints excluded: chain N residue 206 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 568 random chunks: chunk 333 optimal weight: 6.9990 chunk 255 optimal weight: 30.0000 chunk 173 optimal weight: 5.9990 chunk 476 optimal weight: 30.0000 chunk 551 optimal weight: 9.9990 chunk 506 optimal weight: 40.0000 chunk 205 optimal weight: 2.9990 chunk 170 optimal weight: 20.0000 chunk 397 optimal weight: 30.0000 chunk 417 optimal weight: 8.9990 chunk 182 optimal weight: 4.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 54 ASN ** T 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 230 HIS E 62 HIS E 170 HIS E 224 GLN ** G 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 119 HIS Q 175 HIS ** O 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 74 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.158153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.114660 restraints weight = 81241.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.112958 restraints weight = 38415.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.113518 restraints weight = 41566.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.114171 restraints weight = 30645.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.116597 restraints weight = 25894.618| |-----------------------------------------------------------------------------| r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.5063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 45783 Z= 0.263 Angle : 0.695 15.264 62415 Z= 0.353 Chirality : 0.048 0.532 7058 Planarity : 0.005 0.053 7966 Dihedral : 6.959 87.463 6872 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.92 % Favored : 95.99 % Rotamer: Outliers : 3.02 % Allowed : 13.96 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 0.55 (0.11), residues: 5734 helix: 1.62 (0.23), residues: 547 sheet: 1.08 (0.12), residues: 1987 loop : -0.29 (0.11), residues: 3200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG Q 87 TYR 0.041 0.002 TYR F 359 PHE 0.027 0.002 PHE C 95 TRP 0.034 0.002 TRP M 53 HIS 0.011 0.001 HIS I 170 Details of bonding type rmsd covalent geometry : bond 0.00614 (45684) covalent geometry : angle 0.67918 (62212) SS BOND : bond 0.00482 ( 73) SS BOND : angle 1.57035 ( 146) hydrogen bonds : bond 0.04006 ( 1445) hydrogen bonds : angle 5.37915 ( 3576) Misc. bond : bond 0.00439 ( 7) link_ALPHA1-3 : bond 0.02235 ( 1) link_ALPHA1-3 : angle 2.31574 ( 3) link_ALPHA1-4 : bond 0.01899 ( 2) link_ALPHA1-4 : angle 2.43096 ( 6) link_BETA1-4 : bond 0.01323 ( 6) link_BETA1-4 : angle 4.55788 ( 18) link_BETA1-6 : bond 0.00675 ( 5) link_BETA1-6 : angle 1.82208 ( 15) link_NAG-ASN : bond 0.00950 ( 5) link_NAG-ASN : angle 6.55598 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11468 Ramachandran restraints generated. 5734 Oldfield, 0 Emsley, 5734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11468 Ramachandran restraints generated. 5734 Oldfield, 0 Emsley, 5734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 725 residues out of total 4906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 577 time to evaluate : 1.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: S 83 MET cc_start: 0.8573 (mtm) cc_final: 0.8146 (mtm) REVERT: S 212 LYS cc_start: 0.8868 (tppt) cc_final: 0.8585 (tppt) REVERT: T 168 ASP cc_start: 0.8279 (t70) cc_final: 0.7174 (t0) REVERT: B 333 MET cc_start: 0.8333 (mmm) cc_final: 0.7969 (tpp) REVERT: B 397 LEU cc_start: 0.9005 (tp) cc_final: 0.8756 (tp) REVERT: B 407 MET cc_start: 0.8100 (ppp) cc_final: 0.7847 (ppp) REVERT: B 419 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8286 (tp) REVERT: C 158 ASP cc_start: 0.8248 (t0) cc_final: 0.7843 (t0) REVERT: C 302 GLU cc_start: 0.8136 (pm20) cc_final: 0.7499 (pm20) REVERT: D 160 LYS cc_start: 0.8616 (OUTLIER) cc_final: 0.8366 (ttmm) REVERT: D 211 LYS cc_start: 0.9216 (mmtt) cc_final: 0.8943 (tppt) REVERT: D 247 ARG cc_start: 0.8903 (OUTLIER) cc_final: 0.8282 (ptm160) REVERT: D 295 SER cc_start: 0.9315 (m) cc_final: 0.8965 (p) REVERT: D 311 ASP cc_start: 0.7791 (p0) cc_final: 0.7458 (p0) REVERT: D 345 GLU cc_start: 0.7435 (mm-30) cc_final: 0.7029 (mm-30) REVERT: D 436 PHE cc_start: 0.8639 (t80) cc_final: 0.8406 (t80) REVERT: E 74 MET cc_start: 0.8080 (mtp) cc_final: 0.7808 (mtm) REVERT: E 158 GLN cc_start: 0.8372 (OUTLIER) cc_final: 0.8042 (mm-40) REVERT: F 97 MET cc_start: 0.8875 (ttp) cc_final: 0.7929 (tmm) REVERT: F 170 HIS cc_start: 0.7935 (OUTLIER) cc_final: 0.7187 (p-80) REVERT: F 221 LYS cc_start: 0.8316 (OUTLIER) cc_final: 0.8085 (pttm) REVERT: F 226 HIS cc_start: 0.6958 (OUTLIER) cc_final: 0.6033 (t-90) REVERT: F 330 TRP cc_start: 0.8746 (t60) cc_final: 0.8295 (t60) REVERT: F 366 MET cc_start: 0.8104 (mtp) cc_final: 0.7798 (mtt) REVERT: F 388 MET cc_start: 0.7858 (mtp) cc_final: 0.7403 (ttm) REVERT: F 400 TYR cc_start: 0.8491 (m-80) cc_final: 0.7877 (m-80) REVERT: G 195 GLN cc_start: 0.8165 (mt0) cc_final: 0.7932 (mt0) REVERT: G 224 GLN cc_start: 0.7794 (mt0) cc_final: 0.7486 (mt0) REVERT: G 390 MET cc_start: 0.8133 (mmm) cc_final: 0.7493 (tmm) REVERT: H 195 GLN cc_start: 0.8951 (OUTLIER) cc_final: 0.8134 (mp10) REVERT: H 394 ARG cc_start: 0.7839 (ttm-80) cc_final: 0.7474 (ttm170) REVERT: I 179 THR cc_start: 0.8516 (m) cc_final: 0.8205 (m) REVERT: I 187 TYR cc_start: 0.7792 (m-80) cc_final: 0.7349 (m-80) REVERT: J 135 MET cc_start: 0.7969 (tpp) cc_final: 0.7503 (tpp) REVERT: J 136 LYS cc_start: 0.7806 (pttp) cc_final: 0.7377 (pttm) REVERT: J 157 SER cc_start: 0.8811 (t) cc_final: 0.8546 (t) REVERT: J 163 GLU cc_start: 0.7664 (mt-10) cc_final: 0.7169 (mp0) REVERT: J 180 HIS cc_start: 0.8361 (p-80) cc_final: 0.8079 (p-80) REVERT: J 184 GLU cc_start: 0.8611 (tt0) cc_final: 0.8158 (mm-30) REVERT: J 215 ARG cc_start: 0.8807 (mtt-85) cc_final: 0.7753 (mtt-85) REVERT: J 219 ASP cc_start: 0.8123 (p0) cc_final: 0.7849 (p0) REVERT: J 223 ARG cc_start: 0.8931 (mtm180) cc_final: 0.8621 (mtm180) REVERT: K 245 TRP cc_start: 0.8241 (p90) cc_final: 0.7859 (p90) REVERT: L 156 ARG cc_start: 0.7836 (OUTLIER) cc_final: 0.7578 (ttt-90) REVERT: L 171 MET cc_start: 0.8347 (ppp) cc_final: 0.7822 (ppp) REVERT: L 223 ARG cc_start: 0.8057 (mtm180) cc_final: 0.7741 (mtm180) REVERT: Q 13 GLN cc_start: 0.8889 (mp10) cc_final: 0.8663 (mp10) REVERT: Q 111 MET cc_start: 0.9085 (OUTLIER) cc_final: 0.7704 (mmm) REVERT: R 17 ASP cc_start: 0.8234 (t0) cc_final: 0.7992 (t0) REVERT: R 103 THR cc_start: 0.8851 (m) cc_final: 0.8436 (p) REVERT: R 124 GLU cc_start: 0.7657 (mp0) cc_final: 0.7292 (mp0) REVERT: R 172 SER cc_start: 0.9262 (m) cc_final: 0.8974 (p) REVERT: O 34 MET cc_start: 0.4869 (mtt) cc_final: 0.3095 (mmm) REVERT: O 181 LEU cc_start: 0.7087 (OUTLIER) cc_final: 0.6302 (pt) REVERT: M 30 ASP cc_start: 0.8996 (p0) cc_final: 0.8546 (p0) REVERT: M 31 ASP cc_start: 0.8666 (t70) cc_final: 0.8083 (t70) REVERT: M 32 TYR cc_start: 0.8397 (m-80) cc_final: 0.7789 (m-80) REVERT: M 114 TRP cc_start: 0.8722 (m100) cc_final: 0.7927 (m100) REVERT: M 186 LEU cc_start: 0.7239 (mp) cc_final: 0.6703 (mp) REVERT: M 187 TYR cc_start: 0.8607 (m-80) cc_final: 0.8065 (m-80) outliers start: 148 outliers final: 115 residues processed: 684 average time/residue: 0.2220 time to fit residues: 254.6376 Evaluate side-chains 687 residues out of total 4906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 561 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 53 TRP Chi-restraints excluded: chain S residue 58 ILE Chi-restraints excluded: chain S residue 107 ASP Chi-restraints excluded: chain S residue 146 THR Chi-restraints excluded: chain S residue 190 SER Chi-restraints excluded: chain S residue 192 VAL Chi-restraints excluded: chain S residue 209 VAL Chi-restraints excluded: chain T residue 31 SER Chi-restraints excluded: chain T residue 92 TYR Chi-restraints excluded: chain T residue 172 SER Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 183 ASP Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 351 GLN Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 401 ASP Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 328 CYS Chi-restraints excluded: chain B residue 347 GLU Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 437 SER Chi-restraints excluded: chain C residue 2 GLU Chi-restraints excluded: chain C residue 78 CYS Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 393 SER Chi-restraints excluded: chain D residue 160 LYS Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 247 ARG Chi-restraints excluded: chain D residue 299 MET Chi-restraints excluded: chain D residue 338 THR Chi-restraints excluded: chain D residue 344 ILE Chi-restraints excluded: chain D residue 396 THR Chi-restraints excluded: chain D residue 397 LEU Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain D residue 410 VAL Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 139 GLU Chi-restraints excluded: chain E residue 147 HIS Chi-restraints excluded: chain E residue 158 GLN Chi-restraints excluded: chain E residue 170 HIS Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 291 HIS Chi-restraints excluded: chain E residue 349 HIS Chi-restraints excluded: chain E residue 355 ILE Chi-restraints excluded: chain E residue 388 MET Chi-restraints excluded: chain F residue 59 ASP Chi-restraints excluded: chain F residue 147 HIS Chi-restraints excluded: chain F residue 170 HIS Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain F residue 218 ASN Chi-restraints excluded: chain F residue 221 LYS Chi-restraints excluded: chain F residue 226 HIS Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 379 LEU Chi-restraints excluded: chain G residue 107 LYS Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain G residue 201 CYS Chi-restraints excluded: chain G residue 226 HIS Chi-restraints excluded: chain G residue 365 THR Chi-restraints excluded: chain G residue 410 PHE Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 170 HIS Chi-restraints excluded: chain H residue 188 VAL Chi-restraints excluded: chain H residue 191 THR Chi-restraints excluded: chain H residue 195 GLN Chi-restraints excluded: chain H residue 226 HIS Chi-restraints excluded: chain H residue 247 GLU Chi-restraints excluded: chain H residue 291 HIS Chi-restraints excluded: chain I residue 139 HIS Chi-restraints excluded: chain I residue 155 LYS Chi-restraints excluded: chain I residue 158 SER Chi-restraints excluded: chain I residue 249 ILE Chi-restraints excluded: chain J residue 227 ILE Chi-restraints excluded: chain J residue 242 VAL Chi-restraints excluded: chain J residue 245 TRP Chi-restraints excluded: chain J residue 249 ILE Chi-restraints excluded: chain K residue 129 LEU Chi-restraints excluded: chain K residue 130 VAL Chi-restraints excluded: chain K residue 179 THR Chi-restraints excluded: chain K residue 243 VAL Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 140 VAL Chi-restraints excluded: chain L residue 156 ARG Chi-restraints excluded: chain L residue 176 SER Chi-restraints excluded: chain L residue 189 TRP Chi-restraints excluded: chain Q residue 2 VAL Chi-restraints excluded: chain Q residue 53 TRP Chi-restraints excluded: chain Q residue 57 SER Chi-restraints excluded: chain Q residue 96 CYS Chi-restraints excluded: chain Q residue 107 ASP Chi-restraints excluded: chain Q residue 111 MET Chi-restraints excluded: chain Q residue 180 VAL Chi-restraints excluded: chain Q residue 189 LEU Chi-restraints excluded: chain Q residue 192 VAL Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain R residue 196 GLU Chi-restraints excluded: chain R residue 198 THR Chi-restraints excluded: chain O residue 53 TRP Chi-restraints excluded: chain O residue 122 VAL Chi-restraints excluded: chain O residue 163 VAL Chi-restraints excluded: chain O residue 181 LEU Chi-restraints excluded: chain O residue 187 TYR Chi-restraints excluded: chain P residue 126 LEU Chi-restraints excluded: chain P residue 147 VAL Chi-restraints excluded: chain M residue 57 SER Chi-restraints excluded: chain M residue 163 VAL Chi-restraints excluded: chain M residue 208 ASN Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 198 THR Chi-restraints excluded: chain N residue 206 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 568 random chunks: chunk 145 optimal weight: 3.9990 chunk 299 optimal weight: 6.9990 chunk 374 optimal weight: 10.0000 chunk 113 optimal weight: 8.9990 chunk 132 optimal weight: 2.9990 chunk 435 optimal weight: 10.0000 chunk 430 optimal weight: 6.9990 chunk 242 optimal weight: 1.9990 chunk 304 optimal weight: 5.9990 chunk 165 optimal weight: 9.9990 chunk 438 optimal weight: 9.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** T 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 167 GLN ** T 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 230 HIS E 224 GLN ** G 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 139 HIS Q 175 HIS ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 167 GLN M 74 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.161977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.107426 restraints weight = 81626.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.111192 restraints weight = 36877.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.113375 restraints weight = 21862.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.114833 restraints weight = 15916.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.114833 restraints weight = 12907.974| |-----------------------------------------------------------------------------| r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.5190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 45783 Z= 0.204 Angle : 0.661 14.780 62415 Z= 0.333 Chirality : 0.047 0.499 7058 Planarity : 0.005 0.052 7966 Dihedral : 6.728 86.339 6872 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.70 % Favored : 96.23 % Rotamer: Outliers : 2.55 % Allowed : 14.80 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.11), residues: 5734 helix: 1.73 (0.23), residues: 541 sheet: 1.00 (0.12), residues: 2008 loop : -0.30 (0.11), residues: 3185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG Q 87 TYR 0.042 0.002 TYR F 359 PHE 0.024 0.002 PHE C 95 TRP 0.035 0.002 TRP H 64 HIS 0.030 0.001 HIS E 170 Details of bonding type rmsd covalent geometry : bond 0.00475 (45684) covalent geometry : angle 0.64558 (62212) SS BOND : bond 0.00392 ( 73) SS BOND : angle 1.35987 ( 146) hydrogen bonds : bond 0.03684 ( 1445) hydrogen bonds : angle 5.26958 ( 3576) Misc. bond : bond 0.00428 ( 7) link_ALPHA1-3 : bond 0.02143 ( 1) link_ALPHA1-3 : angle 2.08076 ( 3) link_ALPHA1-4 : bond 0.01784 ( 2) link_ALPHA1-4 : angle 2.56175 ( 6) link_BETA1-4 : bond 0.01379 ( 6) link_BETA1-4 : angle 4.53771 ( 18) link_BETA1-6 : bond 0.00567 ( 5) link_BETA1-6 : angle 1.68160 ( 15) link_NAG-ASN : bond 0.00972 ( 5) link_NAG-ASN : angle 6.42869 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11468 Ramachandran restraints generated. 5734 Oldfield, 0 Emsley, 5734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11468 Ramachandran restraints generated. 5734 Oldfield, 0 Emsley, 5734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 701 residues out of total 4906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 576 time to evaluate : 1.007 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: S 83 MET cc_start: 0.8573 (mtm) cc_final: 0.8050 (mtm) REVERT: S 106 ASP cc_start: 0.8317 (m-30) cc_final: 0.7728 (m-30) REVERT: S 212 LYS cc_start: 0.8914 (tppt) cc_final: 0.8696 (tppt) REVERT: T 18 ARG cc_start: 0.8422 (ttm-80) cc_final: 0.8103 (mtp85) REVERT: T 168 ASP cc_start: 0.7676 (t70) cc_final: 0.7043 (t70) REVERT: B 333 MET cc_start: 0.8414 (mmm) cc_final: 0.8036 (tpp) REVERT: B 419 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8234 (tp) REVERT: C 158 ASP cc_start: 0.8263 (t0) cc_final: 0.7857 (t0) REVERT: C 302 GLU cc_start: 0.8142 (pm20) cc_final: 0.7278 (pm20) REVERT: C 364 GLU cc_start: 0.8130 (pt0) cc_final: 0.7881 (pm20) REVERT: D 160 LYS cc_start: 0.8604 (OUTLIER) cc_final: 0.8358 (ttmm) REVERT: D 211 LYS cc_start: 0.9154 (mmtt) cc_final: 0.8926 (tppt) REVERT: D 238 SER cc_start: 0.8841 (t) cc_final: 0.8552 (p) REVERT: D 295 SER cc_start: 0.9345 (m) cc_final: 0.8985 (p) REVERT: D 311 ASP cc_start: 0.7893 (p0) cc_final: 0.7637 (p0) REVERT: D 345 GLU cc_start: 0.7449 (mm-30) cc_final: 0.7004 (mm-30) REVERT: D 436 PHE cc_start: 0.8653 (t80) cc_final: 0.8375 (t80) REVERT: E 74 MET cc_start: 0.8082 (mtp) cc_final: 0.7839 (mtm) REVERT: E 158 GLN cc_start: 0.8418 (OUTLIER) cc_final: 0.8080 (mm-40) REVERT: F 97 MET cc_start: 0.8922 (ttp) cc_final: 0.8025 (tmm) REVERT: F 170 HIS cc_start: 0.7918 (OUTLIER) cc_final: 0.7156 (p-80) REVERT: F 226 HIS cc_start: 0.6779 (OUTLIER) cc_final: 0.5848 (t-90) REVERT: F 330 TRP cc_start: 0.8732 (t60) cc_final: 0.8178 (t60) REVERT: F 366 MET cc_start: 0.8172 (mtp) cc_final: 0.7794 (mtm) REVERT: F 388 MET cc_start: 0.7843 (mtp) cc_final: 0.7343 (ttm) REVERT: F 400 TYR cc_start: 0.8428 (m-80) cc_final: 0.7811 (m-80) REVERT: G 74 MET cc_start: 0.7885 (mmm) cc_final: 0.7651 (mmt) REVERT: G 195 GLN cc_start: 0.8259 (mt0) cc_final: 0.7879 (mt0) REVERT: G 224 GLN cc_start: 0.8071 (mt0) cc_final: 0.7805 (mt0) REVERT: G 285 MET cc_start: 0.8779 (ptm) cc_final: 0.8434 (ptm) REVERT: G 390 MET cc_start: 0.8095 (mmm) cc_final: 0.7418 (tmm) REVERT: H 165 GLU cc_start: 0.7667 (tp30) cc_final: 0.7442 (tp30) REVERT: H 195 GLN cc_start: 0.8940 (OUTLIER) cc_final: 0.8107 (mp10) REVERT: H 247 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.8060 (pt0) REVERT: H 394 ARG cc_start: 0.7760 (ttm-80) cc_final: 0.7413 (ttm170) REVERT: I 179 THR cc_start: 0.8294 (m) cc_final: 0.7991 (m) REVERT: I 187 TYR cc_start: 0.7678 (m-80) cc_final: 0.7248 (m-80) REVERT: J 135 MET cc_start: 0.7921 (tpp) cc_final: 0.7466 (tpp) REVERT: J 136 LYS cc_start: 0.7783 (pttp) cc_final: 0.7360 (pttm) REVERT: J 157 SER cc_start: 0.8752 (t) cc_final: 0.8481 (t) REVERT: J 163 GLU cc_start: 0.7653 (mt-10) cc_final: 0.7140 (mp0) REVERT: J 180 HIS cc_start: 0.8346 (p-80) cc_final: 0.8038 (p-80) REVERT: J 184 GLU cc_start: 0.8568 (tt0) cc_final: 0.8162 (mm-30) REVERT: J 215 ARG cc_start: 0.8764 (mtt-85) cc_final: 0.7746 (mtt-85) REVERT: J 219 ASP cc_start: 0.8063 (p0) cc_final: 0.7230 (p0) REVERT: J 223 ARG cc_start: 0.8946 (mtm180) cc_final: 0.8283 (mtm180) REVERT: L 156 ARG cc_start: 0.7819 (OUTLIER) cc_final: 0.7525 (ttt-90) REVERT: L 166 GLN cc_start: 0.7442 (mm110) cc_final: 0.6706 (tp40) REVERT: L 171 MET cc_start: 0.8406 (ppp) cc_final: 0.7856 (ppp) REVERT: L 223 ARG cc_start: 0.8087 (mtm180) cc_final: 0.7688 (mtm180) REVERT: Q 13 GLN cc_start: 0.8852 (mp10) cc_final: 0.8608 (mp10) REVERT: Q 111 MET cc_start: 0.8882 (OUTLIER) cc_final: 0.7368 (mmm) REVERT: R 17 ASP cc_start: 0.8266 (t0) cc_final: 0.8019 (t0) REVERT: R 103 THR cc_start: 0.8807 (m) cc_final: 0.8366 (p) REVERT: R 124 GLU cc_start: 0.7695 (mp0) cc_final: 0.7277 (mp0) REVERT: R 172 SER cc_start: 0.9214 (m) cc_final: 0.8988 (p) REVERT: R 196 GLU cc_start: 0.7533 (OUTLIER) cc_final: 0.5858 (tp30) REVERT: O 34 MET cc_start: 0.4842 (mtt) cc_final: 0.3030 (mmm) REVERT: O 181 LEU cc_start: 0.7209 (OUTLIER) cc_final: 0.6388 (pt) REVERT: M 30 ASP cc_start: 0.8984 (p0) cc_final: 0.8558 (p0) REVERT: M 31 ASP cc_start: 0.8719 (t70) cc_final: 0.8108 (t70) REVERT: M 32 TYR cc_start: 0.8381 (m-80) cc_final: 0.7812 (m-80) REVERT: M 107 ASP cc_start: 0.8483 (p0) cc_final: 0.8202 (p0) REVERT: M 114 TRP cc_start: 0.8692 (m100) cc_final: 0.7868 (m100) REVERT: M 186 LEU cc_start: 0.7227 (mp) cc_final: 0.6752 (mp) REVERT: M 219 ASP cc_start: 0.5974 (m-30) cc_final: 0.5664 (t0) REVERT: N 18 ARG cc_start: 0.8088 (mmm-85) cc_final: 0.7770 (ttm-80) outliers start: 125 outliers final: 105 residues processed: 664 average time/residue: 0.1805 time to fit residues: 202.3250 Evaluate side-chains 682 residues out of total 4906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 566 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 53 TRP Chi-restraints excluded: chain S residue 58 ILE Chi-restraints excluded: chain S residue 107 ASP Chi-restraints excluded: chain S residue 146 THR Chi-restraints excluded: chain S residue 190 SER Chi-restraints excluded: chain S residue 192 VAL Chi-restraints excluded: chain S residue 209 VAL Chi-restraints excluded: chain T residue 31 SER Chi-restraints excluded: chain T residue 33 LEU Chi-restraints excluded: chain T residue 92 TYR Chi-restraints excluded: chain T residue 172 SER Chi-restraints excluded: chain T residue 190 HIS Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 183 ASP Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 351 GLN Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 401 ASP Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 328 CYS Chi-restraints excluded: chain B residue 347 GLU Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 437 SER Chi-restraints excluded: chain C residue 78 CYS Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 393 SER Chi-restraints excluded: chain D residue 160 LYS Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 299 MET Chi-restraints excluded: chain D residue 344 ILE Chi-restraints excluded: chain D residue 370 CYS Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain D residue 410 VAL Chi-restraints excluded: chain D residue 423 VAL Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 431 VAL Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 139 GLU Chi-restraints excluded: chain E residue 147 HIS Chi-restraints excluded: chain E residue 158 GLN Chi-restraints excluded: chain E residue 291 HIS Chi-restraints excluded: chain E residue 349 HIS Chi-restraints excluded: chain E residue 355 ILE Chi-restraints excluded: chain E residue 388 MET Chi-restraints excluded: chain F residue 59 ASP Chi-restraints excluded: chain F residue 147 HIS Chi-restraints excluded: chain F residue 170 HIS Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain F residue 218 ASN Chi-restraints excluded: chain F residue 226 HIS Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 379 LEU Chi-restraints excluded: chain G residue 107 LYS Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain G residue 201 CYS Chi-restraints excluded: chain G residue 410 PHE Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 170 HIS Chi-restraints excluded: chain H residue 188 VAL Chi-restraints excluded: chain H residue 191 THR Chi-restraints excluded: chain H residue 195 GLN Chi-restraints excluded: chain H residue 226 HIS Chi-restraints excluded: chain H residue 247 GLU Chi-restraints excluded: chain H residue 291 HIS Chi-restraints excluded: chain H residue 372 SER Chi-restraints excluded: chain I residue 155 LYS Chi-restraints excluded: chain I residue 158 SER Chi-restraints excluded: chain I residue 249 ILE Chi-restraints excluded: chain J residue 245 TRP Chi-restraints excluded: chain K residue 129 LEU Chi-restraints excluded: chain K residue 130 VAL Chi-restraints excluded: chain K residue 243 VAL Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 140 VAL Chi-restraints excluded: chain L residue 156 ARG Chi-restraints excluded: chain L residue 176 SER Chi-restraints excluded: chain L residue 189 TRP Chi-restraints excluded: chain Q residue 2 VAL Chi-restraints excluded: chain Q residue 53 TRP Chi-restraints excluded: chain Q residue 57 SER Chi-restraints excluded: chain Q residue 100 MET Chi-restraints excluded: chain Q residue 107 ASP Chi-restraints excluded: chain Q residue 111 MET Chi-restraints excluded: chain Q residue 180 VAL Chi-restraints excluded: chain Q residue 189 LEU Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain R residue 196 GLU Chi-restraints excluded: chain R residue 198 THR Chi-restraints excluded: chain O residue 53 TRP Chi-restraints excluded: chain O residue 122 VAL Chi-restraints excluded: chain O residue 163 VAL Chi-restraints excluded: chain O residue 181 LEU Chi-restraints excluded: chain O residue 187 TYR Chi-restraints excluded: chain P residue 126 LEU Chi-restraints excluded: chain P residue 147 VAL Chi-restraints excluded: chain M residue 57 SER Chi-restraints excluded: chain M residue 163 VAL Chi-restraints excluded: chain M residue 208 ASN Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 198 THR Chi-restraints excluded: chain N residue 206 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 568 random chunks: chunk 260 optimal weight: 3.9990 chunk 196 optimal weight: 5.9990 chunk 540 optimal weight: 20.0000 chunk 17 optimal weight: 10.0000 chunk 222 optimal weight: 9.9990 chunk 62 optimal weight: 0.0570 chunk 28 optimal weight: 20.0000 chunk 480 optimal weight: 30.0000 chunk 300 optimal weight: 0.8980 chunk 473 optimal weight: 0.0770 chunk 47 optimal weight: 2.9990 overall best weight: 1.6060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 54 ASN ** T 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 230 HIS E 224 GLN ** G 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 74 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.152408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.113068 restraints weight = 75960.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.108915 restraints weight = 49837.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.110215 restraints weight = 53129.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.110515 restraints weight = 36719.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.112197 restraints weight = 30748.870| |-----------------------------------------------------------------------------| r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.5236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 45783 Z= 0.118 Angle : 0.614 13.895 62415 Z= 0.307 Chirality : 0.045 0.444 7058 Planarity : 0.004 0.056 7966 Dihedral : 6.340 86.167 6872 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.96 % Favored : 96.95 % Rotamer: Outliers : 2.08 % Allowed : 15.47 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 0.69 (0.11), residues: 5734 helix: 1.86 (0.24), residues: 539 sheet: 1.13 (0.12), residues: 2013 loop : -0.21 (0.11), residues: 3182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG Q 87 TYR 0.040 0.001 TYR F 359 PHE 0.028 0.001 PHE M 68 TRP 0.037 0.001 TRP H 64 HIS 0.012 0.001 HIS I 170 Details of bonding type rmsd covalent geometry : bond 0.00267 (45684) covalent geometry : angle 0.59860 (62212) SS BOND : bond 0.00266 ( 73) SS BOND : angle 1.18193 ( 146) hydrogen bonds : bond 0.03168 ( 1445) hydrogen bonds : angle 5.07304 ( 3576) Misc. bond : bond 0.00415 ( 7) link_ALPHA1-3 : bond 0.02101 ( 1) link_ALPHA1-3 : angle 1.87494 ( 3) link_ALPHA1-4 : bond 0.01660 ( 2) link_ALPHA1-4 : angle 2.77593 ( 6) link_BETA1-4 : bond 0.01390 ( 6) link_BETA1-4 : angle 4.59787 ( 18) link_BETA1-6 : bond 0.00554 ( 5) link_BETA1-6 : angle 1.47636 ( 15) link_NAG-ASN : bond 0.01018 ( 5) link_NAG-ASN : angle 6.18291 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11468 Ramachandran restraints generated. 5734 Oldfield, 0 Emsley, 5734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11468 Ramachandran restraints generated. 5734 Oldfield, 0 Emsley, 5734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 703 residues out of total 4906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 601 time to evaluate : 1.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: S 83 MET cc_start: 0.8475 (mtm) cc_final: 0.8090 (mtm) REVERT: S 212 LYS cc_start: 0.8929 (tppt) cc_final: 0.8698 (tppt) REVERT: T 18 ARG cc_start: 0.8201 (ttm-80) cc_final: 0.7970 (mtp85) REVERT: T 143 ARG cc_start: 0.7555 (ttp80) cc_final: 0.7171 (tpt-90) REVERT: T 168 ASP cc_start: 0.7715 (t70) cc_final: 0.7278 (t70) REVERT: B 333 MET cc_start: 0.8080 (mmm) cc_final: 0.7730 (tpp) REVERT: B 419 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8225 (tp) REVERT: C 302 GLU cc_start: 0.8039 (pm20) cc_final: 0.7322 (pm20) REVERT: D 211 LYS cc_start: 0.9213 (mmtt) cc_final: 0.8928 (tppt) REVERT: D 238 SER cc_start: 0.8799 (t) cc_final: 0.8548 (p) REVERT: D 289 ARG cc_start: 0.7437 (mtp-110) cc_final: 0.7233 (mtp85) REVERT: D 295 SER cc_start: 0.9206 (m) cc_final: 0.8897 (p) REVERT: D 311 ASP cc_start: 0.7649 (p0) cc_final: 0.7358 (p0) REVERT: D 436 PHE cc_start: 0.8472 (t80) cc_final: 0.8198 (t80) REVERT: E 74 MET cc_start: 0.7981 (mtp) cc_final: 0.7750 (mtm) REVERT: E 158 GLN cc_start: 0.8317 (OUTLIER) cc_final: 0.8029 (mm-40) REVERT: E 302 GLU cc_start: 0.8254 (mm-30) cc_final: 0.8052 (tp30) REVERT: F 97 MET cc_start: 0.8693 (ttp) cc_final: 0.7961 (tmm) REVERT: F 226 HIS cc_start: 0.6939 (OUTLIER) cc_final: 0.6042 (t-90) REVERT: F 330 TRP cc_start: 0.8547 (t60) cc_final: 0.7472 (t60) REVERT: F 400 TYR cc_start: 0.8252 (m-80) cc_final: 0.7742 (m-80) REVERT: G 195 GLN cc_start: 0.8224 (mt0) cc_final: 0.7947 (mt0) REVERT: G 224 GLN cc_start: 0.7700 (mt0) cc_final: 0.7446 (mt0) REVERT: G 390 MET cc_start: 0.8115 (mmm) cc_final: 0.7558 (tmm) REVERT: H 181 MET cc_start: 0.8213 (tpp) cc_final: 0.7446 (mmt) REVERT: H 195 GLN cc_start: 0.8857 (OUTLIER) cc_final: 0.8389 (mp10) REVERT: H 394 ARG cc_start: 0.7874 (ttm-80) cc_final: 0.7533 (ttm170) REVERT: I 134 VAL cc_start: 0.7684 (t) cc_final: 0.7388 (m) REVERT: I 179 THR cc_start: 0.8134 (m) cc_final: 0.7878 (m) REVERT: I 195 GLN cc_start: 0.7412 (tm-30) cc_final: 0.7145 (pp30) REVERT: J 135 MET cc_start: 0.7762 (tpp) cc_final: 0.7398 (tpp) REVERT: J 136 LYS cc_start: 0.8016 (pttp) cc_final: 0.7797 (pttm) REVERT: J 157 SER cc_start: 0.8755 (t) cc_final: 0.8531 (t) REVERT: J 163 GLU cc_start: 0.7509 (mt-10) cc_final: 0.7274 (mp0) REVERT: J 180 HIS cc_start: 0.8272 (p-80) cc_final: 0.7990 (p-80) REVERT: J 184 GLU cc_start: 0.8539 (tt0) cc_final: 0.8239 (mm-30) REVERT: J 215 ARG cc_start: 0.8804 (mtt-85) cc_final: 0.7846 (mtt-85) REVERT: J 219 ASP cc_start: 0.7971 (p0) cc_final: 0.7216 (p0) REVERT: J 223 ARG cc_start: 0.8959 (mtm180) cc_final: 0.8471 (mtm180) REVERT: K 245 TRP cc_start: 0.8145 (p90) cc_final: 0.7574 (p90) REVERT: L 156 ARG cc_start: 0.7598 (OUTLIER) cc_final: 0.7311 (ttt-90) REVERT: L 166 GLN cc_start: 0.7443 (mm110) cc_final: 0.6702 (tp40) REVERT: L 171 MET cc_start: 0.8226 (ppp) cc_final: 0.7989 (ppp) REVERT: L 223 ARG cc_start: 0.8146 (mtm180) cc_final: 0.7675 (mtm180) REVERT: Q 13 GLN cc_start: 0.8710 (mp10) cc_final: 0.8487 (mp10) REVERT: Q 102 TYR cc_start: 0.8699 (p90) cc_final: 0.8382 (p90) REVERT: Q 111 MET cc_start: 0.8945 (OUTLIER) cc_final: 0.7145 (mmm) REVERT: R 103 THR cc_start: 0.8870 (m) cc_final: 0.8543 (p) REVERT: R 124 GLU cc_start: 0.7836 (mp0) cc_final: 0.7399 (mp0) REVERT: R 172 SER cc_start: 0.9232 (m) cc_final: 0.8884 (p) REVERT: O 34 MET cc_start: 0.4588 (mtt) cc_final: 0.2859 (mmm) REVERT: O 107 ASP cc_start: 0.7960 (p0) cc_final: 0.7567 (t0) REVERT: O 181 LEU cc_start: 0.7105 (OUTLIER) cc_final: 0.6305 (pt) REVERT: M 30 ASP cc_start: 0.8945 (p0) cc_final: 0.8427 (p0) REVERT: M 31 ASP cc_start: 0.8741 (t70) cc_final: 0.8173 (t70) REVERT: M 32 TYR cc_start: 0.8320 (m-80) cc_final: 0.7757 (m-80) REVERT: M 114 TRP cc_start: 0.8565 (m100) cc_final: 0.7790 (m100) REVERT: M 155 ASP cc_start: 0.7574 (t70) cc_final: 0.7018 (t70) REVERT: M 186 LEU cc_start: 0.7103 (mp) cc_final: 0.6804 (mp) REVERT: N 18 ARG cc_start: 0.8061 (mmm-85) cc_final: 0.7807 (ttm-80) outliers start: 102 outliers final: 87 residues processed: 672 average time/residue: 0.1635 time to fit residues: 185.3858 Evaluate side-chains 670 residues out of total 4906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 576 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 53 TRP Chi-restraints excluded: chain S residue 58 ILE Chi-restraints excluded: chain S residue 107 ASP Chi-restraints excluded: chain S residue 146 THR Chi-restraints excluded: chain S residue 190 SER Chi-restraints excluded: chain S residue 209 VAL Chi-restraints excluded: chain T residue 31 SER Chi-restraints excluded: chain T residue 92 TYR Chi-restraints excluded: chain T residue 172 SER Chi-restraints excluded: chain T residue 190 HIS Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 183 ASP Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 351 GLN Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 401 ASP Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 437 SER Chi-restraints excluded: chain C residue 78 CYS Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 393 SER Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 370 CYS Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain E residue 139 GLU Chi-restraints excluded: chain E residue 147 HIS Chi-restraints excluded: chain E residue 158 GLN Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 291 HIS Chi-restraints excluded: chain E residue 349 HIS Chi-restraints excluded: chain E residue 355 ILE Chi-restraints excluded: chain E residue 388 MET Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain F residue 218 ASN Chi-restraints excluded: chain F residue 226 HIS Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain G residue 201 CYS Chi-restraints excluded: chain G residue 410 PHE Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 170 HIS Chi-restraints excluded: chain H residue 191 THR Chi-restraints excluded: chain H residue 195 GLN Chi-restraints excluded: chain H residue 226 HIS Chi-restraints excluded: chain H residue 291 HIS Chi-restraints excluded: chain H residue 372 SER Chi-restraints excluded: chain I residue 155 LYS Chi-restraints excluded: chain I residue 203 ILE Chi-restraints excluded: chain I residue 249 ILE Chi-restraints excluded: chain J residue 245 TRP Chi-restraints excluded: chain K residue 129 LEU Chi-restraints excluded: chain K residue 130 VAL Chi-restraints excluded: chain K residue 243 VAL Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 140 VAL Chi-restraints excluded: chain L residue 156 ARG Chi-restraints excluded: chain L residue 189 TRP Chi-restraints excluded: chain Q residue 2 VAL Chi-restraints excluded: chain Q residue 53 TRP Chi-restraints excluded: chain Q residue 57 SER Chi-restraints excluded: chain Q residue 100 MET Chi-restraints excluded: chain Q residue 107 ASP Chi-restraints excluded: chain Q residue 111 MET Chi-restraints excluded: chain Q residue 180 VAL Chi-restraints excluded: chain Q residue 189 LEU Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain R residue 196 GLU Chi-restraints excluded: chain R residue 198 THR Chi-restraints excluded: chain O residue 53 TRP Chi-restraints excluded: chain O residue 122 VAL Chi-restraints excluded: chain O residue 163 VAL Chi-restraints excluded: chain O residue 181 LEU Chi-restraints excluded: chain O residue 187 TYR Chi-restraints excluded: chain P residue 147 VAL Chi-restraints excluded: chain M residue 163 VAL Chi-restraints excluded: chain M residue 208 ASN Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 198 THR Chi-restraints excluded: chain N residue 206 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 568 random chunks: chunk 53 optimal weight: 7.9990 chunk 431 optimal weight: 10.0000 chunk 61 optimal weight: 6.9990 chunk 387 optimal weight: 6.9990 chunk 23 optimal weight: 20.0000 chunk 67 optimal weight: 3.9990 chunk 396 optimal weight: 6.9990 chunk 480 optimal weight: 8.9990 chunk 400 optimal weight: 8.9990 chunk 402 optimal weight: 10.0000 chunk 432 optimal weight: 8.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** T 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 230 HIS E 224 GLN F 127 HIS F 147 HIS F 224 GLN ** G 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 211 ASN ** O 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 74 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.148383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.100220 restraints weight = 76718.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.101661 restraints weight = 49393.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.101376 restraints weight = 30279.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.101639 restraints weight = 29536.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.101945 restraints weight = 27494.323| |-----------------------------------------------------------------------------| r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.5437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.083 45783 Z= 0.294 Angle : 0.730 15.451 62415 Z= 0.371 Chirality : 0.049 0.515 7058 Planarity : 0.005 0.055 7966 Dihedral : 6.553 88.417 6872 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.62 % Favored : 95.27 % Rotamer: Outliers : 2.41 % Allowed : 15.45 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 0.36 (0.11), residues: 5734 helix: 1.67 (0.23), residues: 541 sheet: 0.87 (0.12), residues: 2020 loop : -0.41 (0.11), residues: 3173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG Q 87 TYR 0.042 0.002 TYR F 359 PHE 0.028 0.002 PHE C 95 TRP 0.036 0.002 TRP H 64 HIS 0.013 0.002 HIS I 170 Details of bonding type rmsd covalent geometry : bond 0.00689 (45684) covalent geometry : angle 0.71538 (62212) SS BOND : bond 0.00507 ( 73) SS BOND : angle 1.47363 ( 146) hydrogen bonds : bond 0.03984 ( 1445) hydrogen bonds : angle 5.34763 ( 3576) Misc. bond : bond 0.00419 ( 7) link_ALPHA1-3 : bond 0.01709 ( 1) link_ALPHA1-3 : angle 1.93563 ( 3) link_ALPHA1-4 : bond 0.01564 ( 2) link_ALPHA1-4 : angle 2.44390 ( 6) link_BETA1-4 : bond 0.01450 ( 6) link_BETA1-4 : angle 4.62746 ( 18) link_BETA1-6 : bond 0.00734 ( 5) link_BETA1-6 : angle 1.88857 ( 15) link_NAG-ASN : bond 0.00895 ( 5) link_NAG-ASN : angle 6.65199 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8350.57 seconds wall clock time: 144 minutes 21.05 seconds (8661.05 seconds total)