Starting phenix.real_space_refine on Thu Mar 5 04:35:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rye_24735/03_2026/7rye_24735.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rye_24735/03_2026/7rye_24735.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7rye_24735/03_2026/7rye_24735.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rye_24735/03_2026/7rye_24735.map" model { file = "/net/cci-nas-00/data/ceres_data/7rye_24735/03_2026/7rye_24735.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rye_24735/03_2026/7rye_24735.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 30 5.16 5 C 12445 2.51 5 N 3227 2.21 5 O 4006 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 101 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: 19708 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 612 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "B" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 612 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "C" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 612 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "D" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 612 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "E" Number of atoms: 604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 604 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "F" Number of atoms: 1627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1627 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 206} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 604 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "H" Number of atoms: 604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 604 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "I" Number of atoms: 604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 604 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "J" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 612 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "K" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 612 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "L" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 612 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "M" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 612 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "N" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 612 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "O" Number of atoms: 1627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1627 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 206} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "P" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 612 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "Q" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 612 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "R" Number of atoms: 1627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1627 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 206} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "S" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 612 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "T" Number of atoms: 604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 604 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "U" Number of atoms: 605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 605 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "V" Number of atoms: 1627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1627 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 206} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "W" Number of atoms: 604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 604 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "X" Number of atoms: 1627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1627 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 206} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.65, per 1000 atoms: 0.24 Number of scatterers: 19708 At special positions: 0 Unit cell: (99.47, 96.04, 214.375, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 30 16.00 O 4006 8.00 N 3227 7.00 C 12445 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 1.84 Conformation dependent library (CDL) restraints added in 643.7 milliseconds 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4854 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 10 sheets defined 79.4% alpha, 2.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 7 through 20 Processing helix chain 'A' and resid 22 through 35 Processing helix chain 'A' and resid 40 through 77 removed outlier: 3.887A pdb=" N ALA A 46 " --> pdb=" O ALA A 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 20 Processing helix chain 'B' and resid 22 through 37 Processing helix chain 'B' and resid 40 through 78 Processing helix chain 'C' and resid 7 through 20 Processing helix chain 'C' and resid 22 through 37 Processing helix chain 'C' and resid 40 through 78 removed outlier: 3.733A pdb=" N ASN C 78 " --> pdb=" O ALA C 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 16 Processing helix chain 'D' and resid 17 through 21 removed outlier: 3.644A pdb=" N ASP D 21 " --> pdb=" O THR D 18 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 37 Processing helix chain 'D' and resid 40 through 77 Processing helix chain 'E' and resid 8 through 16 Processing helix chain 'E' and resid 17 through 35 removed outlier: 3.918A pdb=" N ASN E 22 " --> pdb=" O THR E 18 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N THR E 25 " --> pdb=" O ASP E 21 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 78 removed outlier: 4.047A pdb=" N LEU E 44 " --> pdb=" O ASP E 40 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE E 68 " --> pdb=" O THR E 64 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS E 69 " --> pdb=" O VAL E 65 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASP E 70 " --> pdb=" O LYS E 66 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ASP E 72 " --> pdb=" O PHE E 68 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ILE E 75 " --> pdb=" O ILE E 71 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ILE E 76 " --> pdb=" O ASP E 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 131 through 147 removed outlier: 3.662A pdb=" N SER F 143 " --> pdb=" O SER F 139 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLY F 146 " --> pdb=" O ILE F 142 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ASP F 147 " --> pdb=" O SER F 143 " (cutoff:3.500A) Processing helix chain 'F' and resid 149 through 175 Processing helix chain 'F' and resid 190 through 206 removed outlier: 3.894A pdb=" N LEU F 194 " --> pdb=" O ASP F 190 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 239 removed outlier: 3.677A pdb=" N ALA F 231 " --> pdb=" O THR F 227 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N GLU F 237 " --> pdb=" O GLN F 233 " (cutoff:3.500A) Processing helix chain 'F' and resid 258 through 268 Processing helix chain 'F' and resid 283 through 311 Processing helix chain 'F' and resid 311 through 323 removed outlier: 4.591A pdb=" N SER F 317 " --> pdb=" O SER F 313 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N LEU F 318 " --> pdb=" O ASN F 314 " (cutoff:3.500A) Processing helix chain 'F' and resid 326 through 331 Processing helix chain 'F' and resid 332 through 340 removed outlier: 3.607A pdb=" N GLU F 335 " --> pdb=" O SER F 332 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N THR F 336 " --> pdb=" O SER F 333 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA F 337 " --> pdb=" O LEU F 334 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 37 removed outlier: 3.976A pdb=" N PHE G 16 " --> pdb=" O VAL G 12 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASP G 17 " --> pdb=" O SER G 13 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N THR G 18 " --> pdb=" O ALA G 14 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N GLY G 19 " --> pdb=" O LYS G 15 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASP G 21 " --> pdb=" O ASP G 17 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ASN G 22 " --> pdb=" O THR G 18 " (cutoff:3.500A) Processing helix chain 'G' and resid 40 through 78 removed outlier: 4.166A pdb=" N LEU G 44 " --> pdb=" O ASP G 40 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU G 53 " --> pdb=" O SER G 49 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ASP G 72 " --> pdb=" O PHE G 68 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ALA G 74 " --> pdb=" O ASP G 70 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ILE G 75 " --> pdb=" O ILE G 71 " (cutoff:3.500A) Processing helix chain 'H' and resid 7 through 37 removed outlier: 3.611A pdb=" N PHE H 16 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR H 18 " --> pdb=" O ALA H 14 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N GLY H 19 " --> pdb=" O LYS H 15 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ASN H 22 " --> pdb=" O THR H 18 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N THR H 28 " --> pdb=" O GLN H 24 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLU H 29 " --> pdb=" O THR H 25 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LYS H 33 " --> pdb=" O GLU H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 41 through 78 removed outlier: 3.867A pdb=" N ALA H 45 " --> pdb=" O PRO H 41 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ALA H 46 " --> pdb=" O ALA H 42 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE H 68 " --> pdb=" O THR H 64 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LYS H 69 " --> pdb=" O VAL H 65 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE H 71 " --> pdb=" O VAL H 67 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ASP H 72 " --> pdb=" O PHE H 68 " (cutoff:3.500A) Processing helix chain 'I' and resid 9 through 37 removed outlier: 4.192A pdb=" N GLY I 19 " --> pdb=" O LYS I 15 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ASN I 22 " --> pdb=" O THR I 18 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU I 23 " --> pdb=" O GLY I 19 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N THR I 28 " --> pdb=" O GLN I 24 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLU I 29 " --> pdb=" O THR I 25 " (cutoff:3.500A) Processing helix chain 'I' and resid 40 through 78 removed outlier: 4.347A pdb=" N LEU I 44 " --> pdb=" O ASP I 40 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ASP I 72 " --> pdb=" O PHE I 68 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA I 74 " --> pdb=" O ASP I 70 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ILE I 75 " --> pdb=" O ILE I 71 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASN I 78 " --> pdb=" O ALA I 74 " (cutoff:3.500A) Processing helix chain 'J' and resid 7 through 20 Processing helix chain 'J' and resid 22 through 35 Processing helix chain 'J' and resid 43 through 79 Processing helix chain 'K' and resid 7 through 20 removed outlier: 3.514A pdb=" N VAL K 20 " --> pdb=" O PHE K 16 " (cutoff:3.500A) Processing helix chain 'K' and resid 22 through 37 Processing helix chain 'K' and resid 40 through 77 Processing helix chain 'L' and resid 7 through 20 Processing helix chain 'L' and resid 22 through 35 Processing helix chain 'L' and resid 40 through 77 Processing helix chain 'M' and resid 7 through 20 Processing helix chain 'M' and resid 22 through 37 Processing helix chain 'M' and resid 40 through 78 Processing helix chain 'N' and resid 7 through 20 Processing helix chain 'N' and resid 22 through 37 Processing helix chain 'N' and resid 40 through 78 removed outlier: 3.709A pdb=" N ASN N 78 " --> pdb=" O ALA N 74 " (cutoff:3.500A) Processing helix chain 'O' and resid 131 through 149 removed outlier: 3.925A pdb=" N TRP O 135 " --> pdb=" O ASP O 131 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ASP O 136 " --> pdb=" O ALA O 132 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASP O 147 " --> pdb=" O SER O 143 " (cutoff:3.500A) Processing helix chain 'O' and resid 149 through 174 removed outlier: 3.541A pdb=" N TYR O 153 " --> pdb=" O TYR O 149 " (cutoff:3.500A) Processing helix chain 'O' and resid 191 through 207 removed outlier: 3.852A pdb=" N GLN O 207 " --> pdb=" O ASN O 203 " (cutoff:3.500A) Processing helix chain 'O' and resid 227 through 239 removed outlier: 3.766A pdb=" N GLU O 237 " --> pdb=" O GLN O 233 " (cutoff:3.500A) Processing helix chain 'O' and resid 258 through 269 removed outlier: 3.817A pdb=" N ASP O 269 " --> pdb=" O VAL O 265 " (cutoff:3.500A) Processing helix chain 'O' and resid 270 through 272 No H-bonds generated for 'chain 'O' and resid 270 through 272' Processing helix chain 'O' and resid 283 through 311 Processing helix chain 'O' and resid 311 through 323 removed outlier: 4.351A pdb=" N SER O 317 " --> pdb=" O SER O 313 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N LEU O 318 " --> pdb=" O ASN O 314 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ASN O 321 " --> pdb=" O SER O 317 " (cutoff:3.500A) Processing helix chain 'O' and resid 326 through 331 Processing helix chain 'O' and resid 333 through 340 removed outlier: 3.881A pdb=" N THR O 336 " --> pdb=" O SER O 333 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ALA O 337 " --> pdb=" O LEU O 334 " (cutoff:3.500A) Processing helix chain 'P' and resid 7 through 20 Processing helix chain 'P' and resid 22 through 37 Processing helix chain 'P' and resid 40 through 78 removed outlier: 3.711A pdb=" N ASN P 78 " --> pdb=" O ALA P 74 " (cutoff:3.500A) Processing helix chain 'Q' and resid 7 through 20 removed outlier: 3.637A pdb=" N VAL Q 20 " --> pdb=" O PHE Q 16 " (cutoff:3.500A) Processing helix chain 'Q' and resid 22 through 37 removed outlier: 4.128A pdb=" N THR Q 28 " --> pdb=" O GLN Q 24 " (cutoff:3.500A) Processing helix chain 'Q' and resid 40 through 79 Processing helix chain 'R' and resid 131 through 145 removed outlier: 4.193A pdb=" N SER R 143 " --> pdb=" O SER R 139 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE R 145 " --> pdb=" O ASN R 141 " (cutoff:3.500A) Processing helix chain 'R' and resid 149 through 175 removed outlier: 3.588A pdb=" N TYR R 153 " --> pdb=" O TYR R 149 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY R 175 " --> pdb=" O LEU R 171 " (cutoff:3.500A) Processing helix chain 'R' and resid 190 through 205 removed outlier: 3.575A pdb=" N LEU R 194 " --> pdb=" O ASP R 190 " (cutoff:3.500A) Processing helix chain 'R' and resid 227 through 239 removed outlier: 3.529A pdb=" N ALA R 231 " --> pdb=" O THR R 227 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N GLU R 237 " --> pdb=" O GLN R 233 " (cutoff:3.500A) Processing helix chain 'R' and resid 258 through 268 Processing helix chain 'R' and resid 269 through 272 removed outlier: 3.722A pdb=" N GLY R 272 " --> pdb=" O ASP R 269 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 269 through 272' Processing helix chain 'R' and resid 283 through 323 removed outlier: 4.117A pdb=" N ALA R 289 " --> pdb=" O ALA R 285 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N TYR R 312 " --> pdb=" O LEU R 308 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N SER R 313 " --> pdb=" O THR R 309 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N SER R 317 " --> pdb=" O SER R 313 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N LEU R 318 " --> pdb=" O ASN R 314 " (cutoff:3.500A) Processing helix chain 'R' and resid 326 through 334 removed outlier: 4.193A pdb=" N SER R 332 " --> pdb=" O SER R 328 " (cutoff:3.500A) Processing helix chain 'R' and resid 335 through 340 Processing helix chain 'S' and resid 7 through 20 removed outlier: 3.638A pdb=" N PHE S 16 " --> pdb=" O VAL S 12 " (cutoff:3.500A) Processing helix chain 'S' and resid 22 through 37 removed outlier: 3.963A pdb=" N THR S 28 " --> pdb=" O GLN S 24 " (cutoff:3.500A) Processing helix chain 'S' and resid 40 through 80 removed outlier: 3.745A pdb=" N ARG S 80 " --> pdb=" O ILE S 76 " (cutoff:3.500A) Processing helix chain 'T' and resid 7 through 37 removed outlier: 3.593A pdb=" N PHE T 16 " --> pdb=" O VAL T 12 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N THR T 18 " --> pdb=" O ALA T 14 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N GLY T 19 " --> pdb=" O LYS T 15 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASN T 22 " --> pdb=" O THR T 18 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N THR T 28 " --> pdb=" O GLN T 24 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU T 29 " --> pdb=" O THR T 25 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYS T 33 " --> pdb=" O GLU T 29 " (cutoff:3.500A) Processing helix chain 'T' and resid 40 through 78 removed outlier: 4.033A pdb=" N LEU T 44 " --> pdb=" O ASP T 40 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL T 65 " --> pdb=" O GLN T 61 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LYS T 66 " --> pdb=" O SER T 62 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N PHE T 68 " --> pdb=" O THR T 64 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE T 71 " --> pdb=" O VAL T 67 " (cutoff:3.500A) Processing helix chain 'U' and resid 7 through 20 Processing helix chain 'U' and resid 22 through 37 removed outlier: 4.283A pdb=" N THR U 28 " --> pdb=" O GLN U 24 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LYS U 37 " --> pdb=" O LYS U 33 " (cutoff:3.500A) Processing helix chain 'U' and resid 40 through 80 Processing helix chain 'V' and resid 132 through 147 removed outlier: 3.527A pdb=" N ASP V 136 " --> pdb=" O ALA V 132 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ASP V 147 " --> pdb=" O SER V 143 " (cutoff:3.500A) Processing helix chain 'V' and resid 149 through 175 removed outlier: 3.521A pdb=" N TYR V 153 " --> pdb=" O TYR V 149 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLY V 175 " --> pdb=" O LEU V 171 " (cutoff:3.500A) Processing helix chain 'V' and resid 191 through 206 Processing helix chain 'V' and resid 227 through 239 Processing helix chain 'V' and resid 258 through 268 Processing helix chain 'V' and resid 269 through 272 Processing helix chain 'V' and resid 283 through 323 removed outlier: 4.133A pdb=" N TYR V 312 " --> pdb=" O LEU V 308 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N SER V 313 " --> pdb=" O THR V 309 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASN V 314 " --> pdb=" O GLN V 310 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N SER V 317 " --> pdb=" O SER V 313 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LEU V 318 " --> pdb=" O ASN V 314 " (cutoff:3.500A) Processing helix chain 'V' and resid 326 through 331 Processing helix chain 'V' and resid 335 through 340 Processing helix chain 'W' and resid 7 through 37 removed outlier: 4.215A pdb=" N GLY W 19 " --> pdb=" O LYS W 15 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ASN W 22 " --> pdb=" O THR W 18 " (cutoff:3.500A) Processing helix chain 'W' and resid 40 through 78 removed outlier: 3.775A pdb=" N LEU W 44 " --> pdb=" O ASP W 40 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE W 71 " --> pdb=" O VAL W 67 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ASP W 72 " --> pdb=" O PHE W 68 " (cutoff:3.500A) Processing helix chain 'X' and resid 132 through 147 removed outlier: 3.949A pdb=" N ASP X 136 " --> pdb=" O ALA X 132 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ASP X 147 " --> pdb=" O SER X 143 " (cutoff:3.500A) Processing helix chain 'X' and resid 149 through 175 removed outlier: 3.759A pdb=" N GLY X 175 " --> pdb=" O LEU X 171 " (cutoff:3.500A) Processing helix chain 'X' and resid 191 through 206 Processing helix chain 'X' and resid 227 through 239 Processing helix chain 'X' and resid 258 through 269 Processing helix chain 'X' and resid 270 through 272 No H-bonds generated for 'chain 'X' and resid 270 through 272' Processing helix chain 'X' and resid 283 through 311 removed outlier: 3.708A pdb=" N ALA X 289 " --> pdb=" O ALA X 285 " (cutoff:3.500A) Processing helix chain 'X' and resid 315 through 323 Processing helix chain 'X' and resid 326 through 334 removed outlier: 3.794A pdb=" N SER X 332 " --> pdb=" O SER X 328 " (cutoff:3.500A) Processing helix chain 'X' and resid 335 through 340 Processing sheet with id=AA1, first strand: chain 'F' and resid 178 through 180 removed outlier: 3.636A pdb=" N LEU F 179 " --> pdb=" O LYS F 188 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 245 through 248 removed outlier: 3.916A pdb=" N GLY F 251 " --> pdb=" O TYR F 248 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'O' and resid 178 through 181 removed outlier: 3.785A pdb=" N THR O 186 " --> pdb=" O GLY O 181 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'O' and resid 213 through 215 removed outlier: 3.897A pdb=" N PHE O 215 " --> pdb=" O VAL O 254 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'R' and resid 178 through 180 removed outlier: 3.920A pdb=" N LEU R 179 " --> pdb=" O LYS R 188 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'R' and resid 245 through 248 removed outlier: 4.025A pdb=" N GLY R 251 " --> pdb=" O TYR R 248 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'V' and resid 178 through 180 removed outlier: 3.614A pdb=" N LEU V 179 " --> pdb=" O LYS V 188 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'V' and resid 245 through 246 Processing sheet with id=AA9, first strand: chain 'X' and resid 178 through 181 removed outlier: 3.623A pdb=" N LEU X 179 " --> pdb=" O LYS X 188 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N THR X 186 " --> pdb=" O GLY X 181 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'X' and resid 245 through 248 removed outlier: 4.033A pdb=" N GLY X 251 " --> pdb=" O TYR X 248 " (cutoff:3.500A) 1524 hydrogen bonds defined for protein. 4512 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.36 Time building geometry restraints manager: 2.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6046 1.34 - 1.45: 2762 1.45 - 1.57: 11189 1.57 - 1.69: 0 1.69 - 1.81: 55 Bond restraints: 20052 Sorted by residual: bond pdb=" CA LYS K 37 " pdb=" CB LYS K 37 " ideal model delta sigma weight residual 1.526 1.540 -0.013 9.30e-03 1.16e+04 2.05e+00 bond pdb=" CG1 ILE G 71 " pdb=" CD1 ILE G 71 " ideal model delta sigma weight residual 1.513 1.463 0.050 3.90e-02 6.57e+02 1.62e+00 bond pdb=" CA LYS O 311 " pdb=" C LYS O 311 " ideal model delta sigma weight residual 1.523 1.539 -0.016 1.34e-02 5.57e+03 1.44e+00 bond pdb=" CG1 ILE A 71 " pdb=" CD1 ILE A 71 " ideal model delta sigma weight residual 1.513 1.467 0.046 3.90e-02 6.57e+02 1.40e+00 bond pdb=" CB ASN W 63 " pdb=" CG ASN W 63 " ideal model delta sigma weight residual 1.516 1.488 0.028 2.50e-02 1.60e+03 1.28e+00 ... (remaining 20047 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 26679 2.01 - 4.01: 505 4.01 - 6.02: 48 6.02 - 8.03: 7 8.03 - 10.03: 4 Bond angle restraints: 27243 Sorted by residual: angle pdb=" C PHE R 215 " pdb=" N PRO R 216 " pdb=" CA PRO R 216 " ideal model delta sigma weight residual 127.00 137.03 -10.03 2.40e+00 1.74e-01 1.75e+01 angle pdb=" N LEU J 43 " pdb=" CA LEU J 43 " pdb=" C LEU J 43 " ideal model delta sigma weight residual 114.04 108.93 5.11 1.24e+00 6.50e-01 1.70e+01 angle pdb=" C PHE R 215 " pdb=" N PRO R 216 " pdb=" CD PRO R 216 " ideal model delta sigma weight residual 120.60 112.51 8.09 2.20e+00 2.07e-01 1.35e+01 angle pdb=" N PRO H 41 " pdb=" CA PRO H 41 " pdb=" C PRO H 41 " ideal model delta sigma weight residual 114.92 111.15 3.77 1.19e+00 7.06e-01 1.00e+01 angle pdb=" N VAL R 325 " pdb=" CA VAL R 325 " pdb=" C VAL R 325 " ideal model delta sigma weight residual 112.04 107.62 4.42 1.40e+00 5.10e-01 9.98e+00 ... (remaining 27238 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 10932 17.96 - 35.91: 944 35.91 - 53.87: 176 53.87 - 71.83: 44 71.83 - 89.78: 17 Dihedral angle restraints: 12113 sinusoidal: 4622 harmonic: 7491 Sorted by residual: dihedral pdb=" CA LYS O 311 " pdb=" C LYS O 311 " pdb=" N TYR O 312 " pdb=" CA TYR O 312 " ideal model delta harmonic sigma weight residual 180.00 159.80 20.20 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" CA GLU V 281 " pdb=" C GLU V 281 " pdb=" N MET V 282 " pdb=" CA MET V 282 " ideal model delta harmonic sigma weight residual 180.00 -160.02 -19.98 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" CA GLU F 228 " pdb=" C GLU F 228 " pdb=" N ALA F 229 " pdb=" CA ALA F 229 " ideal model delta harmonic sigma weight residual -180.00 -162.47 -17.53 0 5.00e+00 4.00e-02 1.23e+01 ... (remaining 12110 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 2054 0.035 - 0.070: 794 0.070 - 0.104: 224 0.104 - 0.139: 41 0.139 - 0.174: 6 Chirality restraints: 3119 Sorted by residual: chirality pdb=" CA GLU P 29 " pdb=" N GLU P 29 " pdb=" C GLU P 29 " pdb=" CB GLU P 29 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.56e-01 chirality pdb=" CA GLN O 266 " pdb=" N GLN O 266 " pdb=" C GLN O 266 " pdb=" CB GLN O 266 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.45e-01 chirality pdb=" CA GLU L 29 " pdb=" N GLU L 29 " pdb=" C GLU L 29 " pdb=" CB GLU L 29 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.82e-01 ... (remaining 3116 not shown) Planarity restraints: 3524 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP X 177 " 0.018 2.00e-02 2.50e+03 1.58e-02 6.24e+00 pdb=" CG TRP X 177 " -0.043 2.00e-02 2.50e+03 pdb=" CD1 TRP X 177 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP X 177 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP X 177 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP X 177 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP X 177 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP X 177 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP X 177 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP X 177 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR P 25 " -0.011 2.00e-02 2.50e+03 2.10e-02 4.43e+00 pdb=" C THR P 25 " 0.036 2.00e-02 2.50e+03 pdb=" O THR P 25 " -0.014 2.00e-02 2.50e+03 pdb=" N GLN P 26 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR V 164 " 0.021 2.00e-02 2.50e+03 1.38e-02 3.79e+00 pdb=" CG TYR V 164 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 TYR V 164 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR V 164 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR V 164 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR V 164 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR V 164 " 0.006 2.00e-02 2.50e+03 pdb=" OH TYR V 164 " 0.003 2.00e-02 2.50e+03 ... (remaining 3521 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 310 2.65 - 3.21: 20461 3.21 - 3.78: 33044 3.78 - 4.34: 41246 4.34 - 4.90: 67330 Nonbonded interactions: 162391 Sorted by model distance: nonbonded pdb=" OD1 ASP D 17 " pdb=" OH TYR D 57 " model vdw 2.090 3.040 nonbonded pdb=" O SER O 328 " pdb=" OG SER O 332 " model vdw 2.095 3.040 nonbonded pdb=" OH TYR I 54 " pdb=" OD2 ASP V 131 " model vdw 2.136 3.040 nonbonded pdb=" O SER R 328 " pdb=" OG SER R 332 " model vdw 2.159 3.040 nonbonded pdb=" OD1 ASN V 314 " pdb=" ND2 ASN X 316 " model vdw 2.176 3.120 ... (remaining 162386 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 4 through 79 or (resid 80 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or \ name NH2)))) selection = (chain 'B' and (resid 4 through 79 or (resid 80 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or \ name NH2)))) selection = (chain 'C' and (resid 4 through 79 or (resid 80 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or \ name NH2)))) selection = (chain 'D' and (resid 4 through 79 or (resid 80 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or \ name NH2)))) selection = chain 'E' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = (chain 'J' and (resid 4 through 79 or (resid 80 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or \ name NH2)))) selection = (chain 'K' and (resid 4 through 79 or (resid 80 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or \ name NH2)))) selection = (chain 'L' and (resid 4 through 79 or (resid 80 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or \ name NH2)))) selection = (chain 'M' and (resid 4 through 79 or (resid 80 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or \ name NH2)))) selection = (chain 'N' and (resid 4 through 79 or (resid 80 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or \ name NH2)))) selection = (chain 'P' and (resid 4 through 79 or (resid 80 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or \ name NH2)))) selection = (chain 'Q' and (resid 4 through 79 or (resid 80 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or \ name NH2)))) selection = (chain 'S' and (resid 4 through 79 or (resid 80 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or \ name NH2)))) selection = chain 'T' selection = (chain 'U' and (resid 4 through 79 or (resid 80 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or \ name NH2)))) selection = chain 'W' } ncs_group { reference = chain 'F' selection = chain 'O' selection = chain 'R' selection = chain 'V' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.030 Set scattering table: 0.060 Process input model: 18.100 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6931 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 : 0.003 0.050 20052 Z= 0.161 Angle : 0.649 10.032 27243 Z= 0.359 Chirality : 0.040 0.174 3119 Planarity : 0.003 0.040 3524 Dihedral : 14.566 89.782 7259 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.17), residues: 2487 helix: 1.59 (0.12), residues: 1813 sheet: -1.31 (0.58), residues: 75 loop : -1.76 (0.23), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 58 TYR 0.032 0.002 TYR V 164 PHE 0.025 0.002 PHE P 16 TRP 0.043 0.002 TRP X 177 Details of bonding type rmsd covalent geometry : bond 0.00346 (20052) covalent geometry : angle 0.64895 (27243) hydrogen bonds : bond 0.11618 ( 1524) hydrogen bonds : angle 4.56306 ( 4512) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 866 residues out of total 2167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 866 time to evaluate : 0.743 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 27 VAL cc_start: 0.9280 (t) cc_final: 0.8821 (p) REVERT: A 31 LEU cc_start: 0.9182 (mt) cc_final: 0.8971 (mm) REVERT: A 48 GLN cc_start: 0.7157 (tm-30) cc_final: 0.6842 (tm-30) REVERT: B 28 THR cc_start: 0.8683 (m) cc_final: 0.8378 (p) REVERT: B 58 ARG cc_start: 0.8420 (mmt180) cc_final: 0.8026 (mmt90) REVERT: C 70 ASP cc_start: 0.7141 (m-30) cc_final: 0.6928 (m-30) REVERT: D 16 PHE cc_start: 0.8560 (t80) cc_final: 0.7899 (t80) REVERT: E 22 ASN cc_start: 0.7932 (p0) cc_final: 0.7150 (t0) REVERT: E 26 GLN cc_start: 0.8128 (mt0) cc_final: 0.6961 (mt0) REVERT: F 215 PHE cc_start: 0.7062 (t80) cc_final: 0.6520 (t80) REVERT: F 263 LYS cc_start: 0.7784 (tppt) cc_final: 0.7562 (tptt) REVERT: F 266 GLN cc_start: 0.7919 (tm-30) cc_final: 0.7614 (pp30) REVERT: F 297 GLN cc_start: 0.6786 (mm110) cc_final: 0.6567 (pp30) REVERT: G 20 VAL cc_start: 0.8241 (t) cc_final: 0.7950 (t) REVERT: G 69 LYS cc_start: 0.7819 (tmtt) cc_final: 0.7447 (tptm) REVERT: H 32 ASP cc_start: 0.7165 (p0) cc_final: 0.6864 (p0) REVERT: I 17 ASP cc_start: 0.7440 (m-30) cc_final: 0.5986 (t70) REVERT: I 31 LEU cc_start: 0.7570 (tp) cc_final: 0.6905 (tp) REVERT: I 68 PHE cc_start: 0.7625 (m-80) cc_final: 0.6942 (m-10) REVERT: J 5 TRP cc_start: 0.8384 (t60) cc_final: 0.8177 (t60) REVERT: J 66 LYS cc_start: 0.8110 (tptm) cc_final: 0.7307 (tptm) REVERT: J 69 LYS cc_start: 0.8480 (tmtt) cc_final: 0.8125 (tptt) REVERT: K 72 ASP cc_start: 0.7319 (m-30) cc_final: 0.6515 (m-30) REVERT: K 79 PHE cc_start: 0.7069 (m-10) cc_final: 0.6806 (m-10) REVERT: L 11 ASP cc_start: 0.8012 (t0) cc_final: 0.7601 (m-30) REVERT: L 21 ASP cc_start: 0.5444 (p0) cc_final: 0.5195 (p0) REVERT: L 22 ASN cc_start: 0.8077 (p0) cc_final: 0.7592 (p0) REVERT: L 25 THR cc_start: 0.8822 (m) cc_final: 0.8433 (m) REVERT: L 63 ASN cc_start: 0.7515 (m-40) cc_final: 0.7249 (m110) REVERT: M 10 ASP cc_start: 0.7794 (t0) cc_final: 0.7531 (t70) REVERT: N 5 TRP cc_start: 0.3194 (t60) cc_final: 0.2699 (p90) REVERT: N 17 ASP cc_start: 0.7345 (m-30) cc_final: 0.6972 (m-30) REVERT: N 31 LEU cc_start: 0.9302 (tp) cc_final: 0.9059 (tp) REVERT: N 58 ARG cc_start: 0.4283 (mtt180) cc_final: 0.3388 (mmt180) REVERT: N 59 ASN cc_start: 0.8082 (t0) cc_final: 0.7844 (t0) REVERT: N 62 SER cc_start: 0.8948 (t) cc_final: 0.8713 (t) REVERT: N 66 LYS cc_start: 0.8215 (tmtt) cc_final: 0.7781 (ttpp) REVERT: O 147 ASP cc_start: 0.7028 (p0) cc_final: 0.6710 (t0) REVERT: O 260 PRO cc_start: 0.9254 (Cg_exo) cc_final: 0.8700 (Cg_endo) REVERT: O 287 TYR cc_start: 0.7868 (t80) cc_final: 0.7441 (t80) REVERT: O 288 GLN cc_start: 0.7700 (mm110) cc_final: 0.7337 (pt0) REVERT: O 326 LEU cc_start: 0.7731 (pp) cc_final: 0.7089 (mt) REVERT: P 24 GLN cc_start: 0.8427 (pm20) cc_final: 0.8121 (mp10) REVERT: P 28 THR cc_start: 0.8833 (m) cc_final: 0.8270 (m) REVERT: P 47 TYR cc_start: 0.8143 (t80) cc_final: 0.7531 (t80) REVERT: P 54 TYR cc_start: 0.7292 (t80) cc_final: 0.6970 (t80) REVERT: P 66 LYS cc_start: 0.7849 (tptm) cc_final: 0.6755 (tptt) REVERT: P 70 ASP cc_start: 0.7271 (m-30) cc_final: 0.7003 (m-30) REVERT: Q 10 ASP cc_start: 0.7731 (m-30) cc_final: 0.7460 (m-30) REVERT: Q 17 ASP cc_start: 0.7905 (t0) cc_final: 0.7557 (t0) REVERT: Q 34 LEU cc_start: 0.8829 (tp) cc_final: 0.8626 (tp) REVERT: Q 67 VAL cc_start: 0.8971 (p) cc_final: 0.8684 (m) REVERT: R 267 ASP cc_start: 0.7780 (m-30) cc_final: 0.7521 (t0) REVERT: T 8 TYR cc_start: 0.7234 (t80) cc_final: 0.7029 (t80) REVERT: T 23 LEU cc_start: 0.8113 (mt) cc_final: 0.7861 (mp) REVERT: T 47 TYR cc_start: 0.7774 (t80) cc_final: 0.7551 (t80) REVERT: T 52 SER cc_start: 0.9050 (t) cc_final: 0.8475 (p) REVERT: U 15 LYS cc_start: 0.7569 (tptp) cc_final: 0.7019 (tmtt) REVERT: V 214 LEU cc_start: 0.6710 (mt) cc_final: 0.6400 (mt) REVERT: V 269 ASP cc_start: 0.7588 (t0) cc_final: 0.7278 (t0) REVERT: W 28 THR cc_start: 0.6176 (m) cc_final: 0.5122 (p) REVERT: W 71 ILE cc_start: 0.9113 (pt) cc_final: 0.8680 (pt) REVERT: X 260 PRO cc_start: 0.8267 (Cg_exo) cc_final: 0.8037 (Cg_endo) REVERT: X 291 GLN cc_start: 0.8069 (mm-40) cc_final: 0.7766 (mm-40) REVERT: X 308 LEU cc_start: 0.7467 (mm) cc_final: 0.5680 (tp) outliers start: 0 outliers final: 0 residues processed: 866 average time/residue: 0.1318 time to fit residues: 178.6031 Evaluate side-chains 524 residues out of total 2167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 524 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 216 optimal weight: 2.9990 chunk 98 optimal weight: 8.9990 chunk 194 optimal weight: 9.9990 chunk 227 optimal weight: 0.8980 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.0470 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 0.1980 chunk 103 optimal weight: 0.9980 chunk 235 optimal weight: 0.5980 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 ASN B 78 ASN D 26 GLN ** F 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 288 GLN G 24 GLN G 59 ASN ** I 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 24 GLN ** K 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 78 ASN L 26 GLN ** L 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 63 ASN N 24 GLN ** N 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 239 ASN P 77 GLN Q 48 GLN Q 63 ASN R 218 GLN R 233 GLN R 310 GLN R 314 ASN ** T 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 199 ASN W 55 ASN ** W 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 63 ASN ** X 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.092103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.080496 restraints weight = 62606.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.082505 restraints weight = 35165.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.083892 restraints weight = 22425.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.084849 restraints weight = 15791.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.085495 restraints weight = 12067.537| |-----------------------------------------------------------------------------| r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7193 moved from start: 0.3301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20052 Z= 0.143 Angle : 0.648 10.859 27243 Z= 0.333 Chirality : 0.041 0.211 3119 Planarity : 0.004 0.061 3524 Dihedral : 4.368 26.337 2693 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.64 % Allowed : 16.83 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.17), residues: 2487 helix: 1.54 (0.12), residues: 1877 sheet: -1.30 (0.58), residues: 75 loop : -1.61 (0.26), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG J 58 TYR 0.038 0.002 TYR J 57 PHE 0.017 0.001 PHE O 215 TRP 0.035 0.002 TRP R 234 Details of bonding type rmsd covalent geometry : bond 0.00301 (20052) covalent geometry : angle 0.64784 (27243) hydrogen bonds : bond 0.04116 ( 1524) hydrogen bonds : angle 4.05377 ( 4512) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 657 residues out of total 2167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 600 time to evaluate : 0.777 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: A 27 VAL cc_start: 0.9433 (t) cc_final: 0.9023 (p) REVERT: A 44 LEU cc_start: 0.8611 (tp) cc_final: 0.8388 (tt) REVERT: A 48 GLN cc_start: 0.7408 (tm-30) cc_final: 0.6661 (tm-30) REVERT: A 72 ASP cc_start: 0.7670 (OUTLIER) cc_final: 0.7373 (t0) REVERT: B 8 TYR cc_start: 0.8171 (t80) cc_final: 0.7792 (t80) REVERT: B 28 THR cc_start: 0.8616 (m) cc_final: 0.8330 (p) REVERT: B 33 LYS cc_start: 0.9032 (tppt) cc_final: 0.8726 (mtpt) REVERT: B 54 TYR cc_start: 0.8401 (t80) cc_final: 0.8120 (t80) REVERT: B 78 ASN cc_start: 0.6747 (m-40) cc_final: 0.6350 (m-40) REVERT: C 53 GLU cc_start: 0.6650 (tt0) cc_final: 0.6387 (mt-10) REVERT: C 66 LYS cc_start: 0.8337 (tptp) cc_final: 0.7498 (tptm) REVERT: C 70 ASP cc_start: 0.7512 (m-30) cc_final: 0.6966 (m-30) REVERT: C 71 ILE cc_start: 0.8907 (mt) cc_final: 0.8664 (mt) REVERT: D 61 GLN cc_start: 0.8120 (pp30) cc_final: 0.7678 (pp30) REVERT: D 66 LYS cc_start: 0.8067 (ttpp) cc_final: 0.7556 (ttpp) REVERT: E 11 ASP cc_start: 0.8614 (m-30) cc_final: 0.7451 (m-30) REVERT: F 215 PHE cc_start: 0.7115 (t80) cc_final: 0.6877 (t80) REVERT: F 287 TYR cc_start: 0.5826 (t80) cc_final: 0.5622 (t80) REVERT: F 301 MET cc_start: 0.7173 (OUTLIER) cc_final: 0.6612 (ppp) REVERT: G 20 VAL cc_start: 0.8091 (t) cc_final: 0.7796 (t) REVERT: G 69 LYS cc_start: 0.8155 (tmtt) cc_final: 0.7766 (tptm) REVERT: G 76 ILE cc_start: 0.6683 (mm) cc_final: 0.6123 (mm) REVERT: H 76 ILE cc_start: 0.8109 (pt) cc_final: 0.7742 (pt) REVERT: I 17 ASP cc_start: 0.7333 (m-30) cc_final: 0.4883 (t70) REVERT: J 59 ASN cc_start: 0.8205 (m110) cc_final: 0.7662 (m110) REVERT: J 66 LYS cc_start: 0.7924 (tptm) cc_final: 0.7133 (tppt) REVERT: J 69 LYS cc_start: 0.8419 (tmtt) cc_final: 0.7888 (tppt) REVERT: J 70 ASP cc_start: 0.7401 (m-30) cc_final: 0.6763 (m-30) REVERT: K 57 TYR cc_start: 0.8407 (t80) cc_final: 0.7350 (t80) REVERT: K 61 GLN cc_start: 0.9035 (tt0) cc_final: 0.8415 (tp40) REVERT: L 11 ASP cc_start: 0.8119 (t0) cc_final: 0.7718 (m-30) REVERT: L 21 ASP cc_start: 0.6697 (p0) cc_final: 0.6246 (p0) REVERT: L 37 LYS cc_start: 0.7567 (tptp) cc_final: 0.7184 (tppt) REVERT: L 63 ASN cc_start: 0.7591 (m-40) cc_final: 0.7328 (m-40) REVERT: M 10 ASP cc_start: 0.7779 (t0) cc_final: 0.7337 (t0) REVERT: M 31 LEU cc_start: 0.8467 (tp) cc_final: 0.8227 (mt) REVERT: N 17 ASP cc_start: 0.7942 (m-30) cc_final: 0.7378 (m-30) REVERT: N 28 THR cc_start: 0.9582 (m) cc_final: 0.9354 (p) REVERT: N 58 ARG cc_start: 0.5001 (mtt180) cc_final: 0.4214 (mmt180) REVERT: N 59 ASN cc_start: 0.8089 (t0) cc_final: 0.7804 (t0) REVERT: N 66 LYS cc_start: 0.7947 (tmtt) cc_final: 0.7734 (ttpp) REVERT: O 288 GLN cc_start: 0.7680 (mm110) cc_final: 0.7261 (pt0) REVERT: O 301 MET cc_start: 0.6897 (mmp) cc_final: 0.6489 (mmt) REVERT: P 10 ASP cc_start: 0.8167 (t0) cc_final: 0.7887 (t0) REVERT: P 27 VAL cc_start: 0.9196 (m) cc_final: 0.8919 (m) REVERT: P 47 TYR cc_start: 0.7972 (t80) cc_final: 0.7743 (t80) REVERT: P 48 GLN cc_start: 0.7548 (pp30) cc_final: 0.7195 (pp30) REVERT: P 70 ASP cc_start: 0.7477 (m-30) cc_final: 0.7241 (m-30) REVERT: P 72 ASP cc_start: 0.7918 (m-30) cc_final: 0.6889 (t0) REVERT: Q 16 PHE cc_start: 0.7792 (OUTLIER) cc_final: 0.7441 (t80) REVERT: Q 31 LEU cc_start: 0.9153 (tp) cc_final: 0.8732 (tp) REVERT: Q 57 TYR cc_start: 0.7483 (t80) cc_final: 0.6843 (t80) REVERT: Q 61 GLN cc_start: 0.8575 (OUTLIER) cc_final: 0.8321 (mt0) REVERT: Q 67 VAL cc_start: 0.8865 (p) cc_final: 0.8649 (m) REVERT: Q 75 ILE cc_start: 0.7427 (tt) cc_final: 0.7130 (tp) REVERT: R 267 ASP cc_start: 0.7715 (m-30) cc_final: 0.7457 (t0) REVERT: R 321 ASN cc_start: 0.8424 (OUTLIER) cc_final: 0.7551 (m-40) REVERT: S 47 TYR cc_start: 0.8257 (t80) cc_final: 0.8048 (t80) REVERT: T 52 SER cc_start: 0.8363 (t) cc_final: 0.8079 (p) REVERT: U 15 LYS cc_start: 0.7515 (tptp) cc_final: 0.6926 (tmtt) REVERT: U 16 PHE cc_start: 0.8145 (OUTLIER) cc_final: 0.7559 (t80) REVERT: V 214 LEU cc_start: 0.7130 (mt) cc_final: 0.6815 (mt) REVERT: V 282 MET cc_start: 0.6025 (tpp) cc_final: 0.5771 (tpp) REVERT: W 28 THR cc_start: 0.5445 (m) cc_final: 0.5150 (p) REVERT: W 72 ASP cc_start: 0.8239 (p0) cc_final: 0.7973 (p0) outliers start: 57 outliers final: 25 residues processed: 626 average time/residue: 0.1241 time to fit residues: 124.5545 Evaluate side-chains 524 residues out of total 2167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 493 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ASP Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain B residue 47 TYR Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain D residue 13 SER Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain F residue 259 THR Chi-restraints excluded: chain F residue 301 MET Chi-restraints excluded: chain I residue 44 LEU Chi-restraints excluded: chain I residue 51 LEU Chi-restraints excluded: chain K residue 25 THR Chi-restraints excluded: chain K residue 47 TYR Chi-restraints excluded: chain M residue 79 PHE Chi-restraints excluded: chain P residue 29 GLU Chi-restraints excluded: chain Q residue 12 VAL Chi-restraints excluded: chain Q residue 16 PHE Chi-restraints excluded: chain Q residue 27 VAL Chi-restraints excluded: chain Q residue 61 GLN Chi-restraints excluded: chain Q residue 62 SER Chi-restraints excluded: chain R residue 221 SER Chi-restraints excluded: chain R residue 261 LEU Chi-restraints excluded: chain R residue 321 ASN Chi-restraints excluded: chain S residue 79 PHE Chi-restraints excluded: chain T residue 75 ILE Chi-restraints excluded: chain U residue 16 PHE Chi-restraints excluded: chain U residue 25 THR Chi-restraints excluded: chain V residue 291 GLN Chi-restraints excluded: chain W residue 61 GLN Chi-restraints excluded: chain X residue 137 MET Chi-restraints excluded: chain X residue 142 ILE Chi-restraints excluded: chain X residue 150 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 0 optimal weight: 10.0000 chunk 16 optimal weight: 6.9990 chunk 223 optimal weight: 4.9990 chunk 108 optimal weight: 0.8980 chunk 135 optimal weight: 0.4980 chunk 70 optimal weight: 7.9990 chunk 50 optimal weight: 0.6980 chunk 169 optimal weight: 7.9990 chunk 62 optimal weight: 2.9990 chunk 78 optimal weight: 0.0980 chunk 219 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 59 ASN I 55 ASN ** I 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 59 ASN ** K 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 78 ASN O 239 ASN O 314 ASN ** O 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 196 ASN R 316 ASN T 26 GLN ** U 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 284 ASN V 300 ASN ** W 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.091634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.080309 restraints weight = 63508.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.082320 restraints weight = 35520.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.083718 restraints weight = 22613.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.084630 restraints weight = 15914.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.085307 restraints weight = 12256.124| |-----------------------------------------------------------------------------| r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.4078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20052 Z= 0.133 Angle : 0.606 10.099 27243 Z= 0.313 Chirality : 0.040 0.161 3119 Planarity : 0.004 0.044 3524 Dihedral : 4.196 23.512 2693 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 3.11 % Allowed : 19.24 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.37 (0.17), residues: 2487 helix: 1.62 (0.12), residues: 1895 sheet: -1.58 (0.78), residues: 50 loop : -1.38 (0.26), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 58 TYR 0.028 0.002 TYR J 57 PHE 0.024 0.001 PHE V 215 TRP 0.026 0.002 TRP R 234 Details of bonding type rmsd covalent geometry : bond 0.00288 (20052) covalent geometry : angle 0.60605 (27243) hydrogen bonds : bond 0.03778 ( 1524) hydrogen bonds : angle 3.86463 ( 4512) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 629 residues out of total 2167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 562 time to evaluate : 0.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 PHE cc_start: 0.8222 (OUTLIER) cc_final: 0.7124 (t80) REVERT: A 31 LEU cc_start: 0.9371 (OUTLIER) cc_final: 0.9142 (mm) REVERT: A 44 LEU cc_start: 0.8706 (tp) cc_final: 0.8458 (tt) REVERT: A 72 ASP cc_start: 0.7988 (OUTLIER) cc_final: 0.7743 (t0) REVERT: B 8 TYR cc_start: 0.7758 (t80) cc_final: 0.7531 (t80) REVERT: B 28 THR cc_start: 0.8673 (m) cc_final: 0.8467 (p) REVERT: B 33 LYS cc_start: 0.9124 (tppt) cc_final: 0.8818 (mtpt) REVERT: B 34 LEU cc_start: 0.8106 (OUTLIER) cc_final: 0.7898 (mt) REVERT: B 80 ARG cc_start: 0.7781 (ptp-170) cc_final: 0.7578 (ptm160) REVERT: C 53 GLU cc_start: 0.7070 (tt0) cc_final: 0.6766 (mt-10) REVERT: C 66 LYS cc_start: 0.8309 (tptp) cc_final: 0.7649 (tptm) REVERT: C 70 ASP cc_start: 0.7544 (m-30) cc_final: 0.7019 (m-30) REVERT: C 71 ILE cc_start: 0.9093 (mt) cc_final: 0.8859 (mt) REVERT: D 66 LYS cc_start: 0.8171 (ttpp) cc_final: 0.7750 (ttpp) REVERT: D 72 ASP cc_start: 0.8242 (m-30) cc_final: 0.7987 (m-30) REVERT: E 11 ASP cc_start: 0.8775 (m-30) cc_final: 0.7495 (m-30) REVERT: E 78 ASN cc_start: 0.7893 (m-40) cc_final: 0.7595 (m-40) REVERT: F 170 ILE cc_start: 0.6958 (mm) cc_final: 0.6650 (mm) REVERT: F 189 LEU cc_start: 0.6370 (tp) cc_final: 0.6033 (mt) REVERT: F 215 PHE cc_start: 0.7111 (t80) cc_final: 0.6832 (t80) REVERT: F 232 ARG cc_start: 0.7011 (mmm-85) cc_final: 0.6741 (tpp80) REVERT: G 69 LYS cc_start: 0.8355 (tmtt) cc_final: 0.7935 (tptm) REVERT: G 76 ILE cc_start: 0.7523 (mm) cc_final: 0.7163 (mm) REVERT: H 13 SER cc_start: 0.9196 (t) cc_final: 0.8948 (p) REVERT: I 17 ASP cc_start: 0.7845 (m-30) cc_final: 0.6393 (t70) REVERT: I 79 PHE cc_start: 0.7672 (m-80) cc_final: 0.7061 (m-10) REVERT: J 59 ASN cc_start: 0.8129 (m-40) cc_final: 0.7822 (m110) REVERT: J 66 LYS cc_start: 0.8068 (tptm) cc_final: 0.7042 (tppt) REVERT: J 69 LYS cc_start: 0.8502 (tmtt) cc_final: 0.7905 (tppt) REVERT: J 70 ASP cc_start: 0.7499 (m-30) cc_final: 0.6688 (m-30) REVERT: K 57 TYR cc_start: 0.8451 (t80) cc_final: 0.7481 (t80) REVERT: K 61 GLN cc_start: 0.9082 (OUTLIER) cc_final: 0.8305 (tp40) REVERT: L 11 ASP cc_start: 0.8151 (t0) cc_final: 0.7761 (m-30) REVERT: L 21 ASP cc_start: 0.7068 (p0) cc_final: 0.6586 (p0) REVERT: L 22 ASN cc_start: 0.8156 (p0) cc_final: 0.7947 (p0) REVERT: L 29 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.8050 (pp20) REVERT: L 63 ASN cc_start: 0.7788 (m-40) cc_final: 0.7439 (m-40) REVERT: M 10 ASP cc_start: 0.7909 (t0) cc_final: 0.7378 (t0) REVERT: M 21 ASP cc_start: 0.7426 (OUTLIER) cc_final: 0.6831 (p0) REVERT: M 40 ASP cc_start: 0.8063 (t70) cc_final: 0.7727 (p0) REVERT: N 17 ASP cc_start: 0.7980 (m-30) cc_final: 0.7427 (m-30) REVERT: N 24 GLN cc_start: 0.7382 (pm20) cc_final: 0.6562 (tp40) REVERT: N 59 ASN cc_start: 0.8032 (t0) cc_final: 0.7660 (t0) REVERT: N 66 LYS cc_start: 0.8112 (tmtt) cc_final: 0.7751 (tmtt) REVERT: O 169 ASP cc_start: 0.7448 (t0) cc_final: 0.7074 (m-30) REVERT: O 288 GLN cc_start: 0.7827 (mm110) cc_final: 0.7325 (pt0) REVERT: O 294 PHE cc_start: 0.7366 (OUTLIER) cc_final: 0.6605 (t80) REVERT: O 301 MET cc_start: 0.7031 (mmp) cc_final: 0.6788 (mmt) REVERT: O 316 ASN cc_start: 0.8285 (m-40) cc_final: 0.7933 (m-40) REVERT: O 322 LEU cc_start: 0.9159 (tp) cc_final: 0.8924 (tp) REVERT: P 10 ASP cc_start: 0.8104 (t0) cc_final: 0.7875 (t0) REVERT: P 27 VAL cc_start: 0.9172 (m) cc_final: 0.8959 (m) REVERT: P 54 TYR cc_start: 0.7591 (t80) cc_final: 0.7317 (t80) REVERT: P 66 LYS cc_start: 0.7445 (tptm) cc_final: 0.6426 (tptt) REVERT: P 72 ASP cc_start: 0.7589 (m-30) cc_final: 0.7319 (m-30) REVERT: Q 16 PHE cc_start: 0.7808 (OUTLIER) cc_final: 0.7391 (t80) REVERT: Q 17 ASP cc_start: 0.7383 (t0) cc_final: 0.6809 (t0) REVERT: Q 31 LEU cc_start: 0.9273 (tp) cc_final: 0.8999 (tp) REVERT: Q 57 TYR cc_start: 0.6941 (t80) cc_final: 0.6351 (t80) REVERT: Q 67 VAL cc_start: 0.8934 (p) cc_final: 0.8731 (m) REVERT: R 264 MET cc_start: 0.6482 (tpp) cc_final: 0.6044 (tpp) REVERT: R 267 ASP cc_start: 0.7774 (m-30) cc_final: 0.7490 (t0) REVERT: R 321 ASN cc_start: 0.8461 (OUTLIER) cc_final: 0.7654 (m-40) REVERT: T 23 LEU cc_start: 0.8035 (mp) cc_final: 0.7575 (mt) REVERT: U 15 LYS cc_start: 0.7508 (tptp) cc_final: 0.6944 (tmtt) REVERT: U 16 PHE cc_start: 0.8230 (OUTLIER) cc_final: 0.7648 (t80) REVERT: V 300 ASN cc_start: 0.7612 (OUTLIER) cc_final: 0.7384 (t0) REVERT: W 28 THR cc_start: 0.6142 (m) cc_final: 0.5638 (p) outliers start: 67 outliers final: 34 residues processed: 599 average time/residue: 0.1224 time to fit residues: 117.0823 Evaluate side-chains 546 residues out of total 2167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 500 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 PHE Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 47 TYR Chi-restraints excluded: chain C residue 79 PHE Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain E residue 16 PHE Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 259 THR Chi-restraints excluded: chain F residue 301 MET Chi-restraints excluded: chain F residue 327 SER Chi-restraints excluded: chain G residue 66 LYS Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain I residue 44 LEU Chi-restraints excluded: chain I residue 51 LEU Chi-restraints excluded: chain K residue 34 LEU Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain K residue 47 TYR Chi-restraints excluded: chain K residue 61 GLN Chi-restraints excluded: chain L residue 25 THR Chi-restraints excluded: chain L residue 29 GLU Chi-restraints excluded: chain M residue 21 ASP Chi-restraints excluded: chain M residue 44 LEU Chi-restraints excluded: chain O residue 245 LEU Chi-restraints excluded: chain O residue 294 PHE Chi-restraints excluded: chain P residue 13 SER Chi-restraints excluded: chain P residue 29 GLU Chi-restraints excluded: chain P residue 55 ASN Chi-restraints excluded: chain Q residue 12 VAL Chi-restraints excluded: chain Q residue 16 PHE Chi-restraints excluded: chain Q residue 61 GLN Chi-restraints excluded: chain Q residue 62 SER Chi-restraints excluded: chain R residue 221 SER Chi-restraints excluded: chain R residue 245 LEU Chi-restraints excluded: chain R residue 294 PHE Chi-restraints excluded: chain R residue 321 ASN Chi-restraints excluded: chain T residue 75 ILE Chi-restraints excluded: chain U residue 16 PHE Chi-restraints excluded: chain V residue 150 LEU Chi-restraints excluded: chain V residue 153 TYR Chi-restraints excluded: chain V residue 291 GLN Chi-restraints excluded: chain V residue 300 ASN Chi-restraints excluded: chain W residue 61 GLN Chi-restraints excluded: chain X residue 137 MET Chi-restraints excluded: chain X residue 150 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 117 optimal weight: 9.9990 chunk 158 optimal weight: 5.9990 chunk 74 optimal weight: 0.5980 chunk 231 optimal weight: 20.0000 chunk 174 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 88 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 120 optimal weight: 7.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 ASN B 24 GLN C 63 ASN ** D 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 300 ASN G 59 ASN H 61 GLN ** I 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 59 ASN ** L 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 26 GLN ** O 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 26 GLN ** U 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 61 GLN ** X 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.085365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.074140 restraints weight = 64502.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.076045 restraints weight = 35474.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.077371 restraints weight = 22461.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.078245 restraints weight = 15836.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.078869 restraints weight = 12188.503| |-----------------------------------------------------------------------------| r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.6891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 20052 Z= 0.206 Angle : 0.723 9.278 27243 Z= 0.381 Chirality : 0.045 0.239 3119 Planarity : 0.004 0.059 3524 Dihedral : 4.666 27.449 2693 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 6.03 % Allowed : 20.35 % Favored : 73.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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 (0.17), residues: 2487 helix: 1.22 (0.12), residues: 1907 sheet: -1.71 (0.78), residues: 50 loop : -1.78 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 58 TYR 0.044 0.003 TYR N 47 PHE 0.032 0.003 PHE V 167 TRP 0.043 0.002 TRP R 234 Details of bonding type rmsd covalent geometry : bond 0.00459 (20052) covalent geometry : angle 0.72289 (27243) hydrogen bonds : bond 0.04642 ( 1524) hydrogen bonds : angle 4.16779 ( 4512) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 681 residues out of total 2167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 551 time to evaluate : 0.745 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: A 47 TYR cc_start: 0.9339 (OUTLIER) cc_final: 0.9076 (t80) REVERT: A 66 LYS cc_start: 0.9095 (tptp) cc_final: 0.8701 (tptp) REVERT: A 72 ASP cc_start: 0.8725 (OUTLIER) cc_final: 0.8415 (t0) REVERT: A 78 ASN cc_start: 0.7803 (m110) cc_final: 0.7327 (m110) REVERT: B 16 PHE cc_start: 0.7790 (OUTLIER) cc_final: 0.7434 (m-80) REVERT: B 28 THR cc_start: 0.9128 (m) cc_final: 0.8082 (p) REVERT: B 33 LYS cc_start: 0.9021 (tppt) cc_final: 0.8698 (mtpt) REVERT: B 63 ASN cc_start: 0.8809 (m-40) cc_final: 0.8456 (m-40) REVERT: C 10 ASP cc_start: 0.8040 (t0) cc_final: 0.7669 (t0) REVERT: C 34 LEU cc_start: 0.8965 (tp) cc_final: 0.8404 (tt) REVERT: C 48 GLN cc_start: 0.8392 (tm-30) cc_final: 0.8070 (tm-30) REVERT: C 53 GLU cc_start: 0.8378 (tt0) cc_final: 0.7795 (mt-10) REVERT: C 66 LYS cc_start: 0.8993 (tptp) cc_final: 0.8296 (tppt) REVERT: C 70 ASP cc_start: 0.8064 (m-30) cc_final: 0.7462 (m-30) REVERT: D 31 LEU cc_start: 0.9565 (tp) cc_final: 0.9313 (tp) REVERT: D 61 GLN cc_start: 0.8921 (pp30) cc_final: 0.8276 (pp30) REVERT: D 62 SER cc_start: 0.9476 (m) cc_final: 0.9247 (p) REVERT: D 66 LYS cc_start: 0.8427 (ttpp) cc_final: 0.7763 (ttpp) REVERT: E 53 GLU cc_start: 0.8360 (tm-30) cc_final: 0.7924 (tm-30) REVERT: E 59 ASN cc_start: 0.7642 (m-40) cc_final: 0.7380 (m-40) REVERT: E 76 ILE cc_start: 0.8948 (pt) cc_final: 0.8676 (mm) REVERT: F 170 ILE cc_start: 0.7506 (mm) cc_final: 0.7199 (mm) REVERT: F 215 PHE cc_start: 0.7827 (t80) cc_final: 0.7272 (t80) REVERT: F 233 GLN cc_start: 0.7922 (tt0) cc_final: 0.7687 (tp-100) REVERT: F 252 TYR cc_start: 0.6878 (m-10) cc_final: 0.6402 (m-10) REVERT: G 66 LYS cc_start: 0.8779 (OUTLIER) cc_final: 0.8577 (ttpt) REVERT: G 69 LYS cc_start: 0.8619 (tmtt) cc_final: 0.8297 (tptm) REVERT: I 11 ASP cc_start: 0.7086 (p0) cc_final: 0.6500 (p0) REVERT: I 17 ASP cc_start: 0.8683 (m-30) cc_final: 0.6940 (t70) REVERT: I 58 ARG cc_start: 0.7993 (ttt180) cc_final: 0.7619 (tpp80) REVERT: J 9 LEU cc_start: 0.8652 (mp) cc_final: 0.8451 (mt) REVERT: J 17 ASP cc_start: 0.8534 (m-30) cc_final: 0.8290 (m-30) REVERT: J 34 LEU cc_start: 0.9115 (OUTLIER) cc_final: 0.8708 (mm) REVERT: J 54 TYR cc_start: 0.8709 (t80) cc_final: 0.8158 (t80) REVERT: J 57 TYR cc_start: 0.7906 (t80) cc_final: 0.7355 (t80) REVERT: J 59 ASN cc_start: 0.8672 (m110) cc_final: 0.8291 (m110) REVERT: J 66 LYS cc_start: 0.8604 (tptm) cc_final: 0.7400 (tppt) REVERT: J 70 ASP cc_start: 0.7264 (m-30) cc_final: 0.7014 (m-30) REVERT: K 25 THR cc_start: 0.8665 (OUTLIER) cc_final: 0.8462 (t) REVERT: K 61 GLN cc_start: 0.9301 (OUTLIER) cc_final: 0.8965 (tt0) REVERT: L 16 PHE cc_start: 0.8473 (OUTLIER) cc_final: 0.7916 (m-10) REVERT: L 21 ASP cc_start: 0.7103 (p0) cc_final: 0.6861 (p0) REVERT: L 29 GLU cc_start: 0.8442 (OUTLIER) cc_final: 0.8222 (pp20) REVERT: L 77 GLN cc_start: 0.8981 (tt0) cc_final: 0.8557 (tm-30) REVERT: M 8 TYR cc_start: 0.7787 (t80) cc_final: 0.6322 (m-80) REVERT: M 10 ASP cc_start: 0.7697 (t0) cc_final: 0.7395 (t0) REVERT: M 21 ASP cc_start: 0.7975 (OUTLIER) cc_final: 0.7384 (p0) REVERT: M 51 LEU cc_start: 0.8833 (tt) cc_final: 0.8499 (tt) REVERT: M 66 LYS cc_start: 0.8765 (tppp) cc_final: 0.8430 (tppt) REVERT: M 76 ILE cc_start: 0.7074 (tt) cc_final: 0.6782 (tt) REVERT: M 77 GLN cc_start: 0.8880 (tm-30) cc_final: 0.8572 (tm-30) REVERT: N 17 ASP cc_start: 0.8251 (m-30) cc_final: 0.7940 (m-30) REVERT: N 24 GLN cc_start: 0.7996 (pm20) cc_final: 0.7622 (pp30) REVERT: N 31 LEU cc_start: 0.9459 (tp) cc_final: 0.9202 (tp) REVERT: N 66 LYS cc_start: 0.8162 (tmtt) cc_final: 0.7717 (tmtt) REVERT: O 169 ASP cc_start: 0.7861 (t0) cc_final: 0.7555 (t70) REVERT: O 253 VAL cc_start: 0.7831 (OUTLIER) cc_final: 0.7508 (p) REVERT: O 294 PHE cc_start: 0.7308 (OUTLIER) cc_final: 0.6072 (t80) REVERT: O 316 ASN cc_start: 0.8613 (m-40) cc_final: 0.8308 (m-40) REVERT: P 16 PHE cc_start: 0.8923 (OUTLIER) cc_final: 0.8398 (t80) REVERT: P 47 TYR cc_start: 0.7888 (t80) cc_final: 0.7594 (t80) REVERT: P 48 GLN cc_start: 0.8552 (pp30) cc_final: 0.8082 (pp30) REVERT: P 54 TYR cc_start: 0.8331 (t80) cc_final: 0.7748 (t80) REVERT: P 70 ASP cc_start: 0.7733 (m-30) cc_final: 0.7429 (m-30) REVERT: P 72 ASP cc_start: 0.8413 (m-30) cc_final: 0.8092 (m-30) REVERT: R 205 TYR cc_start: 0.7283 (m-80) cc_final: 0.7069 (m-10) REVERT: R 234 TRP cc_start: 0.6463 (m100) cc_final: 0.6042 (t-100) REVERT: R 252 TYR cc_start: 0.7428 (m-10) cc_final: 0.7214 (m-10) REVERT: R 264 MET cc_start: 0.6851 (tpp) cc_final: 0.6312 (tpp) REVERT: S 31 LEU cc_start: 0.9088 (tp) cc_final: 0.8823 (tp) REVERT: S 68 PHE cc_start: 0.8459 (m-80) cc_final: 0.8242 (m-10) REVERT: S 79 PHE cc_start: 0.2734 (OUTLIER) cc_final: 0.2220 (t80) REVERT: T 8 TYR cc_start: 0.7907 (t80) cc_final: 0.7500 (t80) REVERT: T 11 ASP cc_start: 0.7467 (m-30) cc_final: 0.6963 (m-30) REVERT: T 23 LEU cc_start: 0.7901 (mp) cc_final: 0.7570 (mt) REVERT: T 55 ASN cc_start: 0.8111 (m-40) cc_final: 0.7335 (m-40) REVERT: U 15 LYS cc_start: 0.7957 (tptp) cc_final: 0.7362 (tmtt) REVERT: U 16 PHE cc_start: 0.8455 (OUTLIER) cc_final: 0.7568 (t80) REVERT: U 47 TYR cc_start: 0.8084 (t80) cc_final: 0.7822 (t80) REVERT: V 300 ASN cc_start: 0.8143 (OUTLIER) cc_final: 0.7750 (t0) REVERT: W 50 LYS cc_start: 0.8517 (mtpt) cc_final: 0.8219 (mtmt) REVERT: X 150 LEU cc_start: 0.7673 (OUTLIER) cc_final: 0.7437 (mp) REVERT: X 298 GLU cc_start: 0.8295 (tp30) cc_final: 0.7903 (tp30) REVERT: X 299 GLU cc_start: 0.8293 (mm-30) cc_final: 0.7891 (mm-30) REVERT: X 300 ASN cc_start: 0.8087 (m110) cc_final: 0.7886 (m110) REVERT: X 334 LEU cc_start: 0.8731 (tt) cc_final: 0.8433 (tt) outliers start: 130 outliers final: 56 residues processed: 640 average time/residue: 0.1245 time to fit residues: 127.8878 Evaluate side-chains 548 residues out of total 2167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 475 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 PHE Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 47 TYR Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain B residue 16 PHE Chi-restraints excluded: chain B residue 47 TYR Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 79 PHE Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 259 THR Chi-restraints excluded: chain F residue 323 VAL Chi-restraints excluded: chain F residue 334 LEU Chi-restraints excluded: chain G residue 66 LYS Chi-restraints excluded: chain H residue 18 THR Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain H residue 76 ILE Chi-restraints excluded: chain I residue 51 LEU Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain K residue 9 LEU Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 25 THR Chi-restraints excluded: chain K residue 34 LEU Chi-restraints excluded: chain K residue 55 ASN Chi-restraints excluded: chain K residue 61 GLN Chi-restraints excluded: chain L residue 8 TYR Chi-restraints excluded: chain L residue 16 PHE Chi-restraints excluded: chain L residue 25 THR Chi-restraints excluded: chain L residue 29 GLU Chi-restraints excluded: chain L residue 40 ASP Chi-restraints excluded: chain M residue 21 ASP Chi-restraints excluded: chain M residue 44 LEU Chi-restraints excluded: chain M residue 71 ILE Chi-restraints excluded: chain M residue 79 PHE Chi-restraints excluded: chain N residue 44 LEU Chi-restraints excluded: chain O residue 136 ASP Chi-restraints excluded: chain O residue 155 ASN Chi-restraints excluded: chain O residue 253 VAL Chi-restraints excluded: chain O residue 258 LEU Chi-restraints excluded: chain O residue 294 PHE Chi-restraints excluded: chain O residue 303 THR Chi-restraints excluded: chain P residue 13 SER Chi-restraints excluded: chain P residue 16 PHE Chi-restraints excluded: chain Q residue 61 GLN Chi-restraints excluded: chain Q residue 62 SER Chi-restraints excluded: chain R residue 145 ILE Chi-restraints excluded: chain R residue 221 SER Chi-restraints excluded: chain R residue 256 VAL Chi-restraints excluded: chain R residue 294 PHE Chi-restraints excluded: chain R residue 321 ASN Chi-restraints excluded: chain S residue 43 LEU Chi-restraints excluded: chain S residue 79 PHE Chi-restraints excluded: chain T residue 75 ILE Chi-restraints excluded: chain U residue 16 PHE Chi-restraints excluded: chain U residue 21 ASP Chi-restraints excluded: chain U residue 32 ASP Chi-restraints excluded: chain U residue 79 PHE Chi-restraints excluded: chain V residue 150 LEU Chi-restraints excluded: chain V residue 157 VAL Chi-restraints excluded: chain V residue 237 GLU Chi-restraints excluded: chain V residue 291 GLN Chi-restraints excluded: chain V residue 300 ASN Chi-restraints excluded: chain W residue 79 PHE Chi-restraints excluded: chain X residue 137 MET Chi-restraints excluded: chain X residue 150 LEU Chi-restraints excluded: chain X residue 189 LEU Chi-restraints excluded: chain X residue 268 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 7 optimal weight: 10.0000 chunk 27 optimal weight: 0.9980 chunk 108 optimal weight: 0.7980 chunk 68 optimal weight: 4.9990 chunk 168 optimal weight: 10.0000 chunk 130 optimal weight: 3.9990 chunk 153 optimal weight: 7.9990 chunk 37 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 93 optimal weight: 4.9990 chunk 112 optimal weight: 4.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 63 ASN ** H 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 61 GLN ** O 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 55 ASN ** R 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 63 ASN ** V 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 300 ASN X 141 ASN ** X 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.083679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.072744 restraints weight = 64303.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.074689 restraints weight = 34054.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.075992 restraints weight = 20955.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.076826 restraints weight = 14475.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.077472 restraints weight = 11048.413| |-----------------------------------------------------------------------------| r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.7886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 20052 Z= 0.192 Angle : 0.665 11.526 27243 Z= 0.347 Chirality : 0.043 0.202 3119 Planarity : 0.004 0.047 3524 Dihedral : 4.504 29.257 2693 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 5.05 % Allowed : 23.13 % Favored : 71.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.17), residues: 2487 helix: 1.44 (0.12), residues: 1916 sheet: -1.74 (0.77), residues: 50 loop : -1.59 (0.26), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG L 58 TYR 0.032 0.002 TYR N 47 PHE 0.020 0.002 PHE T 16 TRP 0.031 0.002 TRP R 234 Details of bonding type rmsd covalent geometry : bond 0.00435 (20052) covalent geometry : angle 0.66504 (27243) hydrogen bonds : bond 0.04116 ( 1524) hydrogen bonds : angle 4.05619 ( 4512) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 639 residues out of total 2167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 530 time to evaluate : 0.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ASN cc_start: 0.8731 (t0) cc_final: 0.8491 (t0) REVERT: A 66 LYS cc_start: 0.9083 (tptp) cc_final: 0.8776 (tptp) REVERT: A 72 ASP cc_start: 0.8783 (OUTLIER) cc_final: 0.8392 (t0) REVERT: B 16 PHE cc_start: 0.8274 (OUTLIER) cc_final: 0.7874 (m-80) REVERT: B 28 THR cc_start: 0.9214 (m) cc_final: 0.8989 (p) REVERT: B 63 ASN cc_start: 0.8838 (m-40) cc_final: 0.8396 (m-40) REVERT: C 10 ASP cc_start: 0.8297 (t0) cc_final: 0.8006 (t0) REVERT: C 34 LEU cc_start: 0.8883 (tp) cc_final: 0.8483 (tt) REVERT: C 53 GLU cc_start: 0.8669 (tt0) cc_final: 0.7989 (mt-10) REVERT: C 66 LYS cc_start: 0.8745 (tptp) cc_final: 0.7838 (tppt) REVERT: C 70 ASP cc_start: 0.8065 (m-30) cc_final: 0.7591 (m-30) REVERT: D 31 LEU cc_start: 0.9565 (tp) cc_final: 0.9348 (tt) REVERT: D 62 SER cc_start: 0.9469 (m) cc_final: 0.9219 (p) REVERT: D 69 LYS cc_start: 0.8902 (tptt) cc_final: 0.8479 (tppp) REVERT: E 11 ASP cc_start: 0.8789 (OUTLIER) cc_final: 0.7886 (m-30) REVERT: E 53 GLU cc_start: 0.8522 (tm-30) cc_final: 0.7936 (tm-30) REVERT: E 76 ILE cc_start: 0.9057 (pt) cc_final: 0.8787 (mm) REVERT: F 215 PHE cc_start: 0.7895 (t80) cc_final: 0.7413 (t80) REVERT: F 252 TYR cc_start: 0.7235 (m-10) cc_final: 0.6717 (m-10) REVERT: F 318 LEU cc_start: 0.7705 (OUTLIER) cc_final: 0.7389 (tt) REVERT: G 69 LYS cc_start: 0.8832 (tmtt) cc_final: 0.8321 (tptm) REVERT: H 77 GLN cc_start: 0.7951 (pp30) cc_final: 0.7706 (pp30) REVERT: I 17 ASP cc_start: 0.8572 (m-30) cc_final: 0.7723 (m-30) REVERT: I 58 ARG cc_start: 0.8020 (ttt180) cc_final: 0.7793 (tpp80) REVERT: J 17 ASP cc_start: 0.8641 (m-30) cc_final: 0.8161 (m-30) REVERT: J 34 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8700 (mm) REVERT: J 37 LYS cc_start: 0.8614 (mmmt) cc_final: 0.8412 (mmmm) REVERT: J 54 TYR cc_start: 0.8627 (t80) cc_final: 0.8215 (t80) REVERT: J 57 TYR cc_start: 0.8252 (t80) cc_final: 0.7820 (t80) REVERT: J 59 ASN cc_start: 0.8759 (m110) cc_final: 0.8355 (m110) REVERT: J 66 LYS cc_start: 0.8660 (tptm) cc_final: 0.7390 (tppt) REVERT: J 69 LYS cc_start: 0.8873 (tptp) cc_final: 0.8614 (tptp) REVERT: J 70 ASP cc_start: 0.7926 (m-30) cc_final: 0.7220 (m-30) REVERT: J 77 GLN cc_start: 0.8444 (pp30) cc_final: 0.8109 (tm-30) REVERT: K 57 TYR cc_start: 0.8872 (t80) cc_final: 0.8534 (t80) REVERT: K 79 PHE cc_start: 0.8087 (m-10) cc_final: 0.7817 (m-80) REVERT: L 17 ASP cc_start: 0.8562 (m-30) cc_final: 0.8242 (m-30) REVERT: L 25 THR cc_start: 0.9092 (OUTLIER) cc_final: 0.8688 (p) REVERT: L 29 GLU cc_start: 0.8543 (OUTLIER) cc_final: 0.8265 (pp20) REVERT: L 34 LEU cc_start: 0.9436 (tp) cc_final: 0.9206 (tt) REVERT: L 77 GLN cc_start: 0.8999 (tt0) cc_final: 0.8450 (tm-30) REVERT: M 10 ASP cc_start: 0.8138 (t0) cc_final: 0.7868 (t0) REVERT: M 21 ASP cc_start: 0.7562 (OUTLIER) cc_final: 0.6967 (p0) REVERT: M 51 LEU cc_start: 0.8928 (tt) cc_final: 0.8625 (tt) REVERT: M 66 LYS cc_start: 0.8778 (tppp) cc_final: 0.8482 (tppp) REVERT: M 76 ILE cc_start: 0.7064 (tt) cc_final: 0.6766 (tt) REVERT: M 77 GLN cc_start: 0.9039 (tm-30) cc_final: 0.8679 (tm-30) REVERT: N 17 ASP cc_start: 0.8441 (m-30) cc_final: 0.8134 (m-30) REVERT: N 24 GLN cc_start: 0.8017 (pm20) cc_final: 0.7472 (tp40) REVERT: N 47 TYR cc_start: 0.8799 (t80) cc_final: 0.8437 (t80) REVERT: N 48 GLN cc_start: 0.8775 (tt0) cc_final: 0.8055 (tm-30) REVERT: N 59 ASN cc_start: 0.8305 (t0) cc_final: 0.7789 (t0) REVERT: O 169 ASP cc_start: 0.8113 (t0) cc_final: 0.7872 (t70) REVERT: O 316 ASN cc_start: 0.8402 (m-40) cc_final: 0.8074 (m-40) REVERT: P 16 PHE cc_start: 0.9022 (OUTLIER) cc_final: 0.8516 (t80) REVERT: P 29 GLU cc_start: 0.7653 (mp0) cc_final: 0.7317 (mp0) REVERT: P 54 TYR cc_start: 0.8705 (t80) cc_final: 0.8369 (t80) REVERT: P 70 ASP cc_start: 0.7711 (m-30) cc_final: 0.7404 (m-30) REVERT: Q 47 TYR cc_start: 0.8488 (t80) cc_final: 0.8251 (t80) REVERT: R 205 TYR cc_start: 0.7185 (m-80) cc_final: 0.6910 (m-10) REVERT: R 252 TYR cc_start: 0.7426 (m-10) cc_final: 0.7103 (m-10) REVERT: S 16 PHE cc_start: 0.6104 (OUTLIER) cc_final: 0.5830 (m-80) REVERT: S 53 GLU cc_start: 0.8345 (mm-30) cc_final: 0.8092 (tp30) REVERT: S 62 SER cc_start: 0.8583 (t) cc_final: 0.8355 (t) REVERT: S 68 PHE cc_start: 0.8563 (m-80) cc_final: 0.8307 (m-10) REVERT: S 79 PHE cc_start: 0.2702 (OUTLIER) cc_final: 0.2014 (t80) REVERT: T 11 ASP cc_start: 0.7902 (m-30) cc_final: 0.7634 (m-30) REVERT: T 31 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8348 (tt) REVERT: U 15 LYS cc_start: 0.8125 (tptp) cc_final: 0.7486 (tmtt) REVERT: U 16 PHE cc_start: 0.8807 (OUTLIER) cc_final: 0.7943 (t80) REVERT: U 47 TYR cc_start: 0.8304 (t80) cc_final: 0.7994 (t80) REVERT: V 150 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8110 (mp) REVERT: V 314 ASN cc_start: 0.7924 (m-40) cc_final: 0.6980 (t0) REVERT: V 340 PHE cc_start: 0.7618 (m-10) cc_final: 0.7232 (m-80) REVERT: W 28 THR cc_start: 0.7432 (m) cc_final: 0.7057 (t) REVERT: W 50 LYS cc_start: 0.8658 (mtpt) cc_final: 0.8324 (mtmt) REVERT: X 161 THR cc_start: 0.8490 (m) cc_final: 0.8175 (p) REVERT: X 261 LEU cc_start: 0.8691 (tt) cc_final: 0.8430 (tt) REVERT: X 282 MET cc_start: 0.7502 (tmm) cc_final: 0.7255 (tmm) REVERT: X 334 LEU cc_start: 0.8815 (tt) cc_final: 0.8556 (tt) outliers start: 109 outliers final: 66 residues processed: 600 average time/residue: 0.1255 time to fit residues: 120.2820 Evaluate side-chains 558 residues out of total 2167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 478 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain B residue 16 PHE Chi-restraints excluded: chain B residue 47 TYR Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 79 PHE Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain E residue 11 ASP Chi-restraints excluded: chain E residue 16 PHE Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 178 LEU Chi-restraints excluded: chain F residue 225 VAL Chi-restraints excluded: chain F residue 240 LEU Chi-restraints excluded: chain F residue 259 THR Chi-restraints excluded: chain F residue 282 MET Chi-restraints excluded: chain F residue 301 MET Chi-restraints excluded: chain F residue 318 LEU Chi-restraints excluded: chain F residue 323 VAL Chi-restraints excluded: chain F residue 326 LEU Chi-restraints excluded: chain G residue 52 SER Chi-restraints excluded: chain H residue 18 THR Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 71 ILE Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain I residue 51 LEU Chi-restraints excluded: chain I residue 53 GLU Chi-restraints excluded: chain I residue 79 PHE Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain K residue 9 LEU Chi-restraints excluded: chain K residue 25 THR Chi-restraints excluded: chain K residue 34 LEU Chi-restraints excluded: chain K residue 75 ILE Chi-restraints excluded: chain L residue 8 TYR Chi-restraints excluded: chain L residue 25 THR Chi-restraints excluded: chain L residue 29 GLU Chi-restraints excluded: chain L residue 57 TYR Chi-restraints excluded: chain M residue 21 ASP Chi-restraints excluded: chain M residue 44 LEU Chi-restraints excluded: chain N residue 16 PHE Chi-restraints excluded: chain O residue 136 ASP Chi-restraints excluded: chain O residue 157 VAL Chi-restraints excluded: chain O residue 258 LEU Chi-restraints excluded: chain O residue 306 GLN Chi-restraints excluded: chain O residue 323 VAL Chi-restraints excluded: chain P residue 13 SER Chi-restraints excluded: chain P residue 16 PHE Chi-restraints excluded: chain P residue 34 LEU Chi-restraints excluded: chain Q residue 61 GLN Chi-restraints excluded: chain Q residue 62 SER Chi-restraints excluded: chain Q residue 65 VAL Chi-restraints excluded: chain R residue 155 ASN Chi-restraints excluded: chain R residue 221 SER Chi-restraints excluded: chain R residue 256 VAL Chi-restraints excluded: chain R residue 261 LEU Chi-restraints excluded: chain R residue 294 PHE Chi-restraints excluded: chain S residue 16 PHE Chi-restraints excluded: chain S residue 57 TYR Chi-restraints excluded: chain S residue 79 PHE Chi-restraints excluded: chain T residue 31 LEU Chi-restraints excluded: chain T residue 75 ILE Chi-restraints excluded: chain U residue 16 PHE Chi-restraints excluded: chain U residue 32 ASP Chi-restraints excluded: chain U residue 57 TYR Chi-restraints excluded: chain U residue 79 PHE Chi-restraints excluded: chain U residue 80 ARG Chi-restraints excluded: chain V residue 143 SER Chi-restraints excluded: chain V residue 150 LEU Chi-restraints excluded: chain V residue 157 VAL Chi-restraints excluded: chain V residue 237 GLU Chi-restraints excluded: chain V residue 264 MET Chi-restraints excluded: chain V residue 265 VAL Chi-restraints excluded: chain V residue 291 GLN Chi-restraints excluded: chain X residue 137 MET Chi-restraints excluded: chain X residue 157 VAL Chi-restraints excluded: chain X residue 268 ILE Chi-restraints excluded: chain X residue 295 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 30 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 228 optimal weight: 8.9990 chunk 176 optimal weight: 4.9990 chunk 180 optimal weight: 5.9990 chunk 19 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 89 optimal weight: 4.9990 chunk 222 optimal weight: 4.9990 chunk 109 optimal weight: 0.8980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 24 GLN E 48 GLN E 59 ASN ** H 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 59 ASN J 24 GLN ** J 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 59 ASN ** O 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 288 GLN ** P 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 48 GLN ** R 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.082521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.071625 restraints weight = 64446.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.073568 restraints weight = 33973.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.074872 restraints weight = 20865.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.075746 restraints weight = 14349.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.076333 restraints weight = 10874.596| |-----------------------------------------------------------------------------| r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.8519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 20052 Z= 0.182 Angle : 0.670 9.364 27243 Z= 0.350 Chirality : 0.043 0.363 3119 Planarity : 0.004 0.052 3524 Dihedral : 4.497 34.262 2693 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 4.78 % Allowed : 25.87 % Favored : 69.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.17), residues: 2487 helix: 1.53 (0.12), residues: 1916 sheet: -1.69 (0.78), residues: 50 loop : -1.56 (0.26), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 58 TYR 0.031 0.002 TYR N 47 PHE 0.017 0.002 PHE X 215 TRP 0.036 0.002 TRP X 177 Details of bonding type rmsd covalent geometry : bond 0.00414 (20052) covalent geometry : angle 0.67046 (27243) hydrogen bonds : bond 0.04121 ( 1524) hydrogen bonds : angle 4.03608 ( 4512) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 597 residues out of total 2167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 494 time to evaluate : 0.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 TYR cc_start: 0.9152 (OUTLIER) cc_final: 0.8914 (t80) REVERT: A 55 ASN cc_start: 0.9011 (t0) cc_final: 0.8754 (t0) REVERT: A 66 LYS cc_start: 0.8989 (tptp) cc_final: 0.8650 (tptp) REVERT: A 72 ASP cc_start: 0.8819 (OUTLIER) cc_final: 0.8572 (t0) REVERT: B 16 PHE cc_start: 0.8230 (OUTLIER) cc_final: 0.7725 (m-80) REVERT: B 29 GLU cc_start: 0.8111 (mm-30) cc_final: 0.7837 (mm-30) REVERT: B 32 ASP cc_start: 0.8137 (m-30) cc_final: 0.7828 (p0) REVERT: B 63 ASN cc_start: 0.8920 (m-40) cc_final: 0.8632 (m-40) REVERT: C 10 ASP cc_start: 0.8409 (t0) cc_final: 0.8121 (t0) REVERT: C 47 TYR cc_start: 0.8517 (t80) cc_final: 0.8212 (t80) REVERT: C 53 GLU cc_start: 0.8653 (tt0) cc_final: 0.8044 (mt-10) REVERT: C 57 TYR cc_start: 0.9052 (OUTLIER) cc_final: 0.8762 (t80) REVERT: C 66 LYS cc_start: 0.8828 (tptp) cc_final: 0.7900 (tppt) REVERT: C 70 ASP cc_start: 0.8156 (m-30) cc_final: 0.7605 (m-30) REVERT: D 62 SER cc_start: 0.9518 (m) cc_final: 0.8928 (p) REVERT: D 69 LYS cc_start: 0.9036 (tptt) cc_final: 0.8510 (tppp) REVERT: D 75 ILE cc_start: 0.9101 (mm) cc_final: 0.8880 (tp) REVERT: D 76 ILE cc_start: 0.9551 (mm) cc_final: 0.9031 (tt) REVERT: E 26 GLN cc_start: 0.8784 (mt0) cc_final: 0.8261 (mt0) REVERT: E 53 GLU cc_start: 0.8565 (tm-30) cc_final: 0.7998 (tm-30) REVERT: E 76 ILE cc_start: 0.9017 (pt) cc_final: 0.8751 (mm) REVERT: E 79 PHE cc_start: 0.8081 (OUTLIER) cc_final: 0.6668 (t80) REVERT: F 215 PHE cc_start: 0.8153 (t80) cc_final: 0.7749 (t80) REVERT: F 252 TYR cc_start: 0.7047 (m-10) cc_final: 0.6454 (m-10) REVERT: F 318 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.8031 (tt) REVERT: F 327 SER cc_start: 0.8153 (OUTLIER) cc_final: 0.7702 (t) REVERT: G 69 LYS cc_start: 0.8940 (tmtt) cc_final: 0.8431 (tptm) REVERT: H 21 ASP cc_start: 0.7271 (m-30) cc_final: 0.6938 (m-30) REVERT: I 17 ASP cc_start: 0.8567 (m-30) cc_final: 0.7780 (m-30) REVERT: J 34 LEU cc_start: 0.9132 (OUTLIER) cc_final: 0.8707 (mm) REVERT: J 57 TYR cc_start: 0.8413 (t80) cc_final: 0.8185 (t80) REVERT: J 59 ASN cc_start: 0.8870 (m110) cc_final: 0.8428 (m110) REVERT: J 69 LYS cc_start: 0.9023 (tptp) cc_final: 0.8805 (tptp) REVERT: J 77 GLN cc_start: 0.8510 (pp30) cc_final: 0.8218 (tm-30) REVERT: K 79 PHE cc_start: 0.8333 (m-10) cc_final: 0.7810 (m-80) REVERT: L 17 ASP cc_start: 0.8750 (m-30) cc_final: 0.8431 (m-30) REVERT: L 25 THR cc_start: 0.9195 (OUTLIER) cc_final: 0.8752 (p) REVERT: L 29 GLU cc_start: 0.8468 (OUTLIER) cc_final: 0.8254 (pp20) REVERT: L 77 GLN cc_start: 0.8787 (tt0) cc_final: 0.8430 (tm-30) REVERT: M 10 ASP cc_start: 0.8487 (t0) cc_final: 0.8142 (t0) REVERT: M 21 ASP cc_start: 0.7683 (OUTLIER) cc_final: 0.7092 (p0) REVERT: M 51 LEU cc_start: 0.8818 (tt) cc_final: 0.8557 (tt) REVERT: M 76 ILE cc_start: 0.7110 (tt) cc_final: 0.6812 (tt) REVERT: M 77 GLN cc_start: 0.9163 (tm-30) cc_final: 0.8754 (tm-30) REVERT: N 17 ASP cc_start: 0.8414 (m-30) cc_final: 0.8068 (m-30) REVERT: N 24 GLN cc_start: 0.7867 (pm20) cc_final: 0.7068 (tp40) REVERT: N 48 GLN cc_start: 0.8856 (tt0) cc_final: 0.8160 (tm-30) REVERT: N 59 ASN cc_start: 0.8356 (t0) cc_final: 0.7573 (t0) REVERT: O 294 PHE cc_start: 0.7780 (OUTLIER) cc_final: 0.7066 (t80) REVERT: O 314 ASN cc_start: 0.8627 (m110) cc_final: 0.8408 (m110) REVERT: O 316 ASN cc_start: 0.8429 (m-40) cc_final: 0.8227 (m-40) REVERT: O 340 PHE cc_start: 0.7119 (m-80) cc_final: 0.6903 (m-80) REVERT: P 16 PHE cc_start: 0.9101 (OUTLIER) cc_final: 0.8563 (t80) REVERT: P 21 ASP cc_start: 0.8843 (OUTLIER) cc_final: 0.8313 (p0) REVERT: P 29 GLU cc_start: 0.7515 (mp0) cc_final: 0.6934 (mp0) REVERT: P 54 TYR cc_start: 0.8831 (t80) cc_final: 0.8524 (t80) REVERT: P 70 ASP cc_start: 0.7989 (m-30) cc_final: 0.7644 (m-30) REVERT: P 77 GLN cc_start: 0.8442 (mm-40) cc_final: 0.8053 (mp10) REVERT: Q 47 TYR cc_start: 0.8519 (t80) cc_final: 0.8175 (t80) REVERT: R 160 TYR cc_start: 0.5779 (t80) cc_final: 0.5450 (t80) REVERT: R 174 MET cc_start: 0.7351 (tpp) cc_final: 0.6449 (ttt) REVERT: R 205 TYR cc_start: 0.7251 (m-80) cc_final: 0.6928 (m-80) REVERT: R 248 TYR cc_start: 0.7078 (t80) cc_final: 0.6875 (t80) REVERT: S 54 TYR cc_start: 0.9106 (t80) cc_final: 0.8787 (t80) REVERT: S 79 PHE cc_start: 0.2330 (OUTLIER) cc_final: 0.1804 (t80) REVERT: T 11 ASP cc_start: 0.8035 (m-30) cc_final: 0.7737 (m-30) REVERT: T 31 LEU cc_start: 0.8739 (tp) cc_final: 0.8508 (tt) REVERT: U 47 TYR cc_start: 0.8189 (t80) cc_final: 0.7839 (t80) REVERT: V 150 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8105 (mp) REVERT: V 314 ASN cc_start: 0.8010 (m-40) cc_final: 0.6817 (t0) REVERT: V 340 PHE cc_start: 0.7608 (m-10) cc_final: 0.7242 (m-80) REVERT: W 50 LYS cc_start: 0.8618 (mtpt) cc_final: 0.8237 (mtmt) REVERT: X 150 LEU cc_start: 0.8350 (OUTLIER) cc_final: 0.7835 (mp) REVERT: X 161 THR cc_start: 0.8522 (m) cc_final: 0.8251 (p) REVERT: X 252 TYR cc_start: 0.6727 (m-80) cc_final: 0.6445 (m-10) REVERT: X 264 MET cc_start: 0.8331 (tpp) cc_final: 0.7944 (tpp) outliers start: 103 outliers final: 61 residues processed: 561 average time/residue: 0.1211 time to fit residues: 110.0472 Evaluate side-chains 527 residues out of total 2167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 449 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 47 TYR Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain B residue 16 PHE Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain C residue 5 TRP Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 57 TYR Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 79 PHE Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 79 PHE Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 225 VAL Chi-restraints excluded: chain F residue 240 LEU Chi-restraints excluded: chain F residue 259 THR Chi-restraints excluded: chain F residue 301 MET Chi-restraints excluded: chain F residue 318 LEU Chi-restraints excluded: chain F residue 323 VAL Chi-restraints excluded: chain F residue 326 LEU Chi-restraints excluded: chain F residue 327 SER Chi-restraints excluded: chain H residue 18 THR Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 71 ILE Chi-restraints excluded: chain I residue 43 LEU Chi-restraints excluded: chain I residue 51 LEU Chi-restraints excluded: chain I residue 53 GLU Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain K residue 9 LEU Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 34 LEU Chi-restraints excluded: chain K residue 47 TYR Chi-restraints excluded: chain L residue 8 TYR Chi-restraints excluded: chain L residue 25 THR Chi-restraints excluded: chain L residue 27 VAL Chi-restraints excluded: chain L residue 29 GLU Chi-restraints excluded: chain L residue 57 TYR Chi-restraints excluded: chain M residue 21 ASP Chi-restraints excluded: chain M residue 44 LEU Chi-restraints excluded: chain M residue 79 PHE Chi-restraints excluded: chain O residue 136 ASP Chi-restraints excluded: chain O residue 138 VAL Chi-restraints excluded: chain O residue 155 ASN Chi-restraints excluded: chain O residue 157 VAL Chi-restraints excluded: chain O residue 258 LEU Chi-restraints excluded: chain O residue 294 PHE Chi-restraints excluded: chain O residue 306 GLN Chi-restraints excluded: chain O residue 323 VAL Chi-restraints excluded: chain P residue 16 PHE Chi-restraints excluded: chain P residue 21 ASP Chi-restraints excluded: chain Q residue 61 GLN Chi-restraints excluded: chain Q residue 62 SER Chi-restraints excluded: chain Q residue 65 VAL Chi-restraints excluded: chain R residue 227 THR Chi-restraints excluded: chain R residue 294 PHE Chi-restraints excluded: chain R residue 323 VAL Chi-restraints excluded: chain S residue 57 TYR Chi-restraints excluded: chain S residue 79 PHE Chi-restraints excluded: chain T residue 75 ILE Chi-restraints excluded: chain U residue 16 PHE Chi-restraints excluded: chain U residue 57 TYR Chi-restraints excluded: chain U residue 79 PHE Chi-restraints excluded: chain U residue 80 ARG Chi-restraints excluded: chain V residue 143 SER Chi-restraints excluded: chain V residue 150 LEU Chi-restraints excluded: chain V residue 157 VAL Chi-restraints excluded: chain V residue 237 GLU Chi-restraints excluded: chain V residue 264 MET Chi-restraints excluded: chain W residue 79 PHE Chi-restraints excluded: chain X residue 137 MET Chi-restraints excluded: chain X residue 150 LEU Chi-restraints excluded: chain X residue 157 VAL Chi-restraints excluded: chain X residue 268 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 68 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 183 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 123 optimal weight: 0.0670 chunk 30 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 231 optimal weight: 0.1980 chunk 228 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 chunk 232 optimal weight: 6.9990 overall best weight: 0.8322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 ASN B 77 GLN C 78 ASN D 61 GLN E 48 GLN ** H 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 59 ASN ** J 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 48 GLN ** P 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 155 ASN U 22 ASN U 26 GLN ** X 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.084934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.073959 restraints weight = 63898.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.075904 restraints weight = 34491.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.077225 restraints weight = 21518.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.078088 restraints weight = 14936.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.078730 restraints weight = 11388.583| |-----------------------------------------------------------------------------| r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.8678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20052 Z= 0.138 Angle : 0.645 10.196 27243 Z= 0.334 Chirality : 0.041 0.227 3119 Planarity : 0.004 0.057 3524 Dihedral : 4.474 57.805 2693 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 4.22 % Allowed : 27.40 % Favored : 68.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.32 (0.17), residues: 2487 helix: 1.58 (0.12), residues: 1926 sheet: -1.65 (0.79), residues: 50 loop : -1.57 (0.27), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG K 80 TYR 0.037 0.002 TYR N 47 PHE 0.016 0.001 PHE O 167 TRP 0.038 0.002 TRP F 234 Details of bonding type rmsd covalent geometry : bond 0.00307 (20052) covalent geometry : angle 0.64515 (27243) hydrogen bonds : bond 0.03857 ( 1524) hydrogen bonds : angle 3.95419 ( 4512) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 595 residues out of total 2167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 504 time to evaluate : 0.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 TYR cc_start: 0.9153 (OUTLIER) cc_final: 0.8916 (t80) REVERT: A 66 LYS cc_start: 0.9005 (tptp) cc_final: 0.8646 (tptp) REVERT: A 72 ASP cc_start: 0.8672 (OUTLIER) cc_final: 0.8361 (t0) REVERT: B 16 PHE cc_start: 0.8076 (OUTLIER) cc_final: 0.7502 (m-80) REVERT: B 63 ASN cc_start: 0.8796 (m-40) cc_final: 0.8304 (m-40) REVERT: C 10 ASP cc_start: 0.8313 (t0) cc_final: 0.7864 (t0) REVERT: C 16 PHE cc_start: 0.8467 (t80) cc_final: 0.8266 (t80) REVERT: C 33 LYS cc_start: 0.9150 (mmtm) cc_final: 0.8853 (mmtm) REVERT: C 57 TYR cc_start: 0.9096 (OUTLIER) cc_final: 0.8721 (t80) REVERT: C 66 LYS cc_start: 0.8832 (tptp) cc_final: 0.7896 (tppt) REVERT: C 70 ASP cc_start: 0.7983 (m-30) cc_final: 0.7494 (m-30) REVERT: D 61 GLN cc_start: 0.8964 (OUTLIER) cc_final: 0.8296 (pp30) REVERT: D 69 LYS cc_start: 0.9032 (tptt) cc_final: 0.8528 (tppp) REVERT: D 75 ILE cc_start: 0.8960 (mm) cc_final: 0.8741 (tp) REVERT: D 77 GLN cc_start: 0.8333 (pp30) cc_final: 0.7670 (pp30) REVERT: E 11 ASP cc_start: 0.8672 (OUTLIER) cc_final: 0.7722 (m-30) REVERT: E 26 GLN cc_start: 0.8719 (mt0) cc_final: 0.8188 (mt0) REVERT: E 53 GLU cc_start: 0.8460 (tm-30) cc_final: 0.7907 (tm-30) REVERT: E 76 ILE cc_start: 0.8897 (pt) cc_final: 0.8692 (mm) REVERT: F 318 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.8034 (tt) REVERT: F 327 SER cc_start: 0.8500 (OUTLIER) cc_final: 0.8001 (t) REVERT: G 69 LYS cc_start: 0.9026 (tmtt) cc_final: 0.8611 (tptm) REVERT: G 70 ASP cc_start: 0.8444 (m-30) cc_final: 0.7846 (m-30) REVERT: H 21 ASP cc_start: 0.7339 (m-30) cc_final: 0.7041 (m-30) REVERT: H 77 GLN cc_start: 0.8065 (tm-30) cc_final: 0.7862 (tm-30) REVERT: I 17 ASP cc_start: 0.8296 (m-30) cc_final: 0.7662 (m-30) REVERT: J 17 ASP cc_start: 0.8565 (m-30) cc_final: 0.8201 (m-30) REVERT: J 34 LEU cc_start: 0.9196 (OUTLIER) cc_final: 0.8751 (mm) REVERT: J 59 ASN cc_start: 0.8815 (m110) cc_final: 0.8311 (m110) REVERT: J 77 GLN cc_start: 0.8410 (pp30) cc_final: 0.8133 (tm-30) REVERT: K 10 ASP cc_start: 0.8302 (m-30) cc_final: 0.7266 (t0) REVERT: K 79 PHE cc_start: 0.8368 (m-10) cc_final: 0.7854 (m-80) REVERT: L 17 ASP cc_start: 0.8637 (m-30) cc_final: 0.8329 (m-30) REVERT: L 24 GLN cc_start: 0.9214 (tp40) cc_final: 0.8834 (tp40) REVERT: L 25 THR cc_start: 0.9173 (m) cc_final: 0.8727 (p) REVERT: L 29 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.8126 (pp20) REVERT: L 34 LEU cc_start: 0.9482 (tp) cc_final: 0.9195 (tt) REVERT: L 77 GLN cc_start: 0.8787 (tt0) cc_final: 0.8409 (tm-30) REVERT: M 21 ASP cc_start: 0.7755 (OUTLIER) cc_final: 0.7197 (p0) REVERT: M 51 LEU cc_start: 0.8815 (tt) cc_final: 0.8565 (tt) REVERT: M 66 LYS cc_start: 0.8698 (tppp) cc_final: 0.8464 (tppt) REVERT: M 76 ILE cc_start: 0.7109 (tt) cc_final: 0.6805 (tt) REVERT: M 77 GLN cc_start: 0.9133 (tm-30) cc_final: 0.8745 (tm-30) REVERT: N 17 ASP cc_start: 0.8401 (m-30) cc_final: 0.8050 (m-30) REVERT: N 24 GLN cc_start: 0.7926 (pm20) cc_final: 0.7286 (tp40) REVERT: N 59 ASN cc_start: 0.8332 (t0) cc_final: 0.7808 (t0) REVERT: O 252 TYR cc_start: 0.5622 (m-10) cc_final: 0.5181 (m-10) REVERT: O 294 PHE cc_start: 0.7728 (OUTLIER) cc_final: 0.6923 (t80) REVERT: O 314 ASN cc_start: 0.8600 (m110) cc_final: 0.8352 (m110) REVERT: O 340 PHE cc_start: 0.6868 (m-80) cc_final: 0.6610 (m-80) REVERT: P 16 PHE cc_start: 0.8941 (OUTLIER) cc_final: 0.8546 (t80) REVERT: P 21 ASP cc_start: 0.8669 (OUTLIER) cc_final: 0.8173 (p0) REVERT: P 29 GLU cc_start: 0.7468 (mp0) cc_final: 0.7236 (mp0) REVERT: P 70 ASP cc_start: 0.7749 (m-30) cc_final: 0.7525 (m-30) REVERT: P 77 GLN cc_start: 0.8515 (mm-40) cc_final: 0.8167 (mp10) REVERT: R 160 TYR cc_start: 0.5482 (t80) cc_final: 0.5151 (t80) REVERT: R 174 MET cc_start: 0.7401 (tpp) cc_final: 0.6526 (ttt) REVERT: S 54 TYR cc_start: 0.9096 (t80) cc_final: 0.8748 (t80) REVERT: S 79 PHE cc_start: 0.2664 (OUTLIER) cc_final: 0.2057 (t80) REVERT: T 11 ASP cc_start: 0.7969 (m-30) cc_final: 0.7746 (m-30) REVERT: T 31 LEU cc_start: 0.8766 (tp) cc_final: 0.8483 (tt) REVERT: U 47 TYR cc_start: 0.8151 (t80) cc_final: 0.7861 (t80) REVERT: V 150 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8059 (mp) REVERT: V 314 ASN cc_start: 0.7836 (m-40) cc_final: 0.7322 (t0) REVERT: V 340 PHE cc_start: 0.7029 (m-10) cc_final: 0.6664 (m-80) REVERT: W 50 LYS cc_start: 0.8634 (mtpt) cc_final: 0.8264 (mtmt) REVERT: X 161 THR cc_start: 0.8445 (m) cc_final: 0.8173 (p) REVERT: X 298 GLU cc_start: 0.7998 (tm-30) cc_final: 0.7755 (tp30) outliers start: 91 outliers final: 56 residues processed: 557 average time/residue: 0.1189 time to fit residues: 107.9648 Evaluate side-chains 536 residues out of total 2167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 464 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 TYR Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain B residue 16 PHE Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 47 TYR Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain C residue 5 TRP Chi-restraints excluded: chain C residue 57 TYR Chi-restraints excluded: chain C residue 79 PHE Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 57 TYR Chi-restraints excluded: chain D residue 61 GLN Chi-restraints excluded: chain E residue 11 ASP Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 225 VAL Chi-restraints excluded: chain F residue 259 THR Chi-restraints excluded: chain F residue 318 LEU Chi-restraints excluded: chain F residue 323 VAL Chi-restraints excluded: chain F residue 326 LEU Chi-restraints excluded: chain F residue 327 SER Chi-restraints excluded: chain H residue 18 THR Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 71 ILE Chi-restraints excluded: chain I residue 51 LEU Chi-restraints excluded: chain I residue 53 GLU Chi-restraints excluded: chain I residue 79 PHE Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain J residue 75 ILE Chi-restraints excluded: chain K residue 13 SER Chi-restraints excluded: chain K residue 25 THR Chi-restraints excluded: chain K residue 34 LEU Chi-restraints excluded: chain K residue 47 TYR Chi-restraints excluded: chain L residue 8 TYR Chi-restraints excluded: chain L residue 29 GLU Chi-restraints excluded: chain L residue 57 TYR Chi-restraints excluded: chain M residue 21 ASP Chi-restraints excluded: chain M residue 44 LEU Chi-restraints excluded: chain M residue 57 TYR Chi-restraints excluded: chain N residue 16 PHE Chi-restraints excluded: chain O residue 136 ASP Chi-restraints excluded: chain O residue 157 VAL Chi-restraints excluded: chain O residue 258 LEU Chi-restraints excluded: chain O residue 294 PHE Chi-restraints excluded: chain O residue 306 GLN Chi-restraints excluded: chain O residue 312 TYR Chi-restraints excluded: chain O residue 323 VAL Chi-restraints excluded: chain P residue 16 PHE Chi-restraints excluded: chain P residue 21 ASP Chi-restraints excluded: chain P residue 48 GLN Chi-restraints excluded: chain P residue 51 LEU Chi-restraints excluded: chain Q residue 62 SER Chi-restraints excluded: chain R residue 155 ASN Chi-restraints excluded: chain R residue 227 THR Chi-restraints excluded: chain R residue 323 VAL Chi-restraints excluded: chain S residue 57 TYR Chi-restraints excluded: chain S residue 79 PHE Chi-restraints excluded: chain T residue 75 ILE Chi-restraints excluded: chain U residue 16 PHE Chi-restraints excluded: chain U residue 57 TYR Chi-restraints excluded: chain U residue 79 PHE Chi-restraints excluded: chain U residue 80 ARG Chi-restraints excluded: chain V residue 143 SER Chi-restraints excluded: chain V residue 150 LEU Chi-restraints excluded: chain V residue 157 VAL Chi-restraints excluded: chain V residue 237 GLU Chi-restraints excluded: chain V residue 264 MET Chi-restraints excluded: chain W residue 71 ILE Chi-restraints excluded: chain W residue 79 PHE Chi-restraints excluded: chain X residue 157 VAL Chi-restraints excluded: chain X residue 268 ILE Chi-restraints excluded: chain X residue 295 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 120 optimal weight: 0.7980 chunk 71 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 129 optimal weight: 0.9990 chunk 40 optimal weight: 6.9990 chunk 181 optimal weight: 0.9990 chunk 151 optimal weight: 2.9990 chunk 66 optimal weight: 0.0670 chunk 108 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 191 optimal weight: 0.9990 overall best weight: 0.7522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 ASN B 61 GLN D 61 GLN E 48 GLN G 77 GLN ** H 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 59 ASN ** J 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 48 GLN Q 61 GLN R 155 ASN U 26 GLN W 24 GLN ** X 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.085079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.074077 restraints weight = 65589.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.076005 restraints weight = 35732.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.077300 restraints weight = 22438.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.078205 restraints weight = 15806.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.078769 restraints weight = 12086.831| |-----------------------------------------------------------------------------| r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.8837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20052 Z= 0.137 Angle : 0.658 11.333 27243 Z= 0.339 Chirality : 0.041 0.244 3119 Planarity : 0.004 0.058 3524 Dihedral : 4.438 56.845 2693 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 3.94 % Allowed : 28.14 % Favored : 67.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.17), residues: 2487 helix: 1.57 (0.12), residues: 1926 sheet: -1.61 (0.79), residues: 50 loop : -1.55 (0.27), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 80 TYR 0.020 0.002 TYR H 54 PHE 0.045 0.001 PHE F 215 TRP 0.036 0.001 TRP X 177 Details of bonding type rmsd covalent geometry : bond 0.00307 (20052) covalent geometry : angle 0.65829 (27243) hydrogen bonds : bond 0.03811 ( 1524) hydrogen bonds : angle 3.94640 ( 4512) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 587 residues out of total 2167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 502 time to evaluate : 0.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 TYR cc_start: 0.9153 (OUTLIER) cc_final: 0.8913 (t80) REVERT: A 55 ASN cc_start: 0.8880 (t0) cc_final: 0.8640 (t0) REVERT: A 66 LYS cc_start: 0.8995 (tptp) cc_final: 0.8644 (tptp) REVERT: A 72 ASP cc_start: 0.8570 (OUTLIER) cc_final: 0.8277 (t0) REVERT: B 16 PHE cc_start: 0.7938 (OUTLIER) cc_final: 0.7201 (m-80) REVERT: B 61 GLN cc_start: 0.8951 (OUTLIER) cc_final: 0.8694 (pp30) REVERT: B 63 ASN cc_start: 0.8781 (m-40) cc_final: 0.8290 (m-40) REVERT: C 10 ASP cc_start: 0.8299 (t0) cc_final: 0.7983 (t0) REVERT: C 33 LYS cc_start: 0.9283 (mmtm) cc_final: 0.8977 (mmtm) REVERT: C 52 SER cc_start: 0.9284 (m) cc_final: 0.9003 (p) REVERT: C 57 TYR cc_start: 0.9055 (OUTLIER) cc_final: 0.8607 (t80) REVERT: C 66 LYS cc_start: 0.8847 (tptp) cc_final: 0.7907 (tppt) REVERT: C 70 ASP cc_start: 0.8037 (m-30) cc_final: 0.7594 (m-30) REVERT: D 61 GLN cc_start: 0.8677 (OUTLIER) cc_final: 0.8204 (pp30) REVERT: D 69 LYS cc_start: 0.9027 (tptt) cc_final: 0.8691 (ttmt) REVERT: D 75 ILE cc_start: 0.9009 (mm) cc_final: 0.8797 (tp) REVERT: D 77 GLN cc_start: 0.8351 (pp30) cc_final: 0.7642 (pp30) REVERT: E 11 ASP cc_start: 0.8550 (OUTLIER) cc_final: 0.7679 (m-30) REVERT: E 26 GLN cc_start: 0.8601 (mt0) cc_final: 0.8152 (mt0) REVERT: E 53 GLU cc_start: 0.8408 (tm-30) cc_final: 0.7835 (tm-30) REVERT: E 79 PHE cc_start: 0.8188 (OUTLIER) cc_final: 0.6899 (t80) REVERT: F 215 PHE cc_start: 0.7852 (t80) cc_final: 0.7549 (t80) REVERT: F 318 LEU cc_start: 0.8357 (OUTLIER) cc_final: 0.8067 (tt) REVERT: G 69 LYS cc_start: 0.9017 (tmtt) cc_final: 0.8560 (tptm) REVERT: G 70 ASP cc_start: 0.8528 (m-30) cc_final: 0.8171 (m-30) REVERT: H 21 ASP cc_start: 0.7349 (m-30) cc_final: 0.7009 (m-30) REVERT: I 17 ASP cc_start: 0.8287 (m-30) cc_final: 0.7649 (m-30) REVERT: J 17 ASP cc_start: 0.8571 (m-30) cc_final: 0.8243 (m-30) REVERT: J 34 LEU cc_start: 0.9189 (OUTLIER) cc_final: 0.8776 (mm) REVERT: J 54 TYR cc_start: 0.8705 (t80) cc_final: 0.8262 (t80) REVERT: J 59 ASN cc_start: 0.8838 (m110) cc_final: 0.8300 (m110) REVERT: J 77 GLN cc_start: 0.8434 (pp30) cc_final: 0.8160 (tm-30) REVERT: K 10 ASP cc_start: 0.8344 (m-30) cc_final: 0.7307 (t0) REVERT: K 29 GLU cc_start: 0.7692 (OUTLIER) cc_final: 0.7416 (pp20) REVERT: K 75 ILE cc_start: 0.9294 (mm) cc_final: 0.9014 (tt) REVERT: K 79 PHE cc_start: 0.8045 (m-10) cc_final: 0.7828 (m-80) REVERT: L 17 ASP cc_start: 0.8637 (m-30) cc_final: 0.8310 (m-30) REVERT: L 24 GLN cc_start: 0.9240 (tp40) cc_final: 0.8798 (tp40) REVERT: L 25 THR cc_start: 0.9189 (m) cc_final: 0.8757 (p) REVERT: L 29 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.8110 (pp20) REVERT: L 34 LEU cc_start: 0.9477 (tp) cc_final: 0.9189 (tt) REVERT: L 77 GLN cc_start: 0.8796 (tt0) cc_final: 0.8428 (tm-30) REVERT: M 21 ASP cc_start: 0.7781 (OUTLIER) cc_final: 0.7179 (p0) REVERT: M 76 ILE cc_start: 0.7098 (tt) cc_final: 0.6790 (tt) REVERT: M 77 GLN cc_start: 0.8995 (tm-30) cc_final: 0.8559 (tm-30) REVERT: N 17 ASP cc_start: 0.8416 (m-30) cc_final: 0.8073 (m-30) REVERT: N 24 GLN cc_start: 0.7549 (pm20) cc_final: 0.7233 (tp40) REVERT: N 59 ASN cc_start: 0.8305 (t0) cc_final: 0.7767 (t0) REVERT: O 252 TYR cc_start: 0.5518 (m-10) cc_final: 0.5132 (m-10) REVERT: O 291 GLN cc_start: 0.8911 (OUTLIER) cc_final: 0.8669 (mm110) REVERT: O 294 PHE cc_start: 0.7718 (OUTLIER) cc_final: 0.6927 (t80) REVERT: P 16 PHE cc_start: 0.8813 (OUTLIER) cc_final: 0.8325 (t80) REVERT: P 21 ASP cc_start: 0.8723 (OUTLIER) cc_final: 0.8272 (p0) REVERT: P 70 ASP cc_start: 0.7732 (m-30) cc_final: 0.7514 (m-30) REVERT: Q 53 GLU cc_start: 0.8235 (tt0) cc_final: 0.7987 (tp30) REVERT: Q 57 TYR cc_start: 0.7795 (t80) cc_final: 0.7437 (t80) REVERT: Q 61 GLN cc_start: 0.7961 (OUTLIER) cc_final: 0.7398 (mm-40) REVERT: R 142 ILE cc_start: 0.8845 (tp) cc_final: 0.8611 (tp) REVERT: R 160 TYR cc_start: 0.5456 (t80) cc_final: 0.5194 (t80) REVERT: R 174 MET cc_start: 0.7509 (tpp) cc_final: 0.6264 (ttt) REVERT: R 264 MET cc_start: 0.5654 (tpp) cc_final: 0.5116 (tpp) REVERT: S 32 ASP cc_start: 0.8083 (m-30) cc_final: 0.7873 (m-30) REVERT: S 54 TYR cc_start: 0.9096 (t80) cc_final: 0.8735 (t80) REVERT: S 62 SER cc_start: 0.8736 (t) cc_final: 0.8428 (t) REVERT: S 79 PHE cc_start: 0.2796 (OUTLIER) cc_final: 0.2130 (t80) REVERT: T 11 ASP cc_start: 0.8079 (m-30) cc_final: 0.7796 (m-30) REVERT: T 31 LEU cc_start: 0.8751 (tp) cc_final: 0.8471 (tt) REVERT: U 47 TYR cc_start: 0.8147 (t80) cc_final: 0.7847 (t80) REVERT: V 150 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.8064 (mp) REVERT: V 314 ASN cc_start: 0.7948 (m-40) cc_final: 0.7361 (t0) REVERT: V 340 PHE cc_start: 0.7020 (m-10) cc_final: 0.6659 (m-80) REVERT: W 24 GLN cc_start: 0.8974 (OUTLIER) cc_final: 0.8620 (tt0) REVERT: W 29 GLU cc_start: 0.8653 (tm-30) cc_final: 0.8334 (tp30) REVERT: W 50 LYS cc_start: 0.8619 (mtpt) cc_final: 0.8280 (mtmt) REVERT: X 161 THR cc_start: 0.8461 (m) cc_final: 0.8176 (p) REVERT: X 298 GLU cc_start: 0.8436 (tm-30) cc_final: 0.8027 (tp30) outliers start: 85 outliers final: 55 residues processed: 556 average time/residue: 0.1225 time to fit residues: 110.5875 Evaluate side-chains 548 residues out of total 2167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 472 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 47 TYR Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain B residue 16 PHE Chi-restraints excluded: chain B residue 47 TYR Chi-restraints excluded: chain B residue 61 GLN Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain C residue 5 TRP Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 57 TYR Chi-restraints excluded: chain C residue 79 PHE Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 61 GLN Chi-restraints excluded: chain E residue 11 ASP Chi-restraints excluded: chain E residue 16 PHE Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 79 PHE Chi-restraints excluded: chain F residue 225 VAL Chi-restraints excluded: chain F residue 318 LEU Chi-restraints excluded: chain F residue 326 LEU Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 71 ILE Chi-restraints excluded: chain I residue 51 LEU Chi-restraints excluded: chain I residue 79 PHE Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain J residue 62 SER Chi-restraints excluded: chain K residue 9 LEU Chi-restraints excluded: chain K residue 25 THR Chi-restraints excluded: chain K residue 29 GLU Chi-restraints excluded: chain K residue 34 LEU Chi-restraints excluded: chain K residue 47 TYR Chi-restraints excluded: chain L residue 8 TYR Chi-restraints excluded: chain L residue 29 GLU Chi-restraints excluded: chain L residue 57 TYR Chi-restraints excluded: chain M residue 21 ASP Chi-restraints excluded: chain M residue 44 LEU Chi-restraints excluded: chain M residue 57 TYR Chi-restraints excluded: chain N residue 16 PHE Chi-restraints excluded: chain O residue 136 ASP Chi-restraints excluded: chain O residue 138 VAL Chi-restraints excluded: chain O residue 157 VAL Chi-restraints excluded: chain O residue 258 LEU Chi-restraints excluded: chain O residue 291 GLN Chi-restraints excluded: chain O residue 294 PHE Chi-restraints excluded: chain O residue 306 GLN Chi-restraints excluded: chain O residue 323 VAL Chi-restraints excluded: chain P residue 16 PHE Chi-restraints excluded: chain P residue 21 ASP Chi-restraints excluded: chain P residue 48 GLN Chi-restraints excluded: chain P residue 51 LEU Chi-restraints excluded: chain Q residue 31 LEU Chi-restraints excluded: chain Q residue 61 GLN Chi-restraints excluded: chain Q residue 62 SER Chi-restraints excluded: chain R residue 155 ASN Chi-restraints excluded: chain R residue 227 THR Chi-restraints excluded: chain R residue 323 VAL Chi-restraints excluded: chain S residue 57 TYR Chi-restraints excluded: chain S residue 79 PHE Chi-restraints excluded: chain T residue 75 ILE Chi-restraints excluded: chain U residue 16 PHE Chi-restraints excluded: chain U residue 53 GLU Chi-restraints excluded: chain U residue 57 TYR Chi-restraints excluded: chain U residue 79 PHE Chi-restraints excluded: chain U residue 80 ARG Chi-restraints excluded: chain V residue 143 SER Chi-restraints excluded: chain V residue 150 LEU Chi-restraints excluded: chain V residue 157 VAL Chi-restraints excluded: chain V residue 237 GLU Chi-restraints excluded: chain V residue 264 MET Chi-restraints excluded: chain W residue 24 GLN Chi-restraints excluded: chain W residue 71 ILE Chi-restraints excluded: chain X residue 157 VAL Chi-restraints excluded: chain X residue 177 TRP Chi-restraints excluded: chain X residue 268 ILE Chi-restraints excluded: chain X residue 295 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 231 optimal weight: 6.9990 chunk 229 optimal weight: 10.0000 chunk 45 optimal weight: 0.9990 chunk 107 optimal weight: 0.9990 chunk 196 optimal weight: 4.9990 chunk 153 optimal weight: 4.9990 chunk 85 optimal weight: 7.9990 chunk 119 optimal weight: 4.9990 chunk 188 optimal weight: 0.9980 chunk 18 optimal weight: 3.9990 chunk 154 optimal weight: 0.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 61 GLN D 61 GLN E 48 GLN ** H 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 59 ASN ** J 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 48 GLN ** Q 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 155 ASN ** R 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 22 ASN U 26 GLN W 24 GLN ** X 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.083184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.072466 restraints weight = 66036.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.074394 restraints weight = 35491.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.075702 restraints weight = 21970.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.076533 restraints weight = 15227.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.077200 restraints weight = 11651.327| |-----------------------------------------------------------------------------| r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.9087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 20052 Z= 0.168 Angle : 0.689 14.661 27243 Z= 0.358 Chirality : 0.043 0.257 3119 Planarity : 0.004 0.057 3524 Dihedral : 4.474 57.382 2693 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 4.36 % Allowed : 28.09 % Favored : 67.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.17), residues: 2487 helix: 1.51 (0.12), residues: 1926 sheet: -1.59 (0.79), residues: 50 loop : -1.56 (0.27), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 80 TYR 0.028 0.002 TYR M 47 PHE 0.033 0.002 PHE F 215 TRP 0.035 0.002 TRP X 177 Details of bonding type rmsd covalent geometry : bond 0.00383 (20052) covalent geometry : angle 0.68927 (27243) hydrogen bonds : bond 0.03976 ( 1524) hydrogen bonds : angle 4.02424 ( 4512) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 567 residues out of total 2167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 473 time to evaluate : 0.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 TYR cc_start: 0.9165 (OUTLIER) cc_final: 0.8916 (t80) REVERT: A 66 LYS cc_start: 0.8977 (tptp) cc_final: 0.8647 (tptp) REVERT: A 72 ASP cc_start: 0.8682 (OUTLIER) cc_final: 0.8412 (t0) REVERT: B 16 PHE cc_start: 0.8174 (OUTLIER) cc_final: 0.7611 (m-80) REVERT: B 29 GLU cc_start: 0.8295 (mm-30) cc_final: 0.7443 (mt-10) REVERT: B 32 ASP cc_start: 0.7882 (p0) cc_final: 0.7178 (p0) REVERT: B 61 GLN cc_start: 0.8997 (OUTLIER) cc_final: 0.8739 (pp30) REVERT: B 63 ASN cc_start: 0.8856 (m-40) cc_final: 0.8371 (m-40) REVERT: C 10 ASP cc_start: 0.8370 (t0) cc_final: 0.8072 (t0) REVERT: C 33 LYS cc_start: 0.9142 (mmtm) cc_final: 0.8699 (mmtm) REVERT: C 52 SER cc_start: 0.9250 (m) cc_final: 0.8947 (p) REVERT: C 57 TYR cc_start: 0.9038 (OUTLIER) cc_final: 0.8588 (t80) REVERT: C 66 LYS cc_start: 0.8906 (tptp) cc_final: 0.7864 (tppt) REVERT: C 70 ASP cc_start: 0.8012 (m-30) cc_final: 0.7551 (m-30) REVERT: D 61 GLN cc_start: 0.8966 (OUTLIER) cc_final: 0.7797 (pp30) REVERT: D 69 LYS cc_start: 0.9074 (tptt) cc_final: 0.8775 (ttmt) REVERT: E 11 ASP cc_start: 0.8669 (OUTLIER) cc_final: 0.7743 (m-30) REVERT: E 26 GLN cc_start: 0.8741 (mt0) cc_final: 0.8280 (mt0) REVERT: E 53 GLU cc_start: 0.8486 (tm-30) cc_final: 0.7897 (tm-30) REVERT: E 76 ILE cc_start: 0.8720 (mm) cc_final: 0.8354 (mm) REVERT: E 79 PHE cc_start: 0.8347 (OUTLIER) cc_final: 0.7175 (t80) REVERT: F 318 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.8095 (tt) REVERT: F 327 SER cc_start: 0.7908 (OUTLIER) cc_final: 0.7369 (t) REVERT: G 26 GLN cc_start: 0.8328 (mt0) cc_final: 0.7917 (mt0) REVERT: G 29 GLU cc_start: 0.7434 (pp20) cc_final: 0.7189 (pp20) REVERT: G 69 LYS cc_start: 0.9030 (tmtt) cc_final: 0.8663 (tptm) REVERT: G 70 ASP cc_start: 0.8505 (m-30) cc_final: 0.8162 (m-30) REVERT: H 21 ASP cc_start: 0.7616 (m-30) cc_final: 0.7303 (m-30) REVERT: H 65 VAL cc_start: 0.9253 (m) cc_final: 0.9043 (p) REVERT: I 17 ASP cc_start: 0.8161 (m-30) cc_final: 0.7229 (m-30) REVERT: J 17 ASP cc_start: 0.8689 (m-30) cc_final: 0.8382 (m-30) REVERT: J 34 LEU cc_start: 0.9220 (OUTLIER) cc_final: 0.8804 (mm) REVERT: J 59 ASN cc_start: 0.8909 (m110) cc_final: 0.8425 (m110) REVERT: J 77 GLN cc_start: 0.8478 (pp30) cc_final: 0.8259 (tm-30) REVERT: K 10 ASP cc_start: 0.8449 (m-30) cc_final: 0.7420 (t0) REVERT: K 79 PHE cc_start: 0.8201 (m-10) cc_final: 0.7919 (m-80) REVERT: L 17 ASP cc_start: 0.8665 (m-30) cc_final: 0.8303 (m-30) REVERT: L 25 THR cc_start: 0.9251 (m) cc_final: 0.8813 (p) REVERT: L 29 GLU cc_start: 0.8424 (OUTLIER) cc_final: 0.8192 (pp20) REVERT: L 34 LEU cc_start: 0.9471 (tp) cc_final: 0.9217 (tt) REVERT: L 77 GLN cc_start: 0.8859 (tt0) cc_final: 0.8440 (tm-30) REVERT: M 21 ASP cc_start: 0.7751 (OUTLIER) cc_final: 0.7198 (p0) REVERT: M 76 ILE cc_start: 0.7121 (tt) cc_final: 0.6808 (tt) REVERT: M 77 GLN cc_start: 0.9016 (tm-30) cc_final: 0.8557 (tm-30) REVERT: N 17 ASP cc_start: 0.8474 (m-30) cc_final: 0.8123 (m-30) REVERT: N 24 GLN cc_start: 0.7059 (pm20) cc_final: 0.6747 (tp40) REVERT: O 252 TYR cc_start: 0.5649 (m-10) cc_final: 0.5207 (m-10) REVERT: O 291 GLN cc_start: 0.8956 (OUTLIER) cc_final: 0.8641 (mm110) REVERT: O 294 PHE cc_start: 0.7783 (OUTLIER) cc_final: 0.7006 (t80) REVERT: P 16 PHE cc_start: 0.8936 (OUTLIER) cc_final: 0.8400 (t80) REVERT: P 21 ASP cc_start: 0.8817 (OUTLIER) cc_final: 0.8357 (p0) REVERT: P 54 TYR cc_start: 0.8886 (t80) cc_final: 0.8164 (t80) REVERT: P 57 TYR cc_start: 0.8470 (t80) cc_final: 0.8120 (t80) REVERT: P 70 ASP cc_start: 0.7767 (m-30) cc_final: 0.7552 (m-30) REVERT: R 142 ILE cc_start: 0.8897 (tp) cc_final: 0.8659 (tp) REVERT: R 160 TYR cc_start: 0.5242 (t80) cc_final: 0.4962 (t80) REVERT: R 264 MET cc_start: 0.5737 (tpp) cc_final: 0.5217 (tpp) REVERT: S 32 ASP cc_start: 0.8139 (m-30) cc_final: 0.7904 (m-30) REVERT: S 53 GLU cc_start: 0.8163 (tp30) cc_final: 0.7953 (tp30) REVERT: S 54 TYR cc_start: 0.9125 (t80) cc_final: 0.8775 (t80) REVERT: S 62 SER cc_start: 0.8750 (t) cc_final: 0.8410 (t) REVERT: S 79 PHE cc_start: 0.2542 (OUTLIER) cc_final: 0.1971 (t80) REVERT: T 31 LEU cc_start: 0.8754 (tp) cc_final: 0.8529 (tt) REVERT: V 150 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8088 (mp) REVERT: V 314 ASN cc_start: 0.8235 (m-40) cc_final: 0.7535 (t0) REVERT: V 340 PHE cc_start: 0.7142 (m-10) cc_final: 0.6755 (m-80) REVERT: W 24 GLN cc_start: 0.9038 (OUTLIER) cc_final: 0.8635 (tt0) REVERT: W 29 GLU cc_start: 0.8680 (tm-30) cc_final: 0.8390 (tp30) REVERT: W 79 PHE cc_start: 0.8681 (t80) cc_final: 0.8421 (t80) REVERT: X 161 THR cc_start: 0.8638 (m) cc_final: 0.8314 (p) REVERT: X 298 GLU cc_start: 0.8437 (tm-30) cc_final: 0.8124 (tp30) REVERT: X 314 ASN cc_start: 0.8863 (m-40) cc_final: 0.8473 (m-40) outliers start: 94 outliers final: 61 residues processed: 531 average time/residue: 0.1199 time to fit residues: 103.7215 Evaluate side-chains 534 residues out of total 2167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 453 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 TYR Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain B residue 16 PHE Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 47 TYR Chi-restraints excluded: chain B residue 61 GLN Chi-restraints excluded: chain C residue 5 TRP Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 57 TYR Chi-restraints excluded: chain C residue 79 PHE Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 61 GLN Chi-restraints excluded: chain E residue 11 ASP Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 79 PHE Chi-restraints excluded: chain F residue 225 VAL Chi-restraints excluded: chain F residue 238 LEU Chi-restraints excluded: chain F residue 318 LEU Chi-restraints excluded: chain F residue 323 VAL Chi-restraints excluded: chain F residue 326 LEU Chi-restraints excluded: chain F residue 327 SER Chi-restraints excluded: chain G residue 32 ASP Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 27 VAL Chi-restraints excluded: chain H residue 71 ILE Chi-restraints excluded: chain I residue 43 LEU Chi-restraints excluded: chain I residue 51 LEU Chi-restraints excluded: chain I residue 53 GLU Chi-restraints excluded: chain I residue 79 PHE Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain J residue 62 SER Chi-restraints excluded: chain K residue 9 LEU Chi-restraints excluded: chain K residue 25 THR Chi-restraints excluded: chain K residue 34 LEU Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain K residue 47 TYR Chi-restraints excluded: chain L residue 8 TYR Chi-restraints excluded: chain L residue 29 GLU Chi-restraints excluded: chain L residue 57 TYR Chi-restraints excluded: chain M residue 21 ASP Chi-restraints excluded: chain M residue 44 LEU Chi-restraints excluded: chain N residue 16 PHE Chi-restraints excluded: chain O residue 136 ASP Chi-restraints excluded: chain O residue 138 VAL Chi-restraints excluded: chain O residue 155 ASN Chi-restraints excluded: chain O residue 157 VAL Chi-restraints excluded: chain O residue 258 LEU Chi-restraints excluded: chain O residue 291 GLN Chi-restraints excluded: chain O residue 294 PHE Chi-restraints excluded: chain O residue 306 GLN Chi-restraints excluded: chain O residue 312 TYR Chi-restraints excluded: chain O residue 323 VAL Chi-restraints excluded: chain P residue 16 PHE Chi-restraints excluded: chain P residue 21 ASP Chi-restraints excluded: chain P residue 48 GLN Chi-restraints excluded: chain P residue 51 LEU Chi-restraints excluded: chain Q residue 31 LEU Chi-restraints excluded: chain Q residue 62 SER Chi-restraints excluded: chain R residue 155 ASN Chi-restraints excluded: chain R residue 227 THR Chi-restraints excluded: chain R residue 323 VAL Chi-restraints excluded: chain S residue 79 PHE Chi-restraints excluded: chain T residue 75 ILE Chi-restraints excluded: chain U residue 16 PHE Chi-restraints excluded: chain U residue 53 GLU Chi-restraints excluded: chain U residue 57 TYR Chi-restraints excluded: chain U residue 79 PHE Chi-restraints excluded: chain U residue 80 ARG Chi-restraints excluded: chain V residue 143 SER Chi-restraints excluded: chain V residue 150 LEU Chi-restraints excluded: chain V residue 157 VAL Chi-restraints excluded: chain V residue 237 GLU Chi-restraints excluded: chain V residue 264 MET Chi-restraints excluded: chain W residue 24 GLN Chi-restraints excluded: chain W residue 71 ILE Chi-restraints excluded: chain X residue 157 VAL Chi-restraints excluded: chain X residue 268 ILE Chi-restraints excluded: chain X residue 295 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 61 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 207 optimal weight: 4.9990 chunk 133 optimal weight: 10.0000 chunk 171 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 127 optimal weight: 7.9990 chunk 179 optimal weight: 0.9990 chunk 31 optimal weight: 0.0770 chunk 129 optimal weight: 0.8980 overall best weight: 1.5944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 61 GLN D 61 GLN E 48 GLN ** H 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 59 ASN ** J 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 48 GLN P 78 ASN Q 61 GLN R 155 ASN ** R 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 22 ASN V 199 ASN V 297 GLN W 24 GLN ** X 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.083135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.072557 restraints weight = 64876.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.074389 restraints weight = 34071.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.075696 restraints weight = 21252.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.076590 restraints weight = 14551.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.077161 restraints weight = 10905.168| |-----------------------------------------------------------------------------| r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.9280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 20052 Z= 0.169 Angle : 0.707 11.655 27243 Z= 0.367 Chirality : 0.043 0.275 3119 Planarity : 0.004 0.056 3524 Dihedral : 4.538 57.828 2693 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 4.27 % Allowed : 28.42 % Favored : 67.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.17), residues: 2487 helix: 1.49 (0.12), residues: 1926 sheet: -1.53 (0.79), residues: 50 loop : -1.57 (0.27), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 80 TYR 0.029 0.002 TYR M 47 PHE 0.042 0.002 PHE F 215 TRP 0.035 0.002 TRP X 177 Details of bonding type rmsd covalent geometry : bond 0.00389 (20052) covalent geometry : angle 0.70691 (27243) hydrogen bonds : bond 0.04036 ( 1524) hydrogen bonds : angle 4.04553 ( 4512) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 556 residues out of total 2167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 464 time to evaluate : 0.773 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: A 47 TYR cc_start: 0.9165 (OUTLIER) cc_final: 0.8922 (t80) REVERT: A 66 LYS cc_start: 0.8980 (tptp) cc_final: 0.8653 (tptp) REVERT: A 72 ASP cc_start: 0.8711 (OUTLIER) cc_final: 0.8429 (t0) REVERT: B 16 PHE cc_start: 0.8188 (OUTLIER) cc_final: 0.7630 (m-80) REVERT: B 29 GLU cc_start: 0.8245 (mm-30) cc_final: 0.7944 (mm-30) REVERT: B 32 ASP cc_start: 0.7751 (p0) cc_final: 0.7528 (p0) REVERT: B 33 LYS cc_start: 0.8907 (OUTLIER) cc_final: 0.8614 (mppt) REVERT: B 61 GLN cc_start: 0.8990 (OUTLIER) cc_final: 0.8678 (pp30) REVERT: B 63 ASN cc_start: 0.8934 (m-40) cc_final: 0.8469 (m-40) REVERT: C 10 ASP cc_start: 0.8402 (t0) cc_final: 0.8062 (t0) REVERT: C 33 LYS cc_start: 0.8950 (mmtm) cc_final: 0.8532 (mmtm) REVERT: C 52 SER cc_start: 0.9229 (m) cc_final: 0.8981 (p) REVERT: C 66 LYS cc_start: 0.8932 (tptp) cc_final: 0.7889 (tppt) REVERT: C 70 ASP cc_start: 0.8045 (m-30) cc_final: 0.7602 (m-30) REVERT: D 69 LYS cc_start: 0.9061 (tptt) cc_final: 0.8787 (ttmt) REVERT: E 11 ASP cc_start: 0.8684 (OUTLIER) cc_final: 0.7809 (m-30) REVERT: E 26 GLN cc_start: 0.8731 (mt0) cc_final: 0.8284 (mt0) REVERT: E 53 GLU cc_start: 0.8526 (tm-30) cc_final: 0.7936 (tm-30) REVERT: E 66 LYS cc_start: 0.9169 (tppt) cc_final: 0.8955 (tppt) REVERT: E 76 ILE cc_start: 0.8883 (mm) cc_final: 0.8657 (mm) REVERT: E 79 PHE cc_start: 0.8340 (OUTLIER) cc_final: 0.7075 (t80) REVERT: F 318 LEU cc_start: 0.8384 (OUTLIER) cc_final: 0.8138 (tt) REVERT: F 327 SER cc_start: 0.7977 (OUTLIER) cc_final: 0.7414 (t) REVERT: G 26 GLN cc_start: 0.7961 (mt0) cc_final: 0.7109 (mt0) REVERT: G 29 GLU cc_start: 0.7391 (pp20) cc_final: 0.7170 (pp20) REVERT: G 69 LYS cc_start: 0.8982 (tmtt) cc_final: 0.8597 (tptm) REVERT: G 70 ASP cc_start: 0.8463 (m-30) cc_final: 0.8135 (m-30) REVERT: H 21 ASP cc_start: 0.7745 (m-30) cc_final: 0.7434 (m-30) REVERT: I 17 ASP cc_start: 0.8127 (m-30) cc_final: 0.7189 (m-30) REVERT: J 17 ASP cc_start: 0.8661 (m-30) cc_final: 0.8334 (m-30) REVERT: J 34 LEU cc_start: 0.9239 (OUTLIER) cc_final: 0.8835 (mm) REVERT: J 59 ASN cc_start: 0.8954 (m110) cc_final: 0.8473 (m110) REVERT: J 77 GLN cc_start: 0.8512 (pp30) cc_final: 0.8296 (tm-30) REVERT: K 10 ASP cc_start: 0.8432 (m-30) cc_final: 0.7435 (t0) REVERT: K 79 PHE cc_start: 0.8094 (m-10) cc_final: 0.7820 (m-80) REVERT: L 17 ASP cc_start: 0.8644 (m-30) cc_final: 0.8287 (m-30) REVERT: L 25 THR cc_start: 0.9267 (m) cc_final: 0.8807 (p) REVERT: L 29 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.8114 (pp20) REVERT: L 34 LEU cc_start: 0.9482 (tp) cc_final: 0.9219 (tt) REVERT: L 77 GLN cc_start: 0.8840 (tt0) cc_final: 0.8430 (tm-30) REVERT: M 21 ASP cc_start: 0.7802 (OUTLIER) cc_final: 0.7275 (p0) REVERT: M 76 ILE cc_start: 0.7158 (tt) cc_final: 0.6823 (tt) REVERT: M 77 GLN cc_start: 0.9002 (tm-30) cc_final: 0.8522 (tm-30) REVERT: N 17 ASP cc_start: 0.8503 (m-30) cc_final: 0.8167 (m-30) REVERT: N 24 GLN cc_start: 0.7258 (pm20) cc_final: 0.6877 (tp40) REVERT: O 252 TYR cc_start: 0.5706 (m-10) cc_final: 0.5316 (m-10) REVERT: O 291 GLN cc_start: 0.8989 (OUTLIER) cc_final: 0.8654 (mm110) REVERT: O 294 PHE cc_start: 0.7890 (OUTLIER) cc_final: 0.7117 (t80) REVERT: P 16 PHE cc_start: 0.8954 (OUTLIER) cc_final: 0.8390 (t80) REVERT: P 21 ASP cc_start: 0.8788 (OUTLIER) cc_final: 0.8323 (p0) REVERT: P 54 TYR cc_start: 0.8879 (t80) cc_final: 0.8138 (t80) REVERT: P 57 TYR cc_start: 0.8539 (t80) cc_final: 0.8150 (t80) REVERT: P 70 ASP cc_start: 0.7770 (m-30) cc_final: 0.7554 (m-30) REVERT: Q 33 LYS cc_start: 0.9029 (mmmt) cc_final: 0.8313 (mppt) REVERT: Q 57 TYR cc_start: 0.8032 (t80) cc_final: 0.7797 (t80) REVERT: Q 61 GLN cc_start: 0.8239 (OUTLIER) cc_final: 0.7938 (mm-40) REVERT: R 142 ILE cc_start: 0.8908 (tp) cc_final: 0.8682 (tp) REVERT: R 160 TYR cc_start: 0.5538 (t80) cc_final: 0.5264 (t80) REVERT: R 174 MET cc_start: 0.6709 (tpp) cc_final: 0.5870 (ttt) REVERT: R 334 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.7997 (mm) REVERT: S 32 ASP cc_start: 0.8155 (m-30) cc_final: 0.7941 (m-30) REVERT: S 53 GLU cc_start: 0.8176 (tp30) cc_final: 0.7961 (tp30) REVERT: S 54 TYR cc_start: 0.9116 (t80) cc_final: 0.8785 (t80) REVERT: S 62 SER cc_start: 0.8738 (t) cc_final: 0.8394 (t) REVERT: S 79 PHE cc_start: 0.2329 (OUTLIER) cc_final: 0.1718 (t80) REVERT: U 52 SER cc_start: 0.8955 (m) cc_final: 0.8701 (m) REVERT: V 150 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8115 (mp) REVERT: V 314 ASN cc_start: 0.8151 (m-40) cc_final: 0.7475 (t0) REVERT: V 340 PHE cc_start: 0.7146 (m-10) cc_final: 0.6750 (m-80) REVERT: W 24 GLN cc_start: 0.9062 (OUTLIER) cc_final: 0.8721 (tt0) REVERT: W 29 GLU cc_start: 0.8668 (tm-30) cc_final: 0.8356 (tp30) REVERT: W 50 LYS cc_start: 0.8660 (mtpt) cc_final: 0.8302 (mtmt) REVERT: W 79 PHE cc_start: 0.8722 (t80) cc_final: 0.8446 (t80) REVERT: X 142 ILE cc_start: 0.8457 (mm) cc_final: 0.8158 (mt) REVERT: X 298 GLU cc_start: 0.8410 (tm-30) cc_final: 0.8081 (tp30) outliers start: 92 outliers final: 65 residues processed: 525 average time/residue: 0.1214 time to fit residues: 103.5837 Evaluate side-chains 536 residues out of total 2167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 450 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 47 TYR Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain B residue 16 PHE Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 33 LYS Chi-restraints excluded: chain B residue 47 TYR Chi-restraints excluded: chain B residue 61 GLN Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 79 PHE Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain E residue 11 ASP Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 79 PHE Chi-restraints excluded: chain F residue 225 VAL Chi-restraints excluded: chain F residue 238 LEU Chi-restraints excluded: chain F residue 240 LEU Chi-restraints excluded: chain F residue 318 LEU Chi-restraints excluded: chain F residue 323 VAL Chi-restraints excluded: chain F residue 326 LEU Chi-restraints excluded: chain F residue 327 SER Chi-restraints excluded: chain G residue 32 ASP Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 27 VAL Chi-restraints excluded: chain H residue 71 ILE Chi-restraints excluded: chain I residue 43 LEU Chi-restraints excluded: chain I residue 51 LEU Chi-restraints excluded: chain I residue 53 GLU Chi-restraints excluded: chain I residue 79 PHE Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain J residue 62 SER Chi-restraints excluded: chain K residue 9 LEU Chi-restraints excluded: chain K residue 25 THR Chi-restraints excluded: chain K residue 34 LEU Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain K residue 47 TYR Chi-restraints excluded: chain L residue 8 TYR Chi-restraints excluded: chain L residue 29 GLU Chi-restraints excluded: chain L residue 57 TYR Chi-restraints excluded: chain M residue 21 ASP Chi-restraints excluded: chain M residue 44 LEU Chi-restraints excluded: chain N residue 16 PHE Chi-restraints excluded: chain O residue 136 ASP Chi-restraints excluded: chain O residue 138 VAL Chi-restraints excluded: chain O residue 155 ASN Chi-restraints excluded: chain O residue 157 VAL Chi-restraints excluded: chain O residue 258 LEU Chi-restraints excluded: chain O residue 291 GLN Chi-restraints excluded: chain O residue 294 PHE Chi-restraints excluded: chain O residue 306 GLN Chi-restraints excluded: chain O residue 312 TYR Chi-restraints excluded: chain O residue 323 VAL Chi-restraints excluded: chain P residue 16 PHE Chi-restraints excluded: chain P residue 21 ASP Chi-restraints excluded: chain P residue 48 GLN Chi-restraints excluded: chain P residue 51 LEU Chi-restraints excluded: chain Q residue 31 LEU Chi-restraints excluded: chain Q residue 61 GLN Chi-restraints excluded: chain Q residue 62 SER Chi-restraints excluded: chain R residue 155 ASN Chi-restraints excluded: chain R residue 227 THR Chi-restraints excluded: chain R residue 323 VAL Chi-restraints excluded: chain R residue 334 LEU Chi-restraints excluded: chain S residue 79 PHE Chi-restraints excluded: chain T residue 75 ILE Chi-restraints excluded: chain U residue 16 PHE Chi-restraints excluded: chain U residue 34 LEU Chi-restraints excluded: chain U residue 53 GLU Chi-restraints excluded: chain U residue 57 TYR Chi-restraints excluded: chain U residue 79 PHE Chi-restraints excluded: chain U residue 80 ARG Chi-restraints excluded: chain V residue 143 SER Chi-restraints excluded: chain V residue 150 LEU Chi-restraints excluded: chain V residue 157 VAL Chi-restraints excluded: chain V residue 237 GLU Chi-restraints excluded: chain V residue 264 MET Chi-restraints excluded: chain W residue 24 GLN Chi-restraints excluded: chain W residue 71 ILE Chi-restraints excluded: chain X residue 137 MET Chi-restraints excluded: chain X residue 157 VAL Chi-restraints excluded: chain X residue 177 TRP Chi-restraints excluded: chain X residue 268 ILE Chi-restraints excluded: chain X residue 295 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 132 optimal weight: 2.9990 chunk 85 optimal weight: 7.9990 chunk 165 optimal weight: 0.9980 chunk 59 optimal weight: 0.2980 chunk 216 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 233 optimal weight: 0.9980 chunk 86 optimal weight: 2.9990 chunk 211 optimal weight: 0.5980 chunk 25 optimal weight: 0.9980 chunk 156 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 61 GLN ** C 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 48 GLN ** G 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 59 ASN ** J 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 48 GLN ** Q 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 155 ASN ** R 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 59 ASN ** T 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 24 GLN ** X 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.084026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.073184 restraints weight = 66225.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.075096 restraints weight = 35859.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.076381 restraints weight = 22499.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.077202 restraints weight = 15760.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.077848 restraints weight = 12169.663| |-----------------------------------------------------------------------------| r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.9379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 20052 Z= 0.143 Angle : 0.697 12.611 27243 Z= 0.359 Chirality : 0.042 0.262 3119 Planarity : 0.004 0.053 3524 Dihedral : 4.531 58.784 2693 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 3.89 % Allowed : 28.98 % Favored : 67.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.17), residues: 2487 helix: 1.50 (0.12), residues: 1926 sheet: -1.49 (0.79), residues: 50 loop : -1.58 (0.27), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 80 TYR 0.029 0.002 TYR M 47 PHE 0.033 0.001 PHE F 215 TRP 0.033 0.001 TRP X 177 Details of bonding type rmsd covalent geometry : bond 0.00323 (20052) covalent geometry : angle 0.69732 (27243) hydrogen bonds : bond 0.03881 ( 1524) hydrogen bonds : angle 4.00212 ( 4512) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3251.45 seconds wall clock time: 57 minutes 32.92 seconds (3452.92 seconds total)