Starting phenix.real_space_refine on Sat Mar 7 08:28:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tl0_25982/03_2026/7tl0_25982_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tl0_25982/03_2026/7tl0_25982.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7tl0_25982/03_2026/7tl0_25982_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tl0_25982/03_2026/7tl0_25982_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7tl0_25982/03_2026/7tl0_25982.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tl0_25982/03_2026/7tl0_25982.map" } resolution = 3.06 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= 0.000 sd= 1.015 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: 5 Type Number sf(0) Gaussians S 126 5.16 5 C 12831 2.51 5 N 3447 2.21 5 O 4056 1.98 5 H 19866 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 40326 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 6577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 6577 Classifications: {'peptide': 433} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 418} Chain breaks: 1 Chain: "B" Number of atoms: 6577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 6577 Classifications: {'peptide': 433} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 418} Chain breaks: 1 Chain: "C" Number of atoms: 6577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 6577 Classifications: {'peptide': 433} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 418} Chain breaks: 1 Chain: "D" Number of atoms: 1857 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 120, 1857 Classifications: {'peptide': 120} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "E" Number of atoms: 1578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 1578 Classifications: {'peptide': 105} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 99} Chain: "F" Number of atoms: 1857 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 120, 1857 Classifications: {'peptide': 120} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "G" Number of atoms: 1578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 1578 Classifications: {'peptide': 105} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 99} Chain: "H" Number of atoms: 1857 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 120, 1857 Classifications: {'peptide': 120} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "I" Number of atoms: 1578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 1578 Classifications: {'peptide': 105} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 99} Chain: "J" Number of atoms: 1838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1838 Classifications: {'peptide': 124} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "K" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 1536 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "L" Number of atoms: 1838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1838 Classifications: {'peptide': 124} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "M" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 1536 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "N" Number of atoms: 1838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1838 Classifications: {'peptide': 124} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "O" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 1536 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 6.90, per 1000 atoms: 0.17 Number of scatterers: 40326 At special positions: 0 Unit cell: (146.256, 147.623, 123.019, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 126 16.00 O 4056 8.00 N 3447 7.00 C 12831 6.00 H 19866 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 28 " - pdb=" SG CYS A 407 " distance=2.03 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 182 " distance=2.03 Simple disulfide: pdb=" SG CYS A 110 " - pdb=" SG CYS A 322 " distance=2.03 Simple disulfide: pdb=" SG CYS A 127 " - pdb=" SG CYS A 153 " distance=2.04 Simple disulfide: pdb=" SG CYS A 140 " - pdb=" SG CYS A 147 " distance=2.04 Simple disulfide: pdb=" SG CYS A 283 " - pdb=" SG CYS A 311 " distance=2.03 Simple disulfide: pdb=" SG CYS A 292 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 326 " - pdb=" SG CYS A 335 " distance=2.03 Simple disulfide: pdb=" SG CYS A 350 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 365 " - pdb=" SG CYS A 463 " distance=2.03 Simple disulfide: pdb=" SG CYS A 384 " - pdb=" SG CYS A 390 " distance=2.02 Simple disulfide: pdb=" SG CYS B 28 " - pdb=" SG CYS B 407 " distance=2.03 Simple disulfide: pdb=" SG CYS B 60 " - pdb=" SG CYS B 182 " distance=2.03 Simple disulfide: pdb=" SG CYS B 110 " - pdb=" SG CYS B 322 " distance=2.03 Simple disulfide: pdb=" SG CYS B 127 " - pdb=" SG CYS B 153 " distance=2.04 Simple disulfide: pdb=" SG CYS B 140 " - pdb=" SG CYS B 147 " distance=2.04 Simple disulfide: pdb=" SG CYS B 283 " - pdb=" SG CYS B 311 " distance=2.03 Simple disulfide: pdb=" SG CYS B 292 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 326 " - pdb=" SG CYS B 335 " distance=2.03 Simple disulfide: pdb=" SG CYS B 350 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 365 " - pdb=" SG CYS B 463 " distance=2.03 Simple disulfide: pdb=" SG CYS B 384 " - pdb=" SG CYS B 390 " distance=2.02 Simple disulfide: pdb=" SG CYS C 28 " - pdb=" SG CYS C 407 " distance=2.03 Simple disulfide: pdb=" SG CYS C 60 " - pdb=" SG CYS C 182 " distance=2.02 Simple disulfide: pdb=" SG CYS C 110 " - pdb=" SG CYS C 322 " distance=2.03 Simple disulfide: pdb=" SG CYS C 127 " - pdb=" SG CYS C 153 " distance=2.04 Simple disulfide: pdb=" SG CYS C 140 " - pdb=" SG CYS C 147 " distance=2.04 Simple disulfide: pdb=" SG CYS C 283 " - pdb=" SG CYS C 311 " distance=2.03 Simple disulfide: pdb=" SG CYS C 292 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 326 " - pdb=" SG CYS C 335 " distance=2.03 Simple disulfide: pdb=" SG CYS C 350 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 365 " - pdb=" SG CYS C 463 " distance=2.03 Simple disulfide: pdb=" SG CYS C 384 " - pdb=" SG CYS C 390 " distance=2.02 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.04 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 92 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.04 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 90 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 96 " distance=2.04 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 90 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.04 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 90 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " NAG-ASN " NAG A 601 " - " ASN A 57 " " NAG A 602 " - " ASN A 353 " " NAG B 601 " - " ASN B 57 " " NAG B 602 " - " ASN B 353 " " NAG C 601 " - " ASN C 57 " " NAG C 602 " - " ASN C 353 " " NAG P 1 " - " ASN A 172 " " NAG Q 1 " - " ASN B 172 " " NAG R 1 " - " ASN C 172 " Time building additional restraints: 4.01 Conformation dependent library (CDL) restraints added in 1.1 seconds 5262 Ramachandran restraints generated. 2631 Oldfield, 0 Emsley, 2631 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4884 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 51 sheets defined 21.4% alpha, 38.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.37 Creating SS restraints... Processing helix chain 'A' and resid 54 through 58 Processing helix chain 'A' and resid 65 through 82 Processing helix chain 'A' and resid 104 through 129 removed outlier: 3.711A pdb=" N ILE A 108 " --> pdb=" O VAL A 104 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLY A 111 " --> pdb=" O ALA A 107 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ILE A 124 " --> pdb=" O ALA A 120 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N CYS A 127 " --> pdb=" O ALA A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 141 removed outlier: 4.124A pdb=" N ALA A 136 " --> pdb=" O SER A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 172 Processing helix chain 'A' and resid 172 through 177 Processing helix chain 'A' and resid 178 through 181 Processing helix chain 'A' and resid 186 through 197 removed outlier: 3.883A pdb=" N ALA A 190 " --> pdb=" O ASP A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 210 Processing helix chain 'A' and resid 223 through 234 Processing helix chain 'A' and resid 237 through 247 Processing helix chain 'A' and resid 247 through 255 Processing helix chain 'A' and resid 338 through 340 No H-bonds generated for 'chain 'A' and resid 338 through 340' Processing helix chain 'A' and resid 344 through 352 removed outlier: 3.607A pdb=" N LYS A 348 " --> pdb=" O GLU A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 446 Processing helix chain 'A' and resid 461 through 463 No H-bonds generated for 'chain 'A' and resid 461 through 463' Processing helix chain 'B' and resid 54 through 58 Processing helix chain 'B' and resid 65 through 82 Processing helix chain 'B' and resid 104 through 129 removed outlier: 4.094A pdb=" N ILE B 108 " --> pdb=" O VAL B 104 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N THR B 114 " --> pdb=" O CYS B 110 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE B 124 " --> pdb=" O ALA B 120 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N CYS B 127 " --> pdb=" O ALA B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 141 Processing helix chain 'B' and resid 163 through 172 Processing helix chain 'B' and resid 172 through 177 Processing helix chain 'B' and resid 178 through 181 Processing helix chain 'B' and resid 186 through 210 removed outlier: 3.912A pdb=" N ALA B 190 " --> pdb=" O ASP B 186 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ARG B 198 " --> pdb=" O SER B 194 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ARG B 199 " --> pdb=" O GLN B 195 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N PHE B 200 " --> pdb=" O PHE B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 233 Processing helix chain 'B' and resid 237 through 247 Processing helix chain 'B' and resid 247 through 255 Processing helix chain 'B' and resid 338 through 340 No H-bonds generated for 'chain 'B' and resid 338 through 340' Processing helix chain 'B' and resid 344 through 352 removed outlier: 3.722A pdb=" N LYS B 348 " --> pdb=" O GLU B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 445 Processing helix chain 'B' and resid 460 through 464 Processing helix chain 'C' and resid 54 through 58 Processing helix chain 'C' and resid 65 through 82 Processing helix chain 'C' and resid 104 through 129 removed outlier: 3.987A pdb=" N ILE C 108 " --> pdb=" O VAL C 104 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N THR C 114 " --> pdb=" O CYS C 110 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE C 124 " --> pdb=" O ALA C 120 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N CYS C 127 " --> pdb=" O ALA C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 141 removed outlier: 3.786A pdb=" N ALA C 136 " --> pdb=" O SER C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 172 Processing helix chain 'C' and resid 172 through 178 Processing helix chain 'C' and resid 186 through 210 removed outlier: 4.014A pdb=" N ALA C 190 " --> pdb=" O ASP C 186 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ARG C 198 " --> pdb=" O SER C 194 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N ARG C 199 " --> pdb=" O GLN C 195 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N PHE C 200 " --> pdb=" O PHE C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 234 Processing helix chain 'C' and resid 237 through 247 Processing helix chain 'C' and resid 247 through 255 Processing helix chain 'C' and resid 344 through 352 removed outlier: 3.925A pdb=" N LYS C 348 " --> pdb=" O GLU C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 441 through 446 Processing helix chain 'C' and resid 461 through 463 No H-bonds generated for 'chain 'C' and resid 461 through 463' Processing helix chain 'D' and resid 28 through 32 removed outlier: 3.697A pdb=" N TYR D 32 " --> pdb=" O PHE D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 75 No H-bonds generated for 'chain 'D' and resid 73 through 75' Processing helix chain 'E' and resid 79 through 83 removed outlier: 3.636A pdb=" N ILE E 83 " --> pdb=" O THR E 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 32 removed outlier: 3.757A pdb=" N TYR F 32 " --> pdb=" O PHE F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 73 through 75 No H-bonds generated for 'chain 'F' and resid 73 through 75' Processing helix chain 'G' and resid 79 through 83 removed outlier: 3.679A pdb=" N ILE G 83 " --> pdb=" O THR G 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.830A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 73 through 75 No H-bonds generated for 'chain 'H' and resid 73 through 75' Processing helix chain 'I' and resid 79 through 83 removed outlier: 3.694A pdb=" N ILE I 83 " --> pdb=" O THR I 80 " (cutoff:3.500A) Processing helix chain 'J' and resid 28 through 32 Processing helix chain 'J' and resid 87 through 91 Processing helix chain 'K' and resid 28 through 32 removed outlier: 3.539A pdb=" N GLY K 32 " --> pdb=" O ILE K 29 " (cutoff:3.500A) Processing helix chain 'K' and resid 81 through 85 Processing helix chain 'L' and resid 28 through 32 Processing helix chain 'L' and resid 87 through 91 Processing helix chain 'M' and resid 28 through 32 Processing helix chain 'M' and resid 81 through 85 Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 87 through 91 Processing helix chain 'O' and resid 28 through 32 removed outlier: 3.510A pdb=" N GLY O 32 " --> pdb=" O ILE O 29 " (cutoff:3.500A) Processing helix chain 'O' and resid 81 through 85 Processing sheet with id=AA1, first strand: chain 'A' and resid 327 through 329 removed outlier: 5.244A pdb=" N ILE A 31 " --> pdb=" O LYS A 287 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N LYS A 287 " --> pdb=" O ILE A 31 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N GLU A 33 " --> pdb=" O ILE A 285 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N ILE A 285 " --> pdb=" O GLU A 33 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N TYR A 35 " --> pdb=" O CYS A 283 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N THR A 281 " --> pdb=" O SER A 37 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N LEU A 39 " --> pdb=" O ILE A 279 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N ILE A 279 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N TRP A 309 " --> pdb=" O TYR A 320 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 327 through 329 removed outlier: 3.507A pdb=" N SER A 29 " --> pdb=" O LEU A 24 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N GLU A 21 " --> pdb=" O HIS A 435 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N ILE A 437 " --> pdb=" O GLU A 21 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N TYR A 23 " --> pdb=" O ILE A 437 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 146 through 150 removed outlier: 5.879A pdb=" N THR A 45 " --> pdb=" O ARG A 156 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N MET A 270 " --> pdb=" O LEU A 259 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N LEU A 259 " --> pdb=" O MET A 270 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N GLN A 272 " --> pdb=" O GLY A 257 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N GLY A 257 " --> pdb=" O GLN A 272 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 291 through 293 removed outlier: 6.843A pdb=" N CYS A 365 " --> pdb=" O PHE A 456 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N PHE A 456 " --> pdb=" O CYS A 365 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 372 through 375 Processing sheet with id=AA6, first strand: chain 'A' and resid 398 through 402 removed outlier: 6.877A pdb=" N ILE A 392 " --> pdb=" O ILE A 400 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N GLN A 402 " --> pdb=" O CYS A 390 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N CYS A 390 " --> pdb=" O GLN A 402 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 278 through 279 removed outlier: 3.507A pdb=" N VAL B 278 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLY B 34 " --> pdb=" O CYS B 283 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N CYS B 283 " --> pdb=" O GLY B 34 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N TRP B 309 " --> pdb=" O TYR B 320 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N THR B 317 " --> pdb=" O VAL B 343 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 327 through 329 removed outlier: 7.979A pdb=" N VAL B 333 " --> pdb=" O GLY B 34 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N LEU B 36 " --> pdb=" O VAL B 333 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N CYS B 335 " --> pdb=" O LEU B 36 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N VAL B 38 " --> pdb=" O CYS B 335 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER B 29 " --> pdb=" O LEU B 24 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N GLU B 21 " --> pdb=" O HIS B 435 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N ILE B 437 " --> pdb=" O GLU B 21 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N TYR B 23 " --> pdb=" O ILE B 437 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 146 through 148 removed outlier: 6.435A pdb=" N MET B 270 " --> pdb=" O LEU B 259 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N LEU B 259 " --> pdb=" O MET B 270 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N GLN B 272 " --> pdb=" O GLY B 257 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N GLY B 257 " --> pdb=" O GLN B 272 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 294 through 295 Processing sheet with id=AB2, first strand: chain 'B' and resid 301 through 304 removed outlier: 7.062A pdb=" N CYS B 365 " --> pdb=" O PHE B 456 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N PHE B 456 " --> pdb=" O CYS B 365 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 372 through 376 removed outlier: 3.592A pdb=" N GLY B 379 " --> pdb=" O SER B 376 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 398 through 402 removed outlier: 6.896A pdb=" N ILE B 392 " --> pdb=" O ILE B 400 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N GLN B 402 " --> pdb=" O CYS B 390 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N CYS B 390 " --> pdb=" O GLN B 402 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 327 through 329 removed outlier: 3.750A pdb=" N GLY C 34 " --> pdb=" O CYS C 283 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N CYS C 283 " --> pdb=" O GLY C 34 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N LEU C 36 " --> pdb=" O THR C 281 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N THR C 281 " --> pdb=" O LEU C 36 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N VAL C 38 " --> pdb=" O ILE C 279 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ILE C 279 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N TRP C 309 " --> pdb=" O TYR C 320 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N THR C 317 " --> pdb=" O VAL C 343 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 327 through 329 removed outlier: 6.281A pdb=" N GLU C 21 " --> pdb=" O HIS C 435 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N ILE C 437 " --> pdb=" O GLU C 21 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N TYR C 23 " --> pdb=" O ILE C 437 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 146 through 148 removed outlier: 6.407A pdb=" N SER C 266 " --> pdb=" O VAL C 262 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N VAL C 262 " --> pdb=" O SER C 266 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ILE C 268 " --> pdb=" O ILE C 260 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 293 through 295 removed outlier: 6.881A pdb=" N CYS C 365 " --> pdb=" O PHE C 456 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N PHE C 456 " --> pdb=" O CYS C 365 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 372 through 376 Processing sheet with id=AC1, first strand: chain 'C' and resid 398 through 402 removed outlier: 6.945A pdb=" N ILE C 392 " --> pdb=" O ILE C 400 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N GLN C 402 " --> pdb=" O CYS C 390 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N CYS C 390 " --> pdb=" O GLN C 402 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 3 through 6 removed outlier: 3.537A pdb=" N LEU D 18 " --> pdb=" O TRP D 82 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.451A pdb=" N ILE D 34 " --> pdb=" O ARG D 50 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N ARG D 50 " --> pdb=" O ILE D 34 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N TRP D 36 " --> pdb=" O MET D 48 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 10 through 12 removed outlier: 4.173A pdb=" N TYR D 102 " --> pdb=" O ARG D 94 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 4 through 7 removed outlier: 3.885A pdb=" N HIS E 70 " --> pdb=" O SER E 67 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.417A pdb=" N LEU E 33 " --> pdb=" O TYR E 49 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N TYR E 49 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 3 through 6 removed outlier: 3.705A pdb=" N VAL F 5 " --> pdb=" O LYS F 23 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU F 18 " --> pdb=" O TRP F 82 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 9 through 12 removed outlier: 6.545A pdb=" N ILE F 34 " --> pdb=" O ARG F 50 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N ARG F 50 " --> pdb=" O ILE F 34 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N TRP F 36 " --> pdb=" O MET F 48 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 9 through 12 removed outlier: 4.110A pdb=" N TYR F 102 " --> pdb=" O ARG F 94 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 4 through 7 removed outlier: 3.809A pdb=" N HIS G 70 " --> pdb=" O SER G 67 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 10 through 11 removed outlier: 6.454A pdb=" N LEU G 33 " --> pdb=" O TYR G 49 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N TYR G 49 " --> pdb=" O LEU G 33 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N TRP G 35 " --> pdb=" O LEU G 47 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.527A pdb=" N LEU H 18 " --> pdb=" O TRP H 82 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 9 through 12 removed outlier: 6.438A pdb=" N ILE H 34 " --> pdb=" O ARG H 50 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ARG H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 9 through 12 removed outlier: 4.108A pdb=" N TYR H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 4 through 7 removed outlier: 3.905A pdb=" N HIS I 70 " --> pdb=" O SER I 67 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.495A pdb=" N LEU I 33 " --> pdb=" O TYR I 49 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N TYR I 49 " --> pdb=" O LEU I 33 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'J' and resid 3 through 7 Processing sheet with id=AD9, first strand: chain 'J' and resid 11 through 12 removed outlier: 3.918A pdb=" N SER J 33 " --> pdb=" O ALA J 99 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N MET J 34 " --> pdb=" O SER J 50 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N SER J 50 " --> pdb=" O MET J 34 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N TRP J 36 " --> pdb=" O VAL J 48 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 11 through 12 removed outlier: 7.056A pdb=" N CYS J 96 " --> pdb=" O TRP J 114 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N TRP J 114 " --> pdb=" O CYS J 96 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ARG J 98 " --> pdb=" O ASP J 112 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'K' and resid 9 through 11 removed outlier: 6.531A pdb=" N TRP K 37 " --> pdb=" O LEU K 49 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'K' and resid 9 through 11 Processing sheet with id=AE4, first strand: chain 'K' and resid 18 through 23 Processing sheet with id=AE5, first strand: chain 'L' and resid 3 through 7 Processing sheet with id=AE6, first strand: chain 'L' and resid 11 through 12 removed outlier: 3.859A pdb=" N SER L 33 " --> pdb=" O ALA L 99 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N MET L 34 " --> pdb=" O SER L 50 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N SER L 50 " --> pdb=" O MET L 34 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N TRP L 36 " --> pdb=" O VAL L 48 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'L' and resid 11 through 12 removed outlier: 7.011A pdb=" N CYS L 96 " --> pdb=" O TRP L 114 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N TRP L 114 " --> pdb=" O CYS L 96 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ARG L 98 " --> pdb=" O ASP L 112 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'M' and resid 9 through 11 removed outlier: 6.525A pdb=" N TRP M 37 " --> pdb=" O LEU M 49 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'M' and resid 9 through 11 Processing sheet with id=AF1, first strand: chain 'M' and resid 18 through 23 Processing sheet with id=AF2, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AF3, first strand: chain 'N' and resid 11 through 12 removed outlier: 3.819A pdb=" N SER N 33 " --> pdb=" O ALA N 99 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N MET N 34 " --> pdb=" O SER N 50 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N SER N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'O' and resid 9 through 11 removed outlier: 6.530A pdb=" N TRP O 37 " --> pdb=" O LEU O 49 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'O' and resid 9 through 11 Processing sheet with id=AF6, first strand: chain 'O' and resid 18 through 23 1001 hydrogen bonds defined for protein. 2445 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: 11.16 Time building geometry restraints manager: 5.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 19846 1.03 - 1.23: 308 1.23 - 1.43: 8533 1.43 - 1.62: 11867 1.62 - 1.82: 162 Bond restraints: 40716 Sorted by residual: bond pdb=" N ARG A 156 " pdb=" H ARG A 156 " ideal model delta sigma weight residual 0.860 1.036 -0.176 2.00e-02 2.50e+03 7.73e+01 bond pdb=" N ASP B 421 " pdb=" H ASP B 421 " ideal model delta sigma weight residual 0.860 1.035 -0.175 2.00e-02 2.50e+03 7.70e+01 bond pdb=" N ARG C 253 " pdb=" H ARG C 253 " ideal model delta sigma weight residual 0.860 1.035 -0.175 2.00e-02 2.50e+03 7.67e+01 bond pdb=" NH2 ARG C 253 " pdb="HH22 ARG C 253 " ideal model delta sigma weight residual 0.860 1.016 -0.156 2.00e-02 2.50e+03 6.11e+01 bond pdb=" NH2 ARG A 156 " pdb="HH22 ARG A 156 " ideal model delta sigma weight residual 0.860 1.016 -0.156 2.00e-02 2.50e+03 6.10e+01 ... (remaining 40711 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.59: 71390 1.59 - 3.18: 1677 3.18 - 4.77: 180 4.77 - 6.36: 16 6.36 - 7.95: 3 Bond angle restraints: 73266 Sorted by residual: angle pdb=" C ASP C 421 " pdb=" CA ASP C 421 " pdb=" CB ASP C 421 " ideal model delta sigma weight residual 116.54 111.14 5.40 1.15e+00 7.56e-01 2.21e+01 angle pdb=" CA ASN C 353 " pdb=" CB ASN C 353 " pdb=" CG ASN C 353 " ideal model delta sigma weight residual 112.60 116.88 -4.28 1.00e+00 1.00e+00 1.83e+01 angle pdb=" C ASP B 421 " pdb=" CA ASP B 421 " pdb=" CB ASP B 421 " ideal model delta sigma weight residual 110.42 118.10 -7.68 1.99e+00 2.53e-01 1.49e+01 angle pdb=" CA ARG A 156 " pdb=" C ARG A 156 " pdb=" O ARG A 156 " ideal model delta sigma weight residual 122.37 117.93 4.44 1.15e+00 7.56e-01 1.49e+01 angle pdb=" N ASP B 421 " pdb=" CA ASP B 421 " pdb=" C ASP B 421 " ideal model delta sigma weight residual 110.80 102.85 7.95 2.13e+00 2.20e-01 1.39e+01 ... (remaining 73261 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 17603 17.82 - 35.64: 1180 35.64 - 53.45: 420 53.45 - 71.27: 379 71.27 - 89.09: 32 Dihedral angle restraints: 19614 sinusoidal: 10728 harmonic: 8886 Sorted by residual: dihedral pdb=" CA LEU I 104 " pdb=" C LEU I 104 " pdb=" N GLU I 105 " pdb=" CA GLU I 105 " ideal model delta harmonic sigma weight residual -180.00 -151.96 -28.04 0 5.00e+00 4.00e-02 3.15e+01 dihedral pdb=" CA VAL H 71 " pdb=" C VAL H 71 " pdb=" N ASP H 72 " pdb=" CA ASP H 72 " ideal model delta harmonic sigma weight residual 180.00 152.65 27.35 0 5.00e+00 4.00e-02 2.99e+01 dihedral pdb=" CA LEU E 104 " pdb=" C LEU E 104 " pdb=" N GLU E 105 " pdb=" CA GLU E 105 " ideal model delta harmonic sigma weight residual -180.00 -152.86 -27.14 0 5.00e+00 4.00e-02 2.95e+01 ... (remaining 19611 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.122: 3199 0.122 - 0.244: 39 0.244 - 0.367: 1 0.367 - 0.489: 0 0.489 - 0.611: 1 Chirality restraints: 3240 Sorted by residual: chirality pdb=" C1 NAG C 602 " pdb=" ND2 ASN C 353 " pdb=" C2 NAG C 602 " pdb=" O5 NAG C 602 " both_signs ideal model delta sigma weight residual False -2.40 -1.79 -0.61 2.00e-01 2.50e+01 9.34e+00 chirality pdb=" CA ASN C 353 " pdb=" N ASN C 353 " pdb=" C ASN C 353 " pdb=" CB ASN C 353 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" C1 NAG B 602 " pdb=" ND2 ASN B 353 " pdb=" C2 NAG B 602 " pdb=" O5 NAG B 602 " both_signs ideal model delta sigma weight residual False -2.40 -2.17 -0.23 2.00e-01 2.50e+01 1.36e+00 ... (remaining 3237 not shown) Planarity restraints: 6165 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG O 56 " -0.326 9.50e-02 1.11e+02 1.20e-01 7.22e+01 pdb=" NE ARG O 56 " -0.044 2.00e-02 2.50e+03 pdb=" CZ ARG O 56 " 0.039 2.00e-02 2.50e+03 pdb=" NH1 ARG O 56 " 0.040 2.00e-02 2.50e+03 pdb=" NH2 ARG O 56 " 0.096 2.00e-02 2.50e+03 pdb="HH11 ARG O 56 " 0.001 2.00e-02 2.50e+03 pdb="HH12 ARG O 56 " -0.026 2.00e-02 2.50e+03 pdb="HH21 ARG O 56 " 0.004 2.00e-02 2.50e+03 pdb="HH22 ARG O 56 " -0.096 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG M 56 " -0.315 9.50e-02 1.11e+02 1.17e-01 7.03e+01 pdb=" NE ARG M 56 " -0.050 2.00e-02 2.50e+03 pdb=" CZ ARG M 56 " 0.046 2.00e-02 2.50e+03 pdb=" NH1 ARG M 56 " 0.055 2.00e-02 2.50e+03 pdb=" NH2 ARG M 56 " 0.084 2.00e-02 2.50e+03 pdb="HH11 ARG M 56 " 0.001 2.00e-02 2.50e+03 pdb="HH12 ARG M 56 " -0.042 2.00e-02 2.50e+03 pdb="HH21 ARG M 56 " 0.003 2.00e-02 2.50e+03 pdb="HH22 ARG M 56 " -0.084 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG K 56 " -0.302 9.50e-02 1.11e+02 1.13e-01 6.88e+01 pdb=" NE ARG K 56 " -0.048 2.00e-02 2.50e+03 pdb=" CZ ARG K 56 " 0.043 2.00e-02 2.50e+03 pdb=" NH1 ARG K 56 " 0.048 2.00e-02 2.50e+03 pdb=" NH2 ARG K 56 " 0.089 2.00e-02 2.50e+03 pdb="HH11 ARG K 56 " 0.001 2.00e-02 2.50e+03 pdb="HH12 ARG K 56 " -0.035 2.00e-02 2.50e+03 pdb="HH21 ARG K 56 " 0.004 2.00e-02 2.50e+03 pdb="HH22 ARG K 56 " -0.089 2.00e-02 2.50e+03 ... (remaining 6162 not shown) Histogram of nonbonded interaction distances: 1.46 - 2.09: 1106 2.09 - 2.72: 70974 2.72 - 3.35: 116700 3.35 - 3.97: 155849 3.97 - 4.60: 246106 Nonbonded interactions: 590735 Sorted by model distance: nonbonded pdb=" OE1 GLU C 51 " pdb=" HG SER C 266 " model vdw 1.464 2.450 nonbonded pdb=" O ILE C 352 " pdb="HD21 ASN C 353 " model vdw 1.526 2.450 nonbonded pdb=" OE1 GLU B 51 " pdb=" HG SER B 266 " model vdw 1.534 2.450 nonbonded pdb=" H LYS D 13 " pdb=" OE2 GLU D 16 " model vdw 1.539 2.450 nonbonded pdb=" O PRO C 290 " pdb=" HH TYR C 385 " model vdw 1.547 2.450 ... (remaining 590730 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'L' selection = chain 'N' } ncs_group { reference = chain 'K' selection = chain 'M' selection = chain 'O' } ncs_group { reference = chain 'P' selection = chain 'Q' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.240 Extract box with map and model: 0.550 Check model and map are aligned: 0.170 Set scattering table: 0.100 Process input model: 39.500 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 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 : 0.008 0.063 20907 Z= 0.359 Angle : 0.744 10.640 28398 Z= 0.414 Chirality : 0.050 0.611 3240 Planarity : 0.008 0.097 3606 Dihedral : 13.544 89.091 7689 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 1.95 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.87 % Favored : 95.10 % Rotamer: Outliers : 1.91 % Allowed : 5.43 % Favored : 92.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.77 (0.16), residues: 2631 helix: -1.42 (0.20), residues: 414 sheet: -0.41 (0.17), residues: 885 loop : -0.09 (0.17), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.003 ARG L 72 TYR 0.039 0.006 TYR C 299 PHE 0.024 0.003 PHE D 90 TRP 0.040 0.006 TRP F 82 HIS 0.015 0.005 HIS M 36 Details of bonding type rmsd covalent geometry : bond 0.00814 (20850) covalent geometry : angle 0.72864 (28272) SS BOND : bond 0.00614 ( 45) SS BOND : angle 1.44959 ( 90) hydrogen bonds : bond 0.18441 ( 942) hydrogen bonds : angle 8.59262 ( 2445) link_BETA1-4 : bond 0.00385 ( 3) link_BETA1-4 : angle 1.38832 ( 9) link_NAG-ASN : bond 0.00759 ( 9) link_NAG-ASN : angle 4.30040 ( 27) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5262 Ramachandran restraints generated. 2631 Oldfield, 0 Emsley, 2631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5262 Ramachandran restraints generated. 2631 Oldfield, 0 Emsley, 2631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 221 time to evaluate : 1.054 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: B 224 ASP cc_start: 0.7792 (OUTLIER) cc_final: 0.7446 (t0) REVERT: B 270 MET cc_start: 0.8901 (ptm) cc_final: 0.8619 (ptt) REVERT: B 389 SER cc_start: 0.9073 (OUTLIER) cc_final: 0.8806 (t) REVERT: C 270 MET cc_start: 0.8762 (ptm) cc_final: 0.8510 (ptm) REVERT: D 64 LYS cc_start: 0.9151 (ttmm) cc_final: 0.8884 (ttmm) REVERT: E 4 MET cc_start: 0.8781 (OUTLIER) cc_final: 0.7946 (mmt) REVERT: F 10 GLU cc_start: 0.7898 (mp0) cc_final: 0.7428 (mp0) REVERT: F 72 ASP cc_start: 0.7869 (m-30) cc_final: 0.7386 (m-30) REVERT: F 108 LEU cc_start: 0.8727 (tt) cc_final: 0.8450 (tt) REVERT: G 1 ASP cc_start: 0.8316 (OUTLIER) cc_final: 0.7999 (m-30) REVERT: G 27 GLN cc_start: 0.8311 (mt0) cc_final: 0.8053 (mt0) REVERT: G 53 ASP cc_start: 0.8174 (m-30) cc_final: 0.7970 (m-30) REVERT: G 103 ARG cc_start: 0.8280 (ptp-110) cc_final: 0.7918 (ptm160) REVERT: H 46 GLU cc_start: 0.8189 (mt-10) cc_final: 0.7908 (mt-10) REVERT: J 83 MET cc_start: 0.9033 (mtm) cc_final: 0.8794 (mtp) REVERT: L 46 GLU cc_start: 0.7780 (mt-10) cc_final: 0.7560 (mt-10) REVERT: L 89 GLU cc_start: 0.8385 (pt0) cc_final: 0.8176 (pt0) outliers start: 43 outliers final: 21 residues processed: 256 average time/residue: 0.4968 time to fit residues: 173.1403 Evaluate side-chains 164 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 139 time to evaluate : 1.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 266 SER Chi-restraints excluded: chain B residue 389 SER Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 266 SER Chi-restraints excluded: chain C residue 353 ASN Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 389 SER Chi-restraints excluded: chain E residue 4 MET Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain G residue 1 ASP Chi-restraints excluded: chain G residue 55 GLU Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain I residue 1 ASP Chi-restraints excluded: chain I residue 4 MET Chi-restraints excluded: chain J residue 55 SER Chi-restraints excluded: chain J residue 108 THR Chi-restraints excluded: chain L residue 108 THR Chi-restraints excluded: chain N residue 108 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 0.9980 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 1.9990 chunk 111 optimal weight: 0.6980 chunk 258 optimal weight: 3.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 342 ASN E 24 GLN F 66 HIS G 24 GLN G 27 GLN I 24 GLN I 79 GLN I 93 ASN M 39 GLN O 81 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.063328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.052011 restraints weight = 143965.219| |-----------------------------------------------------------------------------| r_work (start): 0.2872 rms_B_bonded: 2.99 r_work: 0.2735 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2571 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2571 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2592 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2592 r_free = 0.2592 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2592 r_free = 0.2592 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2592 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 20907 Z= 0.170 Angle : 0.628 7.445 28398 Z= 0.341 Chirality : 0.047 0.506 3240 Planarity : 0.005 0.040 3606 Dihedral : 7.689 54.340 3167 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.69 % Allowed : 7.30 % Favored : 91.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.44 (0.16), residues: 2631 helix: -0.03 (0.24), residues: 414 sheet: -0.59 (0.17), residues: 852 loop : 0.00 (0.17), residues: 1365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 175 TYR 0.014 0.001 TYR C 385 PHE 0.013 0.001 PHE N 29 TRP 0.015 0.002 TRP F 33 HIS 0.011 0.002 HIS B 368 Details of bonding type rmsd covalent geometry : bond 0.00357 (20850) covalent geometry : angle 0.61929 (28272) SS BOND : bond 0.00945 ( 45) SS BOND : angle 0.91043 ( 90) hydrogen bonds : bond 0.04633 ( 942) hydrogen bonds : angle 6.22631 ( 2445) link_BETA1-4 : bond 0.00725 ( 3) link_BETA1-4 : angle 0.96641 ( 9) link_NAG-ASN : bond 0.00484 ( 9) link_NAG-ASN : angle 3.22465 ( 27) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5262 Ramachandran restraints generated. 2631 Oldfield, 0 Emsley, 2631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5262 Ramachandran restraints generated. 2631 Oldfield, 0 Emsley, 2631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 156 time to evaluate : 1.152 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: B 70 GLU cc_start: 0.8318 (mm-30) cc_final: 0.7915 (mm-30) REVERT: B 72 ASP cc_start: 0.7920 (m-30) cc_final: 0.7473 (m-30) REVERT: B 110 CYS cc_start: 0.7654 (OUTLIER) cc_final: 0.7290 (m) REVERT: B 224 ASP cc_start: 0.8106 (OUTLIER) cc_final: 0.7736 (t0) REVERT: B 389 SER cc_start: 0.8875 (OUTLIER) cc_final: 0.8657 (t) REVERT: C 110 CYS cc_start: 0.7902 (OUTLIER) cc_final: 0.7700 (m) REVERT: C 205 ARG cc_start: 0.8167 (ttm-80) cc_final: 0.7879 (ttm-80) REVERT: D 64 LYS cc_start: 0.9276 (ttmm) cc_final: 0.8889 (ttmm) REVERT: D 83 LYS cc_start: 0.8393 (mtmm) cc_final: 0.8190 (mtmm) REVERT: F 11 VAL cc_start: 0.9192 (m) cc_final: 0.8937 (p) REVERT: F 72 ASP cc_start: 0.7982 (m-30) cc_final: 0.7331 (m-30) REVERT: G 27 GLN cc_start: 0.8672 (mt0) cc_final: 0.8330 (mt0) REVERT: G 103 ARG cc_start: 0.8478 (ptp-110) cc_final: 0.8259 (ttm110) REVERT: I 11 LEU cc_start: 0.8258 (OUTLIER) cc_final: 0.7965 (tt) REVERT: I 53 ASP cc_start: 0.8396 (m-30) cc_final: 0.8098 (m-30) REVERT: J 83 MET cc_start: 0.9055 (mtm) cc_final: 0.8708 (mtp) REVERT: K 84 ASP cc_start: 0.8878 (m-30) cc_final: 0.8438 (m-30) REVERT: L 46 GLU cc_start: 0.8288 (mt-10) cc_final: 0.8001 (mt-10) REVERT: L 112 ASP cc_start: 0.8200 (p0) cc_final: 0.7945 (p0) REVERT: M 83 GLU cc_start: 0.8774 (mp0) cc_final: 0.8196 (mp0) REVERT: M 84 ASP cc_start: 0.8787 (m-30) cc_final: 0.8321 (m-30) REVERT: M 106 LYS cc_start: 0.8563 (ttmm) cc_final: 0.7990 (tptt) outliers start: 38 outliers final: 24 residues processed: 188 average time/residue: 0.4435 time to fit residues: 116.6863 Evaluate side-chains 162 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 133 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 147 CYS Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 110 CYS Chi-restraints excluded: chain B residue 147 CYS Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 266 SER Chi-restraints excluded: chain B residue 389 SER Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 110 CYS Chi-restraints excluded: chain C residue 147 CYS Chi-restraints excluded: chain C residue 353 ASN Chi-restraints excluded: chain C residue 389 SER Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain E residue 4 MET Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain F residue 16 GLU Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain I residue 4 MET Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain J residue 108 THR Chi-restraints excluded: chain L residue 108 THR Chi-restraints excluded: chain L residue 113 ILE Chi-restraints excluded: chain N residue 108 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 9 optimal weight: 2.9990 chunk 248 optimal weight: 3.9990 chunk 239 optimal weight: 1.9990 chunk 252 optimal weight: 4.9990 chunk 222 optimal weight: 4.9990 chunk 122 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 116 optimal weight: 3.9990 chunk 118 optimal weight: 1.9990 chunk 145 optimal weight: 0.9990 chunk 100 optimal weight: 3.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 312 GLN B 342 ASN I 30 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.062158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.050523 restraints weight = 145277.428| |-----------------------------------------------------------------------------| r_work (start): 0.2830 rms_B_bonded: 3.09 r_work: 0.2696 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2534 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2534 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2547 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2547 r_free = 0.2547 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2547 r_free = 0.2547 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2547 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 20907 Z= 0.243 Angle : 0.590 7.374 28398 Z= 0.317 Chirality : 0.045 0.434 3240 Planarity : 0.004 0.051 3606 Dihedral : 6.961 56.080 3156 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.69 % Allowed : 7.74 % Favored : 90.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.48 (0.16), residues: 2631 helix: 0.29 (0.25), residues: 408 sheet: -0.72 (0.17), residues: 822 loop : -0.09 (0.17), residues: 1401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 396 TYR 0.017 0.002 TYR H 91 PHE 0.012 0.002 PHE E 73 TRP 0.013 0.002 TRP H 82 HIS 0.008 0.002 HIS B 368 Details of bonding type rmsd covalent geometry : bond 0.00534 (20850) covalent geometry : angle 0.58162 (28272) SS BOND : bond 0.00475 ( 45) SS BOND : angle 0.96122 ( 90) hydrogen bonds : bond 0.04013 ( 942) hydrogen bonds : angle 5.71950 ( 2445) link_BETA1-4 : bond 0.00158 ( 3) link_BETA1-4 : angle 1.11443 ( 9) link_NAG-ASN : bond 0.00497 ( 9) link_NAG-ASN : angle 2.82971 ( 27) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5262 Ramachandran restraints generated. 2631 Oldfield, 0 Emsley, 2631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5262 Ramachandran restraints generated. 2631 Oldfield, 0 Emsley, 2631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 141 time to evaluate : 1.122 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: B 110 CYS cc_start: 0.7730 (OUTLIER) cc_final: 0.7401 (m) REVERT: B 224 ASP cc_start: 0.8310 (OUTLIER) cc_final: 0.8023 (t0) REVERT: B 389 SER cc_start: 0.8958 (OUTLIER) cc_final: 0.8713 (t) REVERT: C 70 GLU cc_start: 0.8128 (mt-10) cc_final: 0.7703 (mt-10) REVERT: C 110 CYS cc_start: 0.7963 (OUTLIER) cc_final: 0.7724 (m) REVERT: D 64 LYS cc_start: 0.9298 (ttmm) cc_final: 0.8806 (tppt) REVERT: F 10 GLU cc_start: 0.8299 (mp0) cc_final: 0.7365 (mp0) REVERT: F 11 VAL cc_start: 0.9151 (m) cc_final: 0.8905 (p) REVERT: F 72 ASP cc_start: 0.8026 (m-30) cc_final: 0.7454 (m-30) REVERT: F 108 LEU cc_start: 0.8676 (tt) cc_final: 0.7605 (mp) REVERT: G 27 GLN cc_start: 0.8758 (mt0) cc_final: 0.8414 (mt0) REVERT: G 100 GLN cc_start: 0.8668 (mm-40) cc_final: 0.8341 (mm-40) REVERT: I 11 LEU cc_start: 0.8314 (OUTLIER) cc_final: 0.8053 (tt) REVERT: I 53 ASP cc_start: 0.8509 (m-30) cc_final: 0.8271 (m-30) REVERT: L 112 ASP cc_start: 0.8290 (p0) cc_final: 0.7963 (p0) REVERT: M 52 ASP cc_start: 0.8859 (m-30) cc_final: 0.8587 (m-30) REVERT: M 83 GLU cc_start: 0.8836 (mp0) cc_final: 0.8236 (mp0) REVERT: M 106 LYS cc_start: 0.8606 (ttmm) cc_final: 0.8093 (tptt) REVERT: N 87 ARG cc_start: 0.7572 (mtt180) cc_final: 0.7368 (mtm-85) REVERT: O 83 GLU cc_start: 0.8418 (mp0) cc_final: 0.8173 (mp0) outliers start: 38 outliers final: 27 residues processed: 172 average time/residue: 0.4414 time to fit residues: 107.6036 Evaluate side-chains 167 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 135 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 147 CYS Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain B residue 110 CYS Chi-restraints excluded: chain B residue 147 CYS Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 266 SER Chi-restraints excluded: chain B residue 389 SER Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 54 ASP Chi-restraints excluded: chain C residue 110 CYS Chi-restraints excluded: chain C residue 353 ASN Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain E residue 4 MET Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain G residue 4 MET Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain I residue 4 MET Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain I residue 27 GLN Chi-restraints excluded: chain J residue 31 SER Chi-restraints excluded: chain J residue 108 THR Chi-restraints excluded: chain L residue 108 THR Chi-restraints excluded: chain L residue 113 ILE Chi-restraints excluded: chain N residue 55 SER Chi-restraints excluded: chain N residue 108 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 253 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 119 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 206 optimal weight: 0.6980 chunk 250 optimal weight: 3.9990 chunk 179 optimal weight: 0.8980 chunk 215 optimal weight: 4.9990 chunk 24 optimal weight: 0.9980 chunk 149 optimal weight: 2.9990 chunk 190 optimal weight: 4.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 426 GLN B 426 GLN C 426 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.063118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.051516 restraints weight = 143927.839| |-----------------------------------------------------------------------------| r_work (start): 0.2858 rms_B_bonded: 3.10 r_work: 0.2718 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2551 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2551 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2570 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2570 r_free = 0.2570 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2570 r_free = 0.2570 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2570 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.2357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 20907 Z= 0.145 Angle : 0.541 7.384 28398 Z= 0.287 Chirality : 0.044 0.374 3240 Planarity : 0.003 0.040 3606 Dihedral : 6.482 55.821 3153 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 2.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.78 % Allowed : 8.37 % Favored : 89.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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 (0.16), residues: 2631 helix: 0.73 (0.25), residues: 408 sheet: -0.78 (0.17), residues: 843 loop : -0.03 (0.17), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 205 TYR 0.013 0.001 TYR H 91 PHE 0.010 0.001 PHE E 73 TRP 0.011 0.001 TRP H 82 HIS 0.005 0.001 HIS D 66 Details of bonding type rmsd covalent geometry : bond 0.00318 (20850) covalent geometry : angle 0.53307 (28272) SS BOND : bond 0.00367 ( 45) SS BOND : angle 1.03632 ( 90) hydrogen bonds : bond 0.03331 ( 942) hydrogen bonds : angle 5.36105 ( 2445) link_BETA1-4 : bond 0.00296 ( 3) link_BETA1-4 : angle 1.08796 ( 9) link_NAG-ASN : bond 0.00418 ( 9) link_NAG-ASN : angle 2.51485 ( 27) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5262 Ramachandran restraints generated. 2631 Oldfield, 0 Emsley, 2631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5262 Ramachandran restraints generated. 2631 Oldfield, 0 Emsley, 2631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 146 time to evaluate : 1.241 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: A 372 MET cc_start: 0.8957 (ptm) cc_final: 0.8739 (ptp) REVERT: B 70 GLU cc_start: 0.8418 (mm-30) cc_final: 0.8014 (mm-30) REVERT: B 224 ASP cc_start: 0.8448 (OUTLIER) cc_final: 0.8063 (t0) REVERT: B 322 CYS cc_start: 0.7830 (t) cc_final: 0.7625 (t) REVERT: D 59 TYR cc_start: 0.9198 (m-80) cc_final: 0.8916 (m-10) REVERT: D 64 LYS cc_start: 0.9315 (ttmm) cc_final: 0.8839 (tppt) REVERT: F 11 VAL cc_start: 0.9150 (m) cc_final: 0.8944 (p) REVERT: F 72 ASP cc_start: 0.8054 (m-30) cc_final: 0.7460 (m-30) REVERT: F 108 LEU cc_start: 0.8655 (tt) cc_final: 0.7962 (mp) REVERT: G 27 GLN cc_start: 0.8768 (mt0) cc_final: 0.8476 (mt0) REVERT: G 100 GLN cc_start: 0.8705 (mm-40) cc_final: 0.8473 (mm-40) REVERT: H 89 ILE cc_start: 0.8643 (mm) cc_final: 0.8314 (mm) REVERT: I 11 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8206 (tt) REVERT: I 100 GLN cc_start: 0.8691 (mm-40) cc_final: 0.8327 (mm-40) REVERT: L 112 ASP cc_start: 0.8355 (p0) cc_final: 0.7996 (p0) REVERT: M 28 ASN cc_start: 0.8326 (OUTLIER) cc_final: 0.8066 (p0) REVERT: M 52 ASP cc_start: 0.8761 (m-30) cc_final: 0.8512 (m-30) REVERT: M 83 GLU cc_start: 0.8830 (mp0) cc_final: 0.8298 (mp0) REVERT: M 106 LYS cc_start: 0.8698 (ttmm) cc_final: 0.8241 (tptt) REVERT: N 87 ARG cc_start: 0.7758 (mtt180) cc_final: 0.7476 (mtm-85) REVERT: O 83 GLU cc_start: 0.8631 (mp0) cc_final: 0.8328 (mp0) outliers start: 40 outliers final: 25 residues processed: 178 average time/residue: 0.4174 time to fit residues: 106.6850 Evaluate side-chains 165 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 137 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 147 CYS Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain B residue 54 ASP Chi-restraints excluded: chain B residue 147 CYS Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 266 SER Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 368 HIS Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 147 CYS Chi-restraints excluded: chain C residue 270 MET Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain F residue 73 LYS Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain G residue 4 MET Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain I residue 4 MET Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain J residue 108 THR Chi-restraints excluded: chain L residue 31 SER Chi-restraints excluded: chain L residue 108 THR Chi-restraints excluded: chain M residue 28 ASN Chi-restraints excluded: chain N residue 31 SER Chi-restraints excluded: chain N residue 108 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 48 optimal weight: 2.9990 chunk 231 optimal weight: 0.7980 chunk 169 optimal weight: 6.9990 chunk 128 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 15 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 22 optimal weight: 0.0570 chunk 174 optimal weight: 2.9990 overall best weight: 1.5502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 312 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.062685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.051091 restraints weight = 143971.003| |-----------------------------------------------------------------------------| r_work (start): 0.2850 rms_B_bonded: 3.09 r_work: 0.2710 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2544 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2544 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2555 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2555 r_free = 0.2555 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2555 r_free = 0.2555 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2555 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 20907 Z= 0.181 Angle : 0.534 6.824 28398 Z= 0.283 Chirality : 0.044 0.351 3240 Planarity : 0.003 0.038 3606 Dihedral : 6.180 55.210 3147 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.69 % Allowed : 8.99 % Favored : 89.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.16), residues: 2631 helix: 0.99 (0.25), residues: 408 sheet: -0.81 (0.17), residues: 852 loop : -0.08 (0.17), residues: 1371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 103 TYR 0.012 0.001 TYR H 91 PHE 0.010 0.001 PHE I 73 TRP 0.010 0.001 TRP H 82 HIS 0.005 0.001 HIS B 368 Details of bonding type rmsd covalent geometry : bond 0.00399 (20850) covalent geometry : angle 0.52613 (28272) SS BOND : bond 0.00385 ( 45) SS BOND : angle 0.95818 ( 90) hydrogen bonds : bond 0.03203 ( 942) hydrogen bonds : angle 5.17387 ( 2445) link_BETA1-4 : bond 0.00138 ( 3) link_BETA1-4 : angle 1.06541 ( 9) link_NAG-ASN : bond 0.00425 ( 9) link_NAG-ASN : angle 2.49002 ( 27) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5262 Ramachandran restraints generated. 2631 Oldfield, 0 Emsley, 2631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5262 Ramachandran restraints generated. 2631 Oldfield, 0 Emsley, 2631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 145 time to evaluate : 0.674 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: A 372 MET cc_start: 0.9009 (ptm) cc_final: 0.8777 (ptp) REVERT: B 70 GLU cc_start: 0.8451 (mm-30) cc_final: 0.8034 (mm-30) REVERT: B 72 ASP cc_start: 0.8245 (m-30) cc_final: 0.7972 (m-30) REVERT: B 224 ASP cc_start: 0.8433 (OUTLIER) cc_final: 0.8100 (t0) REVERT: C 389 SER cc_start: 0.9045 (OUTLIER) cc_final: 0.8829 (t) REVERT: D 59 TYR cc_start: 0.9191 (m-80) cc_final: 0.8932 (m-10) REVERT: D 83 LYS cc_start: 0.8539 (mtmt) cc_final: 0.8289 (mttt) REVERT: E 11 LEU cc_start: 0.8488 (tp) cc_final: 0.8265 (tp) REVERT: F 11 VAL cc_start: 0.9208 (m) cc_final: 0.8939 (p) REVERT: F 72 ASP cc_start: 0.8068 (m-30) cc_final: 0.7480 (m-30) REVERT: F 108 LEU cc_start: 0.8710 (tt) cc_final: 0.7967 (mp) REVERT: G 27 GLN cc_start: 0.8779 (mt0) cc_final: 0.8469 (mt0) REVERT: H 16 GLU cc_start: 0.8436 (tt0) cc_final: 0.7863 (tp30) REVERT: H 89 ILE cc_start: 0.8641 (mm) cc_final: 0.8305 (mm) REVERT: I 11 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.8267 (tt) REVERT: L 59 ASP cc_start: 0.8560 (m-30) cc_final: 0.8281 (m-30) REVERT: L 112 ASP cc_start: 0.8374 (p0) cc_final: 0.7999 (p0) REVERT: M 28 ASN cc_start: 0.8277 (OUTLIER) cc_final: 0.8012 (p0) REVERT: M 83 GLU cc_start: 0.8862 (mp0) cc_final: 0.8321 (mp0) REVERT: M 106 LYS cc_start: 0.8681 (ttmm) cc_final: 0.8229 (tptt) REVERT: O 83 GLU cc_start: 0.8713 (mp0) cc_final: 0.8416 (mp0) outliers start: 38 outliers final: 29 residues processed: 178 average time/residue: 0.4307 time to fit residues: 109.2256 Evaluate side-chains 172 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 139 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 147 CYS Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain B residue 54 ASP Chi-restraints excluded: chain B residue 147 CYS Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 368 HIS Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain C residue 54 ASP Chi-restraints excluded: chain C residue 147 CYS Chi-restraints excluded: chain C residue 389 SER Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain F residue 73 LYS Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain G residue 4 MET Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain I residue 4 MET Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain I residue 27 GLN Chi-restraints excluded: chain J residue 31 SER Chi-restraints excluded: chain J residue 59 ASP Chi-restraints excluded: chain J residue 108 THR Chi-restraints excluded: chain L residue 31 SER Chi-restraints excluded: chain L residue 108 THR Chi-restraints excluded: chain M residue 28 ASN Chi-restraints excluded: chain N residue 55 SER Chi-restraints excluded: chain N residue 108 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 118 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 95 optimal weight: 0.6980 chunk 198 optimal weight: 4.9990 chunk 189 optimal weight: 0.6980 chunk 215 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 chunk 256 optimal weight: 4.9990 chunk 156 optimal weight: 0.5980 chunk 146 optimal weight: 5.9990 chunk 251 optimal weight: 0.3980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 93 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.063293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.051707 restraints weight = 143839.130| |-----------------------------------------------------------------------------| r_work (start): 0.2862 rms_B_bonded: 3.11 r_work: 0.2722 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2556 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2556 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2575 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2575 r_free = 0.2575 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2575 r_free = 0.2575 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2575 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.2739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20907 Z= 0.135 Angle : 0.512 6.978 28398 Z= 0.270 Chirality : 0.043 0.319 3240 Planarity : 0.003 0.061 3606 Dihedral : 5.892 54.602 3144 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.47 % Allowed : 9.79 % Favored : 88.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.22 (0.16), residues: 2631 helix: 1.36 (0.25), residues: 414 sheet: -0.87 (0.17), residues: 864 loop : 0.03 (0.17), residues: 1353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 103 TYR 0.011 0.001 TYR C 385 PHE 0.009 0.001 PHE I 73 TRP 0.012 0.001 TRP H 82 HIS 0.005 0.001 HIS B 368 Details of bonding type rmsd covalent geometry : bond 0.00298 (20850) covalent geometry : angle 0.50611 (28272) SS BOND : bond 0.00338 ( 45) SS BOND : angle 0.80549 ( 90) hydrogen bonds : bond 0.02951 ( 942) hydrogen bonds : angle 5.00953 ( 2445) link_BETA1-4 : bond 0.00298 ( 3) link_BETA1-4 : angle 1.03632 ( 9) link_NAG-ASN : bond 0.00379 ( 9) link_NAG-ASN : angle 2.27253 ( 27) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5262 Ramachandran restraints generated. 2631 Oldfield, 0 Emsley, 2631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5262 Ramachandran restraints generated. 2631 Oldfield, 0 Emsley, 2631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 150 time to evaluate : 1.069 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: B 70 GLU cc_start: 0.8454 (mm-30) cc_final: 0.8055 (mm-30) REVERT: B 72 ASP cc_start: 0.8263 (m-30) cc_final: 0.8030 (m-30) REVERT: D 13 LYS cc_start: 0.8358 (mmmt) cc_final: 0.7661 (mmmt) REVERT: D 16 GLU cc_start: 0.8618 (mt-10) cc_final: 0.7850 (mt-10) REVERT: D 59 TYR cc_start: 0.9153 (m-80) cc_final: 0.8879 (m-10) REVERT: D 83 LYS cc_start: 0.8503 (mtmt) cc_final: 0.8303 (mttt) REVERT: F 72 ASP cc_start: 0.8033 (m-30) cc_final: 0.7410 (m-30) REVERT: F 108 LEU cc_start: 0.8704 (tt) cc_final: 0.7973 (mp) REVERT: G 27 GLN cc_start: 0.8812 (mt0) cc_final: 0.8516 (mt0) REVERT: G 100 GLN cc_start: 0.8570 (mm-40) cc_final: 0.8273 (mp10) REVERT: H 16 GLU cc_start: 0.8462 (tt0) cc_final: 0.7856 (tp30) REVERT: H 89 ILE cc_start: 0.8629 (mm) cc_final: 0.8303 (mm) REVERT: I 11 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.8225 (tt) REVERT: L 59 ASP cc_start: 0.8586 (m-30) cc_final: 0.8273 (m-30) REVERT: L 112 ASP cc_start: 0.8363 (p0) cc_final: 0.7980 (p0) REVERT: M 28 ASN cc_start: 0.8210 (OUTLIER) cc_final: 0.7944 (p0) REVERT: M 83 GLU cc_start: 0.8870 (mp0) cc_final: 0.8339 (mp0) REVERT: M 106 LYS cc_start: 0.8653 (ttmm) cc_final: 0.8247 (tptt) REVERT: O 83 GLU cc_start: 0.8726 (mp0) cc_final: 0.8294 (mp0) outliers start: 33 outliers final: 28 residues processed: 177 average time/residue: 0.4323 time to fit residues: 108.1553 Evaluate side-chains 173 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 143 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 147 CYS Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain B residue 147 CYS Chi-restraints excluded: chain B residue 280 ASP Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 368 HIS Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 147 CYS Chi-restraints excluded: chain C residue 266 SER Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain F residue 73 LYS Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain G residue 4 MET Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain I residue 4 MET Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain I residue 27 GLN Chi-restraints excluded: chain J residue 108 THR Chi-restraints excluded: chain L residue 31 SER Chi-restraints excluded: chain L residue 108 THR Chi-restraints excluded: chain M residue 28 ASN Chi-restraints excluded: chain N residue 31 SER Chi-restraints excluded: chain N residue 62 ASP Chi-restraints excluded: chain N residue 108 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 44 optimal weight: 0.9990 chunk 111 optimal weight: 2.9990 chunk 76 optimal weight: 0.4980 chunk 142 optimal weight: 6.9990 chunk 229 optimal weight: 4.9990 chunk 109 optimal weight: 2.9990 chunk 164 optimal weight: 6.9990 chunk 12 optimal weight: 2.9990 chunk 206 optimal weight: 2.9990 chunk 169 optimal weight: 5.9990 chunk 236 optimal weight: 5.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 GLN I 24 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.062147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.050574 restraints weight = 144059.617| |-----------------------------------------------------------------------------| r_work (start): 0.2835 rms_B_bonded: 3.09 r_work: 0.2696 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2530 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2530 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2547 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2547 r_free = 0.2547 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2547 r_free = 0.2547 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2547 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 20907 Z= 0.231 Angle : 0.543 6.929 28398 Z= 0.286 Chirality : 0.043 0.320 3240 Planarity : 0.004 0.062 3606 Dihedral : 5.854 53.447 3140 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.69 % Allowed : 9.92 % Favored : 88.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.26 (0.16), residues: 2631 helix: 1.36 (0.25), residues: 414 sheet: -0.78 (0.17), residues: 852 loop : -0.11 (0.17), residues: 1365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 18 TYR 0.012 0.001 TYR A 319 PHE 0.012 0.001 PHE G 73 TRP 0.012 0.001 TRP H 82 HIS 0.006 0.001 HIS B 368 Details of bonding type rmsd covalent geometry : bond 0.00510 (20850) covalent geometry : angle 0.53622 (28272) SS BOND : bond 0.00384 ( 45) SS BOND : angle 0.89750 ( 90) hydrogen bonds : bond 0.03128 ( 942) hydrogen bonds : angle 5.00669 ( 2445) link_BETA1-4 : bond 0.00170 ( 3) link_BETA1-4 : angle 1.16626 ( 9) link_NAG-ASN : bond 0.00437 ( 9) link_NAG-ASN : angle 2.39813 ( 27) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5262 Ramachandran restraints generated. 2631 Oldfield, 0 Emsley, 2631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5262 Ramachandran restraints generated. 2631 Oldfield, 0 Emsley, 2631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 146 time to evaluate : 1.011 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: A 372 MET cc_start: 0.8952 (ptm) cc_final: 0.8749 (ptp) REVERT: B 70 GLU cc_start: 0.8514 (mm-30) cc_final: 0.8128 (mm-30) REVERT: B 72 ASP cc_start: 0.8290 (m-30) cc_final: 0.8054 (m-30) REVERT: B 110 CYS cc_start: 0.7934 (OUTLIER) cc_final: 0.7594 (m) REVERT: D 59 TYR cc_start: 0.9180 (m-80) cc_final: 0.8938 (m-10) REVERT: D 83 LYS cc_start: 0.8581 (mtmt) cc_final: 0.8319 (mttt) REVERT: F 72 ASP cc_start: 0.8038 (m-30) cc_final: 0.7410 (m-30) REVERT: F 108 LEU cc_start: 0.8700 (tt) cc_final: 0.7947 (mp) REVERT: G 27 GLN cc_start: 0.8805 (mt0) cc_final: 0.8488 (mt0) REVERT: H 16 GLU cc_start: 0.8554 (tt0) cc_final: 0.7924 (tp30) REVERT: H 89 ILE cc_start: 0.8626 (mm) cc_final: 0.8306 (mm) REVERT: I 11 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.8216 (tt) REVERT: L 59 ASP cc_start: 0.8608 (m-30) cc_final: 0.8293 (m-30) REVERT: L 112 ASP cc_start: 0.8428 (p0) cc_final: 0.7954 (p0) REVERT: M 83 GLU cc_start: 0.8858 (mp0) cc_final: 0.8342 (mp0) REVERT: M 106 LYS cc_start: 0.8682 (ttmm) cc_final: 0.8254 (tptt) REVERT: N 87 ARG cc_start: 0.7858 (mtt180) cc_final: 0.7637 (mtm-85) REVERT: O 83 GLU cc_start: 0.8742 (mp0) cc_final: 0.8379 (mp0) outliers start: 38 outliers final: 32 residues processed: 177 average time/residue: 0.4180 time to fit residues: 105.9915 Evaluate side-chains 176 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 142 time to evaluate : 1.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 147 CYS Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain B residue 54 ASP Chi-restraints excluded: chain B residue 110 CYS Chi-restraints excluded: chain B residue 147 CYS Chi-restraints excluded: chain B residue 280 ASP Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 368 HIS Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 54 ASP Chi-restraints excluded: chain C residue 147 CYS Chi-restraints excluded: chain C residue 266 SER Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain F residue 73 LYS Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain G residue 4 MET Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain I residue 4 MET Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain I residue 27 GLN Chi-restraints excluded: chain J residue 31 SER Chi-restraints excluded: chain J residue 59 ASP Chi-restraints excluded: chain J residue 108 THR Chi-restraints excluded: chain L residue 31 SER Chi-restraints excluded: chain L residue 108 THR Chi-restraints excluded: chain N residue 31 SER Chi-restraints excluded: chain N residue 55 SER Chi-restraints excluded: chain N residue 62 ASP Chi-restraints excluded: chain N residue 108 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 207 optimal weight: 0.0870 chunk 201 optimal weight: 1.9990 chunk 170 optimal weight: 4.9990 chunk 129 optimal weight: 2.9990 chunk 217 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 199 optimal weight: 2.9990 chunk 188 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 238 optimal weight: 3.9990 overall best weight: 1.5964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.064457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.053811 restraints weight = 141812.659| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 2.73 r_work: 0.2803 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2641 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2641 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2652 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2652 r_free = 0.2652 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2652 r_free = 0.2652 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2652 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 20907 Z= 0.177 Angle : 0.526 9.944 28398 Z= 0.276 Chirality : 0.043 0.304 3240 Planarity : 0.003 0.066 3606 Dihedral : 5.727 52.432 3139 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 1.51 % Allowed : 10.37 % Favored : 88.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.23 (0.16), residues: 2631 helix: 1.50 (0.25), residues: 414 sheet: -0.88 (0.16), residues: 885 loop : -0.00 (0.17), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG I 103 TYR 0.011 0.001 TYR C 385 PHE 0.010 0.001 PHE I 73 TRP 0.012 0.001 TRP H 82 HIS 0.005 0.001 HIS B 368 Details of bonding type rmsd covalent geometry : bond 0.00393 (20850) covalent geometry : angle 0.51994 (28272) SS BOND : bond 0.00336 ( 45) SS BOND : angle 0.78993 ( 90) hydrogen bonds : bond 0.03002 ( 942) hydrogen bonds : angle 4.94984 ( 2445) link_BETA1-4 : bond 0.00169 ( 3) link_BETA1-4 : angle 1.05398 ( 9) link_NAG-ASN : bond 0.00379 ( 9) link_NAG-ASN : angle 2.27268 ( 27) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5262 Ramachandran restraints generated. 2631 Oldfield, 0 Emsley, 2631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5262 Ramachandran restraints generated. 2631 Oldfield, 0 Emsley, 2631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 146 time to evaluate : 1.183 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: B 70 GLU cc_start: 0.8493 (mm-30) cc_final: 0.8108 (mm-30) REVERT: B 72 ASP cc_start: 0.8250 (m-30) cc_final: 0.8037 (m-30) REVERT: B 110 CYS cc_start: 0.7939 (OUTLIER) cc_final: 0.7626 (m) REVERT: D 59 TYR cc_start: 0.9118 (m-80) cc_final: 0.8883 (m-10) REVERT: D 83 LYS cc_start: 0.8684 (mtmt) cc_final: 0.8414 (mttt) REVERT: F 72 ASP cc_start: 0.8079 (m-30) cc_final: 0.7475 (m-30) REVERT: F 108 LEU cc_start: 0.8772 (tt) cc_final: 0.8063 (mp) REVERT: G 27 GLN cc_start: 0.8802 (mt0) cc_final: 0.8532 (mt0) REVERT: H 16 GLU cc_start: 0.8310 (tt0) cc_final: 0.7854 (tp30) REVERT: H 89 ILE cc_start: 0.8702 (mm) cc_final: 0.8417 (mm) REVERT: L 59 ASP cc_start: 0.8608 (m-30) cc_final: 0.8318 (m-30) REVERT: M 83 GLU cc_start: 0.8835 (mp0) cc_final: 0.8404 (mp0) REVERT: M 106 LYS cc_start: 0.8753 (ttmm) cc_final: 0.8405 (tptt) REVERT: O 83 GLU cc_start: 0.8683 (mp0) cc_final: 0.8386 (mp0) outliers start: 34 outliers final: 31 residues processed: 174 average time/residue: 0.4387 time to fit residues: 109.6508 Evaluate side-chains 171 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 139 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 147 CYS Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain B residue 54 ASP Chi-restraints excluded: chain B residue 110 CYS Chi-restraints excluded: chain B residue 147 CYS Chi-restraints excluded: chain B residue 280 ASP Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 368 HIS Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 147 CYS Chi-restraints excluded: chain C residue 266 SER Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain F residue 73 LYS Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain G residue 4 MET Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain I residue 4 MET Chi-restraints excluded: chain I residue 27 GLN Chi-restraints excluded: chain J residue 31 SER Chi-restraints excluded: chain J residue 108 THR Chi-restraints excluded: chain L residue 31 SER Chi-restraints excluded: chain L residue 108 THR Chi-restraints excluded: chain N residue 31 SER Chi-restraints excluded: chain N residue 55 SER Chi-restraints excluded: chain N residue 62 ASP Chi-restraints excluded: chain N residue 108 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 193 optimal weight: 0.9980 chunk 59 optimal weight: 0.0570 chunk 167 optimal weight: 0.5980 chunk 96 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 46 optimal weight: 0.5980 chunk 107 optimal weight: 3.9990 chunk 240 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 199 optimal weight: 3.9990 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.065163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.054607 restraints weight = 141414.742| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 2.72 r_work: 0.2825 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2663 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2679 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2679 r_free = 0.2679 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2679 r_free = 0.2679 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2679 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.3047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 20907 Z= 0.106 Angle : 0.504 7.159 28398 Z= 0.263 Chirality : 0.043 0.282 3240 Planarity : 0.003 0.066 3606 Dihedral : 5.519 51.947 3139 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.11 % Allowed : 10.95 % Favored : 87.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.05 (0.16), residues: 2631 helix: 1.72 (0.26), residues: 417 sheet: -0.77 (0.17), residues: 864 loop : 0.07 (0.17), residues: 1350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG N 87 TYR 0.011 0.001 TYR C 385 PHE 0.007 0.001 PHE E 73 TRP 0.012 0.001 TRP H 82 HIS 0.005 0.001 HIS B 368 Details of bonding type rmsd covalent geometry : bond 0.00237 (20850) covalent geometry : angle 0.49913 (28272) SS BOND : bond 0.00271 ( 45) SS BOND : angle 0.65993 ( 90) hydrogen bonds : bond 0.02718 ( 942) hydrogen bonds : angle 4.80322 ( 2445) link_BETA1-4 : bond 0.00287 ( 3) link_BETA1-4 : angle 0.98502 ( 9) link_NAG-ASN : bond 0.00371 ( 9) link_NAG-ASN : angle 2.15245 ( 27) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5262 Ramachandran restraints generated. 2631 Oldfield, 0 Emsley, 2631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5262 Ramachandran restraints generated. 2631 Oldfield, 0 Emsley, 2631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 151 time to evaluate : 1.054 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: A 70 GLU cc_start: 0.8480 (mm-30) cc_final: 0.8155 (mm-30) REVERT: B 72 ASP cc_start: 0.8255 (m-30) cc_final: 0.8007 (m-30) REVERT: D 59 TYR cc_start: 0.9064 (m-80) cc_final: 0.8803 (m-10) REVERT: F 72 ASP cc_start: 0.8055 (m-30) cc_final: 0.7457 (m-30) REVERT: F 108 LEU cc_start: 0.8765 (tt) cc_final: 0.8073 (mp) REVERT: G 27 GLN cc_start: 0.8840 (mt0) cc_final: 0.8582 (mt0) REVERT: H 16 GLU cc_start: 0.8328 (tt0) cc_final: 0.7902 (tp30) REVERT: H 89 ILE cc_start: 0.8694 (mm) cc_final: 0.8406 (mm) REVERT: L 57 TYR cc_start: 0.9074 (m-80) cc_final: 0.8666 (m-80) REVERT: L 59 ASP cc_start: 0.8591 (m-30) cc_final: 0.8312 (m-30) REVERT: M 83 GLU cc_start: 0.8858 (mp0) cc_final: 0.8433 (mp0) REVERT: M 106 LYS cc_start: 0.8709 (ttmm) cc_final: 0.8392 (tptt) REVERT: O 83 GLU cc_start: 0.8676 (mp0) cc_final: 0.8410 (mp0) outliers start: 25 outliers final: 24 residues processed: 170 average time/residue: 0.4127 time to fit residues: 100.2627 Evaluate side-chains 169 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 145 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain B residue 147 CYS Chi-restraints excluded: chain B residue 280 ASP Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain C residue 147 CYS Chi-restraints excluded: chain C residue 234 MET Chi-restraints excluded: chain C residue 266 SER Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain F residue 73 LYS Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain I residue 4 MET Chi-restraints excluded: chain I residue 27 GLN Chi-restraints excluded: chain J residue 31 SER Chi-restraints excluded: chain J residue 108 THR Chi-restraints excluded: chain L residue 108 THR Chi-restraints excluded: chain N residue 31 SER Chi-restraints excluded: chain N residue 55 SER Chi-restraints excluded: chain N residue 62 ASP Chi-restraints excluded: chain N residue 108 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 179 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 32 optimal weight: 0.3980 chunk 91 optimal weight: 2.9990 chunk 200 optimal weight: 3.9990 chunk 106 optimal weight: 0.1980 chunk 79 optimal weight: 2.9990 chunk 254 optimal weight: 2.9990 chunk 14 optimal weight: 0.0370 chunk 222 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 overall best weight: 1.1262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 116 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.064947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.054486 restraints weight = 140979.843| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 2.68 r_work: 0.2822 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2661 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2684 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2684 r_free = 0.2684 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2684 r_free = 0.2684 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2684 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.3092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20907 Z= 0.142 Angle : 0.510 7.198 28398 Z= 0.266 Chirality : 0.043 0.280 3240 Planarity : 0.003 0.069 3606 Dihedral : 5.471 50.659 3139 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.25 % Allowed : 10.90 % Favored : 87.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.01 (0.16), residues: 2631 helix: 1.79 (0.26), residues: 417 sheet: -0.71 (0.17), residues: 864 loop : 0.07 (0.17), residues: 1350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG I 103 TYR 0.010 0.001 TYR C 385 PHE 0.008 0.001 PHE G 73 TRP 0.010 0.001 TRP H 82 HIS 0.005 0.001 HIS B 368 Details of bonding type rmsd covalent geometry : bond 0.00317 (20850) covalent geometry : angle 0.50528 (28272) SS BOND : bond 0.00288 ( 45) SS BOND : angle 0.69333 ( 90) hydrogen bonds : bond 0.02744 ( 942) hydrogen bonds : angle 4.76615 ( 2445) link_BETA1-4 : bond 0.00211 ( 3) link_BETA1-4 : angle 0.98647 ( 9) link_NAG-ASN : bond 0.00344 ( 9) link_NAG-ASN : angle 2.13131 ( 27) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5262 Ramachandran restraints generated. 2631 Oldfield, 0 Emsley, 2631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5262 Ramachandran restraints generated. 2631 Oldfield, 0 Emsley, 2631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 149 time to evaluate : 1.046 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: A 70 GLU cc_start: 0.8474 (mm-30) cc_final: 0.8166 (mm-30) REVERT: B 72 ASP cc_start: 0.8269 (m-30) cc_final: 0.8021 (m-30) REVERT: B 110 CYS cc_start: 0.7590 (OUTLIER) cc_final: 0.7213 (m) REVERT: D 59 TYR cc_start: 0.9080 (m-80) cc_final: 0.8833 (m-10) REVERT: F 40 MET cc_start: 0.8356 (mmm) cc_final: 0.8097 (mmm) REVERT: F 72 ASP cc_start: 0.8073 (m-30) cc_final: 0.7487 (m-30) REVERT: F 108 LEU cc_start: 0.8763 (tt) cc_final: 0.8061 (mp) REVERT: G 27 GLN cc_start: 0.8831 (mt0) cc_final: 0.8588 (mt0) REVERT: H 16 GLU cc_start: 0.8295 (tt0) cc_final: 0.7908 (tp30) REVERT: H 89 ILE cc_start: 0.8704 (mm) cc_final: 0.8421 (mm) REVERT: L 57 TYR cc_start: 0.9074 (m-80) cc_final: 0.8651 (m-80) REVERT: L 59 ASP cc_start: 0.8586 (m-30) cc_final: 0.8302 (m-30) REVERT: M 83 GLU cc_start: 0.8855 (mp0) cc_final: 0.8429 (mp0) REVERT: M 106 LYS cc_start: 0.8712 (ttmm) cc_final: 0.8399 (tptt) REVERT: O 83 GLU cc_start: 0.8686 (mp0) cc_final: 0.8447 (mp0) outliers start: 28 outliers final: 26 residues processed: 171 average time/residue: 0.4141 time to fit residues: 101.9355 Evaluate side-chains 172 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 145 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain B residue 110 CYS Chi-restraints excluded: chain B residue 147 CYS Chi-restraints excluded: chain B residue 280 ASP Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 368 HIS Chi-restraints excluded: chain C residue 147 CYS Chi-restraints excluded: chain C residue 234 MET Chi-restraints excluded: chain C residue 266 SER Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain C residue 392 ILE Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain F residue 73 LYS Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain I residue 4 MET Chi-restraints excluded: chain I residue 27 GLN Chi-restraints excluded: chain J residue 108 THR Chi-restraints excluded: chain L residue 108 THR Chi-restraints excluded: chain N residue 31 SER Chi-restraints excluded: chain N residue 55 SER Chi-restraints excluded: chain N residue 62 ASP Chi-restraints excluded: chain N residue 108 THR Chi-restraints excluded: chain N residue 116 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 113 optimal weight: 4.9990 chunk 191 optimal weight: 7.9990 chunk 224 optimal weight: 2.9990 chunk 231 optimal weight: 0.9990 chunk 178 optimal weight: 0.0370 chunk 89 optimal weight: 1.9990 chunk 244 optimal weight: 0.9980 chunk 131 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 175 optimal weight: 0.9980 chunk 139 optimal weight: 1.9990 overall best weight: 1.0062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 116 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.065062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.054496 restraints weight = 141988.725| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 2.70 r_work: 0.2814 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2654 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2685 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2685 r_free = 0.2685 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2685 r_free = 0.2685 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2685 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.3108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.108 20907 Z= 0.148 Angle : 0.680 59.198 28398 Z= 0.390 Chirality : 0.044 0.424 3240 Planarity : 0.003 0.068 3606 Dihedral : 5.468 50.632 3139 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.25 % Allowed : 10.99 % Favored : 87.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.01 (0.16), residues: 2631 helix: 1.80 (0.26), residues: 417 sheet: -0.70 (0.17), residues: 864 loop : 0.06 (0.17), residues: 1350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 103 TYR 0.010 0.001 TYR C 385 PHE 0.008 0.001 PHE E 73 TRP 0.010 0.001 TRP H 82 HIS 0.011 0.001 HIS D 66 Details of bonding type rmsd covalent geometry : bond 0.00325 (20850) covalent geometry : angle 0.67667 (28272) SS BOND : bond 0.00286 ( 45) SS BOND : angle 0.67915 ( 90) hydrogen bonds : bond 0.02742 ( 942) hydrogen bonds : angle 4.76558 ( 2445) link_BETA1-4 : bond 0.00295 ( 3) link_BETA1-4 : angle 1.27023 ( 9) link_NAG-ASN : bond 0.00345 ( 9) link_NAG-ASN : angle 2.13083 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8890.18 seconds wall clock time: 151 minutes 36.63 seconds (9096.63 seconds total)