Starting phenix.real_space_refine on Mon Jun 16 23:19:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rye_24735/06_2025/7rye_24735.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rye_24735/06_2025/7rye_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_24735/06_2025/7rye_24735.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rye_24735/06_2025/7rye_24735.map" model { file = "/net/cci-nas-00/data/ceres_data/7rye_24735/06_2025/7rye_24735.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rye_24735/06_2025/7rye_24735.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 11.91, per 1000 atoms: 0.60 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: 5.07 Conformation dependent library (CDL) restraints added in 2.5 seconds 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: 1.65 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: 6.27 Time building geometry restraints manager: 6.01 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: 0.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.760 Check model and map are aligned: 0.150 Set scattering table: 0.180 Process input model: 44.860 Find NCS groups from input model: 0.920 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6931 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 : 14.13 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.043 0.002 TRP X 177 PHE 0.025 0.002 PHE P 16 TYR 0.032 0.002 TYR V 164 ARG 0.009 0.001 ARG H 58 Details of bonding type rmsd hydrogen bonds : bond 0.11618 ( 1524) hydrogen bonds : angle 4.56306 ( 4512) covalent geometry : bond 0.00346 (20052) covalent geometry : angle 0.64895 (27243) *********************** 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 : 2.276 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: A 27 VAL cc_start: 0.9280 (t) cc_final: 0.8823 (p) REVERT: A 31 LEU cc_start: 0.9182 (mt) cc_final: 0.8968 (mm) REVERT: A 48 GLN cc_start: 0.7157 (tm-30) cc_final: 0.6837 (tm-30) REVERT: B 28 THR cc_start: 0.8683 (m) cc_final: 0.8376 (p) REVERT: B 58 ARG cc_start: 0.8420 (mmt180) cc_final: 0.8025 (mmt90) REVERT: C 70 ASP cc_start: 0.7141 (m-30) cc_final: 0.6932 (m-30) REVERT: D 16 PHE cc_start: 0.8560 (t80) cc_final: 0.7892 (t80) REVERT: E 22 ASN cc_start: 0.7932 (p0) cc_final: 0.7152 (t0) REVERT: E 26 GLN cc_start: 0.8128 (mt0) cc_final: 0.6962 (mt0) REVERT: F 215 PHE cc_start: 0.7062 (t80) cc_final: 0.6521 (t80) REVERT: F 266 GLN cc_start: 0.7919 (tm-30) cc_final: 0.7605 (pp30) REVERT: G 20 VAL cc_start: 0.8241 (t) cc_final: 0.7948 (t) REVERT: G 69 LYS cc_start: 0.7819 (tmtt) cc_final: 0.7472 (tptm) REVERT: H 32 ASP cc_start: 0.7165 (p0) cc_final: 0.6871 (p0) REVERT: I 17 ASP cc_start: 0.7440 (m-30) cc_final: 0.5992 (t70) REVERT: I 31 LEU cc_start: 0.7570 (tp) cc_final: 0.6907 (tp) REVERT: I 68 PHE cc_start: 0.7625 (m-80) cc_final: 0.6949 (m-10) REVERT: J 5 TRP cc_start: 0.8384 (t60) cc_final: 0.8178 (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: 0.8120 (tptt) REVERT: K 72 ASP cc_start: 0.7319 (m-30) cc_final: 0.6512 (m-30) REVERT: K 79 PHE cc_start: 0.7069 (m-10) cc_final: 0.6811 (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: 0.5193 (p0) REVERT: L 22 ASN cc_start: 0.8077 (p0) cc_final: 0.7593 (p0) REVERT: L 25 THR cc_start: 0.8822 (m) cc_final: 0.8432 (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: 0.7530 (t70) REVERT: N 5 TRP cc_start: 0.3194 (t60) cc_final: 0.2703 (p90) REVERT: N 17 ASP cc_start: 0.7345 (m-30) cc_final: 0.6909 (m-30) REVERT: N 31 LEU cc_start: 0.9302 (tp) cc_final: 0.9054 (tp) REVERT: N 58 ARG cc_start: 0.4283 (mtt180) cc_final: 0.3385 (mmt180) REVERT: N 59 ASN cc_start: 0.8082 (t0) cc_final: 0.7843 (t0) REVERT: N 62 SER cc_start: 0.8948 (t) cc_final: 0.8704 (t) REVERT: N 66 LYS cc_start: 0.8215 (tmtt) cc_final: 0.7786 (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: 0.8703 (Cg_endo) REVERT: O 287 TYR cc_start: 0.7868 (t80) cc_final: 0.7442 (t80) REVERT: O 288 GLN cc_start: 0.7700 (mm110) cc_final: 0.7335 (pt0) REVERT: O 326 LEU cc_start: 0.7731 (pp) cc_final: 0.7090 (mt) REVERT: P 24 GLN cc_start: 0.8427 (pm20) cc_final: 0.8123 (mp10) REVERT: P 28 THR cc_start: 0.8833 (m) cc_final: 0.8271 (m) REVERT: P 47 TYR cc_start: 0.8143 (t80) cc_final: 0.7523 (t80) REVERT: P 54 TYR cc_start: 0.7292 (t80) cc_final: 0.6974 (t80) REVERT: P 66 LYS cc_start: 0.7849 (tptm) cc_final: 0.6756 (tptt) REVERT: P 70 ASP cc_start: 0.7271 (m-30) cc_final: 0.6999 (m-30) REVERT: Q 10 ASP cc_start: 0.7731 (m-30) cc_final: 0.7459 (m-30) REVERT: Q 17 ASP cc_start: 0.7905 (t0) cc_final: 0.7554 (t0) REVERT: Q 34 LEU cc_start: 0.8829 (tp) cc_final: 0.8624 (tp) REVERT: Q 57 TYR cc_start: 0.6781 (t80) cc_final: 0.6578 (t80) REVERT: Q 67 VAL cc_start: 0.8971 (p) cc_final: 0.8684 (m) REVERT: R 171 LEU cc_start: 0.7924 (tp) cc_final: 0.7723 (tt) REVERT: R 267 ASP cc_start: 0.7780 (m-30) cc_final: 0.7527 (t0) 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: 0.7552 (t80) REVERT: T 52 SER cc_start: 0.9050 (t) cc_final: 0.8474 (p) REVERT: U 15 LYS cc_start: 0.7569 (tptp) cc_final: 0.7018 (tmtt) REVERT: V 171 LEU cc_start: 0.7861 (tt) cc_final: 0.7656 (tt) 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: 0.7276 (t0) REVERT: W 28 THR cc_start: 0.6176 (m) cc_final: 0.5123 (p) REVERT: W 71 ILE cc_start: 0.9113 (pt) cc_final: 0.8678 (pt) REVERT: X 260 PRO cc_start: 0.8267 (Cg_exo) cc_final: 0.8044 (Cg_endo) REVERT: X 291 GLN cc_start: 0.8069 (mm-40) cc_final: 0.7769 (mm-40) REVERT: X 308 LEU cc_start: 0.7467 (mm) cc_final: 0.5676 (tp) outliers start: 0 outliers final: 0 residues processed: 866 average time/residue: 0.3286 time to fit residues: 437.6652 Evaluate side-chains 518 residues out of total 2167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 518 time to evaluate : 2.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 200 optimal weight: 3.9990 chunk 180 optimal weight: 6.9990 chunk 100 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 chunk 96 optimal weight: 0.8980 chunk 186 optimal weight: 0.7980 chunk 72 optimal weight: 3.9990 chunk 113 optimal weight: 5.9990 chunk 138 optimal weight: 4.9990 chunk 216 optimal weight: 0.8980 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 55 ASN ** I 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 78 ASN ** L 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ** O 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 77 GLN Q 48 GLN R 218 GLN R 233 GLN ** R 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 63 ASN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.089527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.078326 restraints weight = 63047.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.080333 restraints weight = 33868.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.081702 restraints weight = 21075.420| |-----------------------------------------------------------------------------| r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.3787 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= 0.171 Angle : 0.667 10.346 27243 Z= 0.346 Chirality : 0.043 0.204 3119 Planarity : 0.004 0.061 3524 Dihedral : 4.462 28.894 2693 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 3.38 % Allowed : 16.92 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.17), residues: 2487 helix: 1.50 (0.12), residues: 1895 sheet: -1.28 (0.58), residues: 75 loop : -1.53 (0.27), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP R 234 PHE 0.019 0.002 PHE F 215 TYR 0.042 0.002 TYR J 57 ARG 0.007 0.001 ARG H 58 Details of bonding type rmsd hydrogen bonds : bond 0.04326 ( 1524) hydrogen bonds : angle 4.08985 ( 4512) covalent geometry : bond 0.00374 (20052) covalent geometry : angle 0.66650 (27243) *********************** 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 662 residues out of total 2167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 589 time to evaluate : 3.250 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 48 GLN cc_start: 0.8009 (tm-30) cc_final: 0.7173 (tm-30) REVERT: A 66 LYS cc_start: 0.8539 (tmmt) cc_final: 0.8253 (ttpt) REVERT: A 72 ASP cc_start: 0.7864 (OUTLIER) cc_final: 0.7566 (t0) REVERT: B 28 THR cc_start: 0.8814 (m) cc_final: 0.8467 (p) REVERT: B 33 LYS cc_start: 0.9117 (tppt) cc_final: 0.8791 (mtmt) REVERT: B 54 TYR cc_start: 0.8614 (t80) cc_final: 0.8197 (t80) REVERT: B 78 ASN cc_start: 0.7215 (m-40) cc_final: 0.6888 (m-40) REVERT: C 53 GLU cc_start: 0.7364 (tt0) cc_final: 0.6874 (mt-10) REVERT: C 66 LYS cc_start: 0.8493 (tptp) cc_final: 0.7661 (tptm) REVERT: C 70 ASP cc_start: 0.7668 (m-30) cc_final: 0.7135 (m-30) REVERT: D 61 GLN cc_start: 0.8380 (pp30) cc_final: 0.7761 (pp30) REVERT: E 11 ASP cc_start: 0.8691 (m-30) cc_final: 0.7409 (m-30) REVERT: E 26 GLN cc_start: 0.8645 (mt0) cc_final: 0.7778 (mp10) REVERT: F 160 TYR cc_start: 0.8434 (t80) cc_final: 0.8158 (t80) REVERT: F 215 PHE cc_start: 0.7470 (t80) cc_final: 0.7199 (t80) REVERT: F 232 ARG cc_start: 0.6349 (tpp80) cc_final: 0.6141 (mmm-85) REVERT: F 300 ASN cc_start: 0.4850 (t0) cc_final: 0.4647 (t0) REVERT: F 301 MET cc_start: 0.7496 (OUTLIER) cc_final: 0.6997 (ppp) REVERT: G 20 VAL cc_start: 0.8208 (t) cc_final: 0.7870 (t) REVERT: G 69 LYS cc_start: 0.8350 (tmtt) cc_final: 0.7951 (tptm) REVERT: G 76 ILE cc_start: 0.6951 (mm) cc_final: 0.6291 (mm) REVERT: H 57 TYR cc_start: 0.8433 (OUTLIER) cc_final: 0.7278 (m-10) REVERT: H 76 ILE cc_start: 0.8417 (pt) cc_final: 0.8196 (pt) REVERT: I 17 ASP cc_start: 0.7949 (m-30) cc_final: 0.5273 (t70) REVERT: I 58 ARG cc_start: 0.7639 (tpp80) cc_final: 0.7230 (ttt180) REVERT: J 8 TYR cc_start: 0.8442 (t80) cc_final: 0.8205 (t80) REVERT: J 9 LEU cc_start: 0.8649 (mp) cc_final: 0.7949 (mt) REVERT: J 59 ASN cc_start: 0.8316 (m110) cc_final: 0.7584 (m110) REVERT: J 66 LYS cc_start: 0.8036 (tptm) cc_final: 0.7178 (tppt) REVERT: J 69 LYS cc_start: 0.8585 (tmtt) cc_final: 0.8032 (tppt) REVERT: J 70 ASP cc_start: 0.7535 (m-30) cc_final: 0.6886 (m-30) REVERT: J 75 ILE cc_start: 0.9180 (mm) cc_final: 0.8882 (mm) REVERT: K 57 TYR cc_start: 0.8599 (t80) cc_final: 0.7759 (t80) REVERT: L 11 ASP cc_start: 0.8224 (t0) cc_final: 0.7782 (m-30) REVERT: L 21 ASP cc_start: 0.7111 (p0) cc_final: 0.6582 (p0) REVERT: M 21 ASP cc_start: 0.7577 (OUTLIER) cc_final: 0.6923 (p0) REVERT: N 5 TRP cc_start: 0.3339 (t60) cc_final: 0.3128 (p90) REVERT: N 16 PHE cc_start: 0.6944 (m-10) cc_final: 0.6590 (m-10) REVERT: N 17 ASP cc_start: 0.8017 (m-30) cc_final: 0.7508 (m-30) REVERT: N 28 THR cc_start: 0.9565 (m) cc_final: 0.9317 (p) REVERT: N 59 ASN cc_start: 0.8058 (t0) cc_final: 0.7733 (t0) REVERT: N 66 LYS cc_start: 0.7957 (tmtt) cc_final: 0.7603 (tmtt) REVERT: O 288 GLN cc_start: 0.7856 (mm110) cc_final: 0.7425 (pt0) REVERT: O 294 PHE cc_start: 0.7115 (OUTLIER) cc_final: 0.5983 (t80) REVERT: O 301 MET cc_start: 0.7070 (mmp) cc_final: 0.6418 (mmt) REVERT: O 316 ASN cc_start: 0.8569 (m-40) cc_final: 0.8185 (m-40) REVERT: P 10 ASP cc_start: 0.8233 (t0) cc_final: 0.7988 (t0) REVERT: P 27 VAL cc_start: 0.9240 (m) cc_final: 0.8975 (m) REVERT: P 48 GLN cc_start: 0.7777 (pp30) cc_final: 0.7437 (pp30) REVERT: P 54 TYR cc_start: 0.7204 (t80) cc_final: 0.6990 (t80) REVERT: P 61 GLN cc_start: 0.8167 (mt0) cc_final: 0.7858 (mm-40) REVERT: P 66 LYS cc_start: 0.7752 (tptm) cc_final: 0.6673 (tptt) REVERT: Q 16 PHE cc_start: 0.7673 (OUTLIER) cc_final: 0.7249 (t80) REVERT: Q 57 TYR cc_start: 0.7121 (t80) cc_final: 0.6913 (t80) REVERT: Q 61 GLN cc_start: 0.7524 (OUTLIER) cc_final: 0.7309 (mt0) REVERT: Q 67 VAL cc_start: 0.8884 (p) cc_final: 0.8656 (m) REVERT: R 160 TYR cc_start: 0.5102 (t80) cc_final: 0.4867 (t80) REVERT: R 267 ASP cc_start: 0.7851 (m-30) cc_final: 0.7401 (t0) REVERT: T 52 SER cc_start: 0.8527 (t) cc_final: 0.8224 (p) REVERT: U 15 LYS cc_start: 0.7507 (tptp) cc_final: 0.6917 (tmtt) REVERT: U 16 PHE cc_start: 0.8073 (OUTLIER) cc_final: 0.7346 (t80) REVERT: V 282 MET cc_start: 0.6382 (tpp) cc_final: 0.6073 (tpp) REVERT: W 28 THR cc_start: 0.6459 (m) cc_final: 0.5878 (p) outliers start: 73 outliers final: 39 residues processed: 630 average time/residue: 0.3142 time to fit residues: 315.3472 Evaluate side-chains 538 residues out of total 2167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 491 time to evaluate : 4.001 ------------------------------------------------------------------------------- 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 31 LEU 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 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 F residue 327 SER Chi-restraints excluded: chain H residue 27 VAL Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 57 TYR Chi-restraints excluded: chain H residue 75 ILE 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 21 ASP Chi-restraints excluded: chain M residue 71 ILE Chi-restraints excluded: chain M residue 79 PHE Chi-restraints excluded: chain O residue 155 ASN 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 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 167 PHE Chi-restraints excluded: chain R residue 221 SER Chi-restraints excluded: chain R residue 245 LEU Chi-restraints excluded: chain R residue 261 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 25 THR Chi-restraints excluded: chain U residue 27 VAL Chi-restraints excluded: chain V residue 157 VAL Chi-restraints excluded: chain V residue 189 LEU 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 158 optimal weight: 4.9990 chunk 220 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 181 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 61 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 198 optimal weight: 5.9990 chunk 138 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 125 optimal weight: 4.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 ASN ** D 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 300 ASN ** G 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 78 ASN ** O 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 196 ASN R 314 ASN ** R 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 77 GLN ** V 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 300 ASN W 61 GLN ** W 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 141 ASN ** 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 = 0.3677 r_free = 0.3677 target = 0.087453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.076167 restraints weight = 63935.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.078092 restraints weight = 35424.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.079382 restraints weight = 22535.084| |-----------------------------------------------------------------------------| r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.5607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 20052 Z= 0.173 Angle : 0.656 10.988 27243 Z= 0.341 Chirality : 0.042 0.228 3119 Planarity : 0.004 0.048 3524 Dihedral : 4.421 26.196 2693 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 4.68 % Allowed : 19.56 % Favored : 75.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.17), residues: 2487 helix: 1.44 (0.12), residues: 1923 sheet: -1.58 (0.79), residues: 50 loop : -1.60 (0.26), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP X 177 PHE 0.026 0.002 PHE V 167 TYR 0.029 0.002 TYR H 54 ARG 0.006 0.001 ARG H 58 Details of bonding type rmsd hydrogen bonds : bond 0.04145 ( 1524) hydrogen bonds : angle 3.93146 ( 4512) covalent geometry : bond 0.00385 (20052) covalent geometry : angle 0.65584 (27243) *********************** 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 659 residues out of total 2167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 558 time to evaluate : 2.981 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: A 16 PHE cc_start: 0.8348 (OUTLIER) cc_final: 0.7661 (t80) REVERT: A 31 LEU cc_start: 0.9339 (mt) cc_final: 0.9133 (mm) REVERT: A 66 LYS cc_start: 0.8872 (tmmt) cc_final: 0.8344 (tptp) REVERT: A 72 ASP cc_start: 0.8241 (OUTLIER) cc_final: 0.7987 (t0) REVERT: B 16 PHE cc_start: 0.7691 (OUTLIER) cc_final: 0.7277 (m-80) REVERT: B 28 THR cc_start: 0.9069 (m) cc_final: 0.7881 (p) REVERT: B 33 LYS cc_start: 0.9094 (tppt) cc_final: 0.8805 (mtpt) REVERT: B 78 ASN cc_start: 0.7493 (m-40) cc_final: 0.7290 (m-40) REVERT: C 33 LYS cc_start: 0.9087 (mmtm) cc_final: 0.8792 (mmtm) REVERT: C 34 LEU cc_start: 0.8306 (tp) cc_final: 0.8063 (tt) REVERT: C 53 GLU cc_start: 0.7788 (tt0) cc_final: 0.7424 (mt-10) REVERT: C 66 LYS cc_start: 0.8629 (tptp) cc_final: 0.7944 (tppt) REVERT: C 70 ASP cc_start: 0.7681 (m-30) cc_final: 0.7148 (m-30) REVERT: D 72 ASP cc_start: 0.8288 (m-30) cc_final: 0.8051 (m-30) REVERT: E 11 ASP cc_start: 0.8875 (m-30) cc_final: 0.7639 (m-30) REVERT: E 17 ASP cc_start: 0.7735 (t70) cc_final: 0.7360 (m-30) REVERT: E 23 LEU cc_start: 0.8812 (tt) cc_final: 0.7990 (tt) REVERT: E 26 GLN cc_start: 0.8595 (mt0) cc_final: 0.7818 (mp10) REVERT: E 53 GLU cc_start: 0.8152 (tm-30) cc_final: 0.7822 (tm-30) REVERT: E 77 GLN cc_start: 0.8600 (tp40) cc_final: 0.8361 (tp40) REVERT: F 215 PHE cc_start: 0.7722 (t80) cc_final: 0.7431 (t80) REVERT: G 24 GLN cc_start: 0.8575 (mm-40) cc_final: 0.7934 (tp40) REVERT: G 66 LYS cc_start: 0.8776 (OUTLIER) cc_final: 0.8563 (ptmt) REVERT: G 69 LYS cc_start: 0.8488 (tmtt) cc_final: 0.8149 (tptm) REVERT: H 57 TYR cc_start: 0.8560 (OUTLIER) cc_final: 0.8059 (m-10) REVERT: I 17 ASP cc_start: 0.8337 (m-30) cc_final: 0.5801 (t70) REVERT: I 32 ASP cc_start: 0.8078 (m-30) cc_final: 0.7860 (m-30) REVERT: J 59 ASN cc_start: 0.8486 (m110) cc_final: 0.8056 (m110) REVERT: J 66 LYS cc_start: 0.8384 (tptm) cc_final: 0.7304 (tppt) REVERT: J 69 LYS cc_start: 0.8978 (tmtt) cc_final: 0.8703 (tptp) REVERT: J 70 ASP cc_start: 0.7242 (m-30) cc_final: 0.6957 (m-30) REVERT: K 57 TYR cc_start: 0.8468 (t80) cc_final: 0.8025 (t80) REVERT: L 12 VAL cc_start: 0.8018 (m) cc_final: 0.7769 (m) REVERT: L 69 LYS cc_start: 0.9050 (mmmm) cc_final: 0.8779 (tppp) REVERT: M 65 VAL cc_start: 0.8777 (t) cc_final: 0.8468 (p) REVERT: M 77 GLN cc_start: 0.9033 (tm-30) cc_final: 0.8729 (tm-30) REVERT: N 5 TRP cc_start: 0.4181 (t60) cc_final: 0.3603 (p90) REVERT: N 17 ASP cc_start: 0.8356 (m-30) cc_final: 0.7820 (m-30) REVERT: N 24 GLN cc_start: 0.7561 (pm20) cc_final: 0.7345 (tp40) REVERT: N 59 ASN cc_start: 0.7932 (t0) cc_final: 0.7636 (t0) REVERT: N 66 LYS cc_start: 0.8228 (tmtt) cc_final: 0.7900 (tmtt) REVERT: O 137 MET cc_start: 0.8334 (tmm) cc_final: 0.7794 (tmm) REVERT: O 169 ASP cc_start: 0.7760 (t0) cc_final: 0.7251 (m-30) REVERT: O 301 MET cc_start: 0.7332 (mmp) cc_final: 0.7128 (tpp) REVERT: O 316 ASN cc_start: 0.8594 (m-40) cc_final: 0.8137 (m110) REVERT: P 47 TYR cc_start: 0.7811 (t80) cc_final: 0.7190 (t80) REVERT: P 66 LYS cc_start: 0.8041 (tptm) cc_final: 0.7291 (tptt) REVERT: Q 31 LEU cc_start: 0.9384 (tp) cc_final: 0.9057 (tp) REVERT: R 160 TYR cc_start: 0.5213 (t80) cc_final: 0.4800 (t80) REVERT: R 165 GLN cc_start: 0.7971 (tp40) cc_final: 0.7577 (tm-30) REVERT: R 264 MET cc_start: 0.5789 (tpp) cc_final: 0.5566 (tpp) REVERT: S 53 GLU cc_start: 0.8189 (mm-30) cc_final: 0.7940 (tp30) REVERT: T 11 ASP cc_start: 0.7362 (m-30) cc_final: 0.6934 (m-30) REVERT: T 23 LEU cc_start: 0.7625 (mp) cc_final: 0.7119 (mt) REVERT: U 15 LYS cc_start: 0.7784 (tptp) cc_final: 0.7146 (tmtt) REVERT: U 16 PHE cc_start: 0.8343 (OUTLIER) cc_final: 0.7517 (t80) REVERT: V 150 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.7900 (mp) REVERT: V 300 ASN cc_start: 0.7971 (OUTLIER) cc_final: 0.7566 (t0) REVERT: W 28 THR cc_start: 0.7053 (m) cc_final: 0.6808 (m) REVERT: X 189 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8266 (pp) REVERT: X 298 GLU cc_start: 0.8047 (tm-30) cc_final: 0.7604 (tp30) outliers start: 101 outliers final: 50 residues processed: 621 average time/residue: 0.3131 time to fit residues: 310.4286 Evaluate side-chains 551 residues out of total 2167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 492 time to evaluate : 3.375 ------------------------------------------------------------------------------- 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 72 ASP Chi-restraints excluded: chain B residue 16 PHE Chi-restraints excluded: chain B residue 34 LEU 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 39 SER Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 259 THR Chi-restraints excluded: chain F residue 327 SER 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 25 THR Chi-restraints excluded: chain H residue 27 VAL Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 57 TYR Chi-restraints excluded: chain I residue 51 LEU Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain K residue 9 LEU Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 62 SER Chi-restraints excluded: chain K residue 75 ILE Chi-restraints excluded: chain L residue 8 TYR Chi-restraints excluded: chain M residue 71 ILE Chi-restraints excluded: chain O residue 136 ASP Chi-restraints excluded: chain O residue 155 ASN Chi-restraints excluded: chain O residue 157 VAL Chi-restraints excluded: chain O residue 159 VAL Chi-restraints excluded: chain O residue 303 THR Chi-restraints excluded: chain P residue 13 SER Chi-restraints excluded: chain P residue 29 GLU Chi-restraints excluded: chain P residue 34 LEU Chi-restraints excluded: chain P residue 55 ASN 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 321 ASN Chi-restraints excluded: chain S residue 79 PHE Chi-restraints excluded: chain U residue 16 PHE Chi-restraints excluded: chain U residue 27 VAL Chi-restraints excluded: chain U residue 34 LEU 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 V residue 301 MET Chi-restraints excluded: chain W residue 79 PHE Chi-restraints excluded: chain X residue 137 MET Chi-restraints excluded: chain X residue 157 VAL Chi-restraints excluded: chain X residue 189 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 154 optimal weight: 5.9990 chunk 229 optimal weight: 0.0270 chunk 177 optimal weight: 4.9990 chunk 19 optimal weight: 0.8980 chunk 119 optimal weight: 1.9990 chunk 220 optimal weight: 2.9990 chunk 174 optimal weight: 1.9990 chunk 103 optimal weight: 0.7980 chunk 58 optimal weight: 0.8980 chunk 50 optimal weight: 3.9990 chunk 87 optimal weight: 0.0770 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 61 GLN F 141 ASN ** G 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 59 ASN ** O 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 63 ASN ** R 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 300 ASN ** W 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.088497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.077112 restraints weight = 63668.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.079096 restraints weight = 35446.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.080433 restraints weight = 22603.951| |-----------------------------------------------------------------------------| r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.6056 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= 0.128 Angle : 0.615 9.246 27243 Z= 0.313 Chirality : 0.040 0.190 3119 Planarity : 0.003 0.050 3524 Dihedral : 4.244 23.311 2693 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 3.89 % Allowed : 23.55 % Favored : 72.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.17), residues: 2487 helix: 1.60 (0.12), residues: 1928 sheet: -1.54 (0.80), residues: 50 loop : -1.48 (0.27), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP X 177 PHE 0.017 0.001 PHE C 16 TYR 0.028 0.002 TYR N 47 ARG 0.006 0.000 ARG S 58 Details of bonding type rmsd hydrogen bonds : bond 0.03696 ( 1524) hydrogen bonds : angle 3.78777 ( 4512) covalent geometry : bond 0.00285 (20052) covalent geometry : angle 0.61455 (27243) *********************** 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 632 residues out of total 2167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 548 time to evaluate : 3.053 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: A 16 PHE cc_start: 0.8443 (OUTLIER) cc_final: 0.7710 (t80) REVERT: A 27 VAL cc_start: 0.9300 (t) cc_final: 0.9028 (p) REVERT: A 31 LEU cc_start: 0.9271 (mt) cc_final: 0.9038 (mm) REVERT: A 66 LYS cc_start: 0.8880 (tmmt) cc_final: 0.8372 (tptp) REVERT: A 72 ASP cc_start: 0.8461 (OUTLIER) cc_final: 0.8207 (t0) REVERT: B 16 PHE cc_start: 0.7715 (OUTLIER) cc_final: 0.7237 (m-10) REVERT: B 28 THR cc_start: 0.8769 (m) cc_final: 0.8382 (p) REVERT: B 63 ASN cc_start: 0.8863 (m-40) cc_final: 0.8617 (m-40) REVERT: C 26 GLN cc_start: 0.8650 (tt0) cc_final: 0.8345 (mt0) REVERT: C 33 LYS cc_start: 0.9095 (mmtm) cc_final: 0.8379 (mmtm) REVERT: C 34 LEU cc_start: 0.8338 (tp) cc_final: 0.7710 (tt) REVERT: C 53 GLU cc_start: 0.7623 (tt0) cc_final: 0.7348 (mt-10) REVERT: C 66 LYS cc_start: 0.8754 (tptp) cc_final: 0.8096 (tppt) REVERT: C 70 ASP cc_start: 0.7669 (m-30) cc_final: 0.7145 (m-30) REVERT: D 69 LYS cc_start: 0.8848 (tptt) cc_final: 0.8426 (ttmt) REVERT: E 11 ASP cc_start: 0.8873 (m-30) cc_final: 0.7958 (m-30) REVERT: E 17 ASP cc_start: 0.7713 (t70) cc_final: 0.7377 (m-30) REVERT: E 23 LEU cc_start: 0.8688 (tt) cc_final: 0.8005 (tt) REVERT: E 26 GLN cc_start: 0.8558 (mt0) cc_final: 0.8149 (mt0) REVERT: E 34 LEU cc_start: 0.8040 (tt) cc_final: 0.7677 (tp) REVERT: E 53 GLU cc_start: 0.8283 (tm-30) cc_final: 0.7749 (tm-30) REVERT: E 63 ASN cc_start: 0.8338 (t0) cc_final: 0.7719 (t0) REVERT: E 77 GLN cc_start: 0.8596 (tp40) cc_final: 0.8392 (tp40) REVERT: F 215 PHE cc_start: 0.7653 (t80) cc_final: 0.7428 (t80) REVERT: G 24 GLN cc_start: 0.8467 (mm-40) cc_final: 0.7728 (tp40) REVERT: G 69 LYS cc_start: 0.8621 (tmtt) cc_final: 0.8285 (tptm) REVERT: H 57 TYR cc_start: 0.8384 (OUTLIER) cc_final: 0.7389 (m-10) REVERT: I 17 ASP cc_start: 0.7772 (m-30) cc_final: 0.5587 (t0) REVERT: I 29 GLU cc_start: 0.8532 (OUTLIER) cc_final: 0.8243 (pt0) REVERT: I 32 ASP cc_start: 0.8096 (m-30) cc_final: 0.7835 (m-30) REVERT: J 57 TYR cc_start: 0.7291 (t80) cc_final: 0.6817 (t80) REVERT: J 59 ASN cc_start: 0.8574 (m110) cc_final: 0.8216 (m110) REVERT: J 66 LYS cc_start: 0.8375 (tptm) cc_final: 0.6870 (tppt) REVERT: J 69 LYS cc_start: 0.8926 (tmtt) cc_final: 0.8146 (tppt) REVERT: J 70 ASP cc_start: 0.7147 (m-30) cc_final: 0.6575 (m-30) REVERT: K 10 ASP cc_start: 0.8160 (m-30) cc_final: 0.6717 (t0) REVERT: L 12 VAL cc_start: 0.8011 (m) cc_final: 0.7808 (m) REVERT: L 21 ASP cc_start: 0.7519 (p0) cc_final: 0.7058 (p0) REVERT: L 22 ASN cc_start: 0.8812 (p0) cc_final: 0.8545 (p0) REVERT: M 8 TYR cc_start: 0.7799 (t80) cc_final: 0.6331 (m-80) REVERT: M 21 ASP cc_start: 0.7715 (OUTLIER) cc_final: 0.7115 (p0) REVERT: M 65 VAL cc_start: 0.8744 (t) cc_final: 0.8402 (p) REVERT: M 77 GLN cc_start: 0.8957 (tm-30) cc_final: 0.8652 (tm-30) REVERT: N 5 TRP cc_start: 0.4550 (t60) cc_final: 0.3830 (p90) REVERT: N 9 LEU cc_start: 0.7543 (OUTLIER) cc_final: 0.7225 (mt) REVERT: N 17 ASP cc_start: 0.8375 (m-30) cc_final: 0.7878 (m-30) REVERT: N 24 GLN cc_start: 0.7799 (pm20) cc_final: 0.7420 (tp-100) REVERT: N 34 LEU cc_start: 0.9083 (mt) cc_final: 0.8860 (mt) REVERT: N 59 ASN cc_start: 0.7917 (t0) cc_final: 0.7565 (t0) REVERT: N 66 LYS cc_start: 0.8219 (tmtt) cc_final: 0.7858 (tmtt) REVERT: O 137 MET cc_start: 0.8365 (tmm) cc_final: 0.8119 (tmm) REVERT: O 169 ASP cc_start: 0.7876 (t0) cc_final: 0.7434 (m-30) REVERT: O 261 LEU cc_start: 0.9410 (OUTLIER) cc_final: 0.9207 (mp) REVERT: O 288 GLN cc_start: 0.7895 (mm110) cc_final: 0.7498 (pt0) REVERT: O 316 ASN cc_start: 0.8609 (m-40) cc_final: 0.8372 (m110) REVERT: P 21 ASP cc_start: 0.8523 (OUTLIER) cc_final: 0.7790 (p0) REVERT: P 29 GLU cc_start: 0.7398 (OUTLIER) cc_final: 0.7095 (mp0) REVERT: P 54 TYR cc_start: 0.8077 (t80) cc_final: 0.7761 (t80) REVERT: P 72 ASP cc_start: 0.7643 (m-30) cc_final: 0.7429 (m-30) REVERT: P 80 ARG cc_start: 0.1535 (mpt180) cc_final: -0.0353 (ptp90) REVERT: Q 16 PHE cc_start: 0.7651 (OUTLIER) cc_final: 0.7342 (t80) REVERT: Q 31 LEU cc_start: 0.9479 (tp) cc_final: 0.9191 (tp) REVERT: Q 47 TYR cc_start: 0.8426 (t80) cc_final: 0.8066 (t80) REVERT: Q 75 ILE cc_start: 0.7493 (tt) cc_final: 0.7183 (tp) REVERT: R 142 ILE cc_start: 0.8377 (tp) cc_final: 0.8146 (tp) REVERT: R 160 TYR cc_start: 0.5112 (t80) cc_final: 0.4910 (t80) REVERT: R 264 MET cc_start: 0.5875 (tpp) cc_final: 0.5554 (tpp) REVERT: S 53 GLU cc_start: 0.8165 (mm-30) cc_final: 0.7877 (tp30) REVERT: T 11 ASP cc_start: 0.7431 (m-30) cc_final: 0.6863 (m-30) REVERT: T 23 LEU cc_start: 0.7939 (mp) cc_final: 0.7566 (mt) REVERT: U 15 LYS cc_start: 0.7746 (tptp) cc_final: 0.7100 (tmtt) REVERT: U 16 PHE cc_start: 0.8367 (OUTLIER) cc_final: 0.7629 (t80) REVERT: V 150 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.8004 (mp) REVERT: V 153 TYR cc_start: 0.7495 (OUTLIER) cc_final: 0.7197 (t80) REVERT: V 282 MET cc_start: 0.6804 (tpp) cc_final: 0.6421 (tpp) REVERT: V 300 ASN cc_start: 0.8148 (OUTLIER) cc_final: 0.7625 (t0) REVERT: X 189 LEU cc_start: 0.8573 (tt) cc_final: 0.8297 (pp) REVERT: X 298 GLU cc_start: 0.8059 (tm-30) cc_final: 0.7724 (tp30) outliers start: 84 outliers final: 42 residues processed: 593 average time/residue: 0.3221 time to fit residues: 301.3739 Evaluate side-chains 559 residues out of total 2167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 502 time to evaluate : 2.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 PHE 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 79 PHE Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain F residue 259 THR Chi-restraints excluded: chain F residue 301 MET Chi-restraints excluded: chain F residue 309 THR Chi-restraints excluded: chain F residue 323 VAL Chi-restraints excluded: chain F residue 327 SER Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 57 TYR Chi-restraints excluded: chain I residue 29 GLU Chi-restraints excluded: chain I residue 51 LEU Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 47 TYR 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 57 TYR Chi-restraints excluded: chain M residue 21 ASP Chi-restraints excluded: chain M residue 43 LEU Chi-restraints excluded: chain M residue 44 LEU Chi-restraints excluded: chain N residue 9 LEU Chi-restraints excluded: chain O residue 161 THR Chi-restraints excluded: chain O residue 261 LEU Chi-restraints excluded: chain O residue 303 THR Chi-restraints excluded: chain O residue 323 VAL Chi-restraints excluded: chain P residue 21 ASP Chi-restraints excluded: chain P residue 29 GLU Chi-restraints excluded: chain P residue 55 ASN 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 167 PHE Chi-restraints excluded: chain R residue 221 SER 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 57 TYR Chi-restraints excluded: chain V residue 150 LEU Chi-restraints excluded: chain V residue 153 TYR 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 291 GLN Chi-restraints excluded: chain V residue 300 ASN Chi-restraints excluded: chain V residue 301 MET Chi-restraints excluded: chain X residue 137 MET Chi-restraints excluded: chain X residue 177 TRP Chi-restraints excluded: chain X residue 268 ILE Chi-restraints excluded: chain X residue 322 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 51 optimal weight: 2.9990 chunk 125 optimal weight: 0.5980 chunk 128 optimal weight: 0.8980 chunk 139 optimal weight: 0.9990 chunk 44 optimal weight: 0.0980 chunk 56 optimal weight: 1.9990 chunk 79 optimal weight: 0.8980 chunk 126 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 218 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 ASN ** A 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 24 GLN E 48 GLN ** G 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 48 GLN ** J 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 55 ASN K 61 GLN N 26 GLN ** O 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 48 GLN ** 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** U 24 GLN ** U 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 300 ASN ** 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 = 0.3685 r_free = 0.3685 target = 0.088106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.076920 restraints weight = 64370.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.078884 restraints weight = 35861.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.080228 restraints weight = 22899.278| |-----------------------------------------------------------------------------| r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.6435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20052 Z= 0.127 Angle : 0.603 8.963 27243 Z= 0.306 Chirality : 0.039 0.199 3119 Planarity : 0.003 0.051 3524 Dihedral : 4.144 25.697 2693 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 3.99 % Allowed : 24.62 % Favored : 71.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.17), residues: 2487 helix: 1.68 (0.12), residues: 1929 sheet: -1.49 (0.79), residues: 50 loop : -1.46 (0.27), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP X 177 PHE 0.020 0.001 PHE H 79 TYR 0.021 0.002 TYR P 47 ARG 0.005 0.000 ARG H 58 Details of bonding type rmsd hydrogen bonds : bond 0.03590 ( 1524) hydrogen bonds : angle 3.71710 ( 4512) covalent geometry : bond 0.00282 (20052) covalent geometry : angle 0.60259 (27243) *********************** 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 610 residues out of total 2167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 524 time to evaluate : 2.917 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: A 16 PHE cc_start: 0.8460 (OUTLIER) cc_final: 0.7623 (t80) REVERT: A 66 LYS cc_start: 0.8907 (tmmt) cc_final: 0.8467 (tptp) REVERT: A 72 ASP cc_start: 0.8554 (OUTLIER) cc_final: 0.8252 (t0) REVERT: B 16 PHE cc_start: 0.7609 (OUTLIER) cc_final: 0.7113 (m-80) REVERT: B 63 ASN cc_start: 0.8811 (m-40) cc_final: 0.8552 (m-40) REVERT: C 33 LYS cc_start: 0.9127 (mmtm) cc_final: 0.8674 (mmtm) REVERT: C 34 LEU cc_start: 0.8614 (tp) cc_final: 0.8251 (tt) REVERT: C 66 LYS cc_start: 0.8814 (tptp) cc_final: 0.8116 (tppt) REVERT: C 70 ASP cc_start: 0.7639 (m-30) cc_final: 0.7052 (m-30) REVERT: D 66 LYS cc_start: 0.8532 (tmmt) cc_final: 0.7956 (tmmt) REVERT: D 69 LYS cc_start: 0.8924 (tptt) cc_final: 0.8566 (ttmt) REVERT: E 11 ASP cc_start: 0.8790 (OUTLIER) cc_final: 0.7919 (m-30) REVERT: E 34 LEU cc_start: 0.8225 (tt) cc_final: 0.7716 (tp) REVERT: E 53 GLU cc_start: 0.8357 (tm-30) cc_final: 0.7770 (tm-30) REVERT: E 63 ASN cc_start: 0.8243 (t0) cc_final: 0.7739 (t0) REVERT: E 76 ILE cc_start: 0.8825 (pt) cc_final: 0.8477 (mm) REVERT: E 77 GLN cc_start: 0.8636 (tp40) cc_final: 0.8313 (tp40) REVERT: F 141 ASN cc_start: 0.8467 (t0) cc_final: 0.8237 (m-40) REVERT: F 215 PHE cc_start: 0.7627 (t80) cc_final: 0.7414 (t80) REVERT: F 318 LEU cc_start: 0.7294 (OUTLIER) cc_final: 0.6793 (tt) REVERT: G 24 GLN cc_start: 0.8622 (mm-40) cc_final: 0.7930 (tp40) REVERT: G 69 LYS cc_start: 0.8709 (tmtt) cc_final: 0.8384 (tptm) REVERT: G 70 ASP cc_start: 0.8364 (m-30) cc_final: 0.8124 (m-30) REVERT: H 57 TYR cc_start: 0.8345 (OUTLIER) cc_final: 0.7721 (m-10) REVERT: I 17 ASP cc_start: 0.8022 (m-30) cc_final: 0.7370 (m-30) REVERT: I 29 GLU cc_start: 0.8523 (tt0) cc_final: 0.8254 (pt0) REVERT: J 57 TYR cc_start: 0.7481 (t80) cc_final: 0.6912 (t80) REVERT: J 59 ASN cc_start: 0.8575 (m110) cc_final: 0.8096 (m110) REVERT: J 66 LYS cc_start: 0.8577 (tptm) cc_final: 0.7057 (tppt) REVERT: J 69 LYS cc_start: 0.8986 (tmtt) cc_final: 0.8298 (tppt) REVERT: J 70 ASP cc_start: 0.7154 (m-30) cc_final: 0.6612 (m-30) REVERT: J 77 GLN cc_start: 0.7984 (pp30) cc_final: 0.7668 (tm-30) REVERT: K 10 ASP cc_start: 0.8141 (m-30) cc_final: 0.6713 (t0) REVERT: K 17 ASP cc_start: 0.7708 (m-30) cc_final: 0.7451 (m-30) REVERT: M 8 TYR cc_start: 0.7804 (t80) cc_final: 0.6393 (m-80) REVERT: M 21 ASP cc_start: 0.7923 (OUTLIER) cc_final: 0.7295 (p0) REVERT: M 23 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8422 (mp) REVERT: M 77 GLN cc_start: 0.8999 (tm-30) cc_final: 0.8658 (tm-30) REVERT: N 5 TRP cc_start: 0.4590 (t60) cc_final: 0.3841 (p90) REVERT: N 17 ASP cc_start: 0.8434 (m-30) cc_final: 0.7927 (m-30) REVERT: N 24 GLN cc_start: 0.7944 (pm20) cc_final: 0.7647 (tp-100) REVERT: N 26 GLN cc_start: 0.8980 (OUTLIER) cc_final: 0.8642 (mt0) REVERT: N 66 LYS cc_start: 0.8199 (tmtt) cc_final: 0.7884 (tmtt) REVERT: O 169 ASP cc_start: 0.7973 (t0) cc_final: 0.7451 (m-30) REVERT: O 261 LEU cc_start: 0.9375 (OUTLIER) cc_final: 0.9172 (mp) REVERT: O 294 PHE cc_start: 0.7251 (OUTLIER) cc_final: 0.5517 (t80) REVERT: O 316 ASN cc_start: 0.8578 (m-40) cc_final: 0.8267 (m-40) REVERT: O 322 LEU cc_start: 0.8883 (tp) cc_final: 0.8598 (tp) REVERT: O 340 PHE cc_start: 0.6436 (m-80) cc_final: 0.6136 (m-80) REVERT: P 21 ASP cc_start: 0.8561 (OUTLIER) cc_final: 0.7792 (p0) REVERT: P 29 GLU cc_start: 0.7400 (OUTLIER) cc_final: 0.7073 (mp0) REVERT: P 54 TYR cc_start: 0.8124 (t80) cc_final: 0.7745 (t80) REVERT: P 55 ASN cc_start: 0.8758 (OUTLIER) cc_final: 0.8544 (t0) REVERT: P 72 ASP cc_start: 0.8182 (m-30) cc_final: 0.7620 (m-30) REVERT: Q 16 PHE cc_start: 0.7663 (OUTLIER) cc_final: 0.7066 (t80) REVERT: Q 17 ASP cc_start: 0.7352 (t0) cc_final: 0.6780 (t0) REVERT: Q 31 LEU cc_start: 0.9487 (tp) cc_final: 0.9168 (tp) REVERT: Q 47 TYR cc_start: 0.8550 (t80) cc_final: 0.8282 (t80) REVERT: Q 57 TYR cc_start: 0.6852 (t80) cc_final: 0.6484 (t80) REVERT: Q 75 ILE cc_start: 0.7539 (tt) cc_final: 0.7282 (tp) REVERT: R 142 ILE cc_start: 0.8450 (tp) cc_final: 0.8241 (tp) REVERT: T 11 ASP cc_start: 0.7482 (m-30) cc_final: 0.7272 (m-30) REVERT: T 23 LEU cc_start: 0.8028 (mp) cc_final: 0.7716 (mt) REVERT: T 29 GLU cc_start: 0.8175 (tp30) cc_final: 0.7826 (tm-30) REVERT: U 15 LYS cc_start: 0.7758 (tptp) cc_final: 0.7096 (tmtt) REVERT: U 16 PHE cc_start: 0.8460 (OUTLIER) cc_final: 0.7809 (t80) REVERT: V 150 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8119 (mp) REVERT: V 300 ASN cc_start: 0.7947 (OUTLIER) cc_final: 0.7353 (t0) REVERT: X 161 THR cc_start: 0.7994 (m) cc_final: 0.7626 (p) REVERT: X 298 GLU cc_start: 0.8041 (tm-30) cc_final: 0.7642 (tp30) outliers start: 86 outliers final: 46 residues processed: 573 average time/residue: 0.3601 time to fit residues: 333.5936 Evaluate side-chains 554 residues out of total 2167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 490 time to evaluate : 3.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 PHE 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 C residue 79 PHE Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain E residue 11 ASP Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain F residue 259 THR Chi-restraints excluded: chain F residue 301 MET Chi-restraints excluded: chain F residue 309 THR Chi-restraints excluded: chain F residue 318 LEU Chi-restraints excluded: chain F residue 323 VAL Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 57 TYR Chi-restraints excluded: chain I residue 51 LEU Chi-restraints excluded: chain I residue 79 PHE Chi-restraints excluded: chain K residue 47 TYR Chi-restraints excluded: chain K residue 61 GLN Chi-restraints excluded: chain K residue 75 ILE Chi-restraints excluded: chain L residue 8 TYR Chi-restraints excluded: chain L residue 57 TYR Chi-restraints excluded: chain M residue 21 ASP Chi-restraints excluded: chain M residue 23 LEU Chi-restraints excluded: chain M residue 44 LEU Chi-restraints excluded: chain M residue 57 TYR Chi-restraints excluded: chain M residue 79 PHE Chi-restraints excluded: chain N residue 16 PHE Chi-restraints excluded: chain N residue 26 GLN Chi-restraints excluded: chain O residue 136 ASP Chi-restraints excluded: chain O residue 157 VAL Chi-restraints excluded: chain O residue 161 THR Chi-restraints excluded: chain O residue 261 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 21 ASP Chi-restraints excluded: chain P residue 29 GLU Chi-restraints excluded: chain P residue 55 ASN Chi-restraints excluded: chain P residue 77 GLN 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 167 PHE 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 57 TYR Chi-restraints excluded: chain U residue 79 PHE Chi-restraints excluded: chain U residue 80 ARG 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 V residue 301 MET Chi-restraints excluded: chain X residue 137 MET Chi-restraints excluded: chain X residue 177 TRP Chi-restraints excluded: chain X residue 268 ILE Chi-restraints excluded: chain X residue 322 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 148 optimal weight: 0.7980 chunk 18 optimal weight: 5.9990 chunk 6 optimal weight: 4.9990 chunk 133 optimal weight: 5.9990 chunk 119 optimal weight: 3.9990 chunk 70 optimal weight: 0.9980 chunk 153 optimal weight: 10.0000 chunk 100 optimal weight: 0.8980 chunk 177 optimal weight: 5.9990 chunk 233 optimal weight: 0.9990 chunk 226 optimal weight: 7.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 48 GLN ** H 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 61 GLN ** H 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 48 GLN ** J 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 59 ASN ** K 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 61 GLN N 26 GLN N 59 ASN O 291 GLN ** O 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 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 = 0.3633 r_free = 0.3633 target = 0.085480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.074422 restraints weight = 65751.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.076307 restraints weight = 36766.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.077622 restraints weight = 23473.334| |-----------------------------------------------------------------------------| r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.7207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 20052 Z= 0.165 Angle : 0.638 9.534 27243 Z= 0.331 Chirality : 0.042 0.184 3119 Planarity : 0.004 0.052 3524 Dihedral : 4.227 28.243 2693 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 4.87 % Allowed : 24.80 % Favored : 70.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.17), residues: 2487 helix: 1.60 (0.12), residues: 1931 sheet: -1.57 (0.77), residues: 50 loop : -1.56 (0.27), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP X 177 PHE 0.016 0.002 PHE H 79 TYR 0.025 0.002 TYR P 47 ARG 0.004 0.000 ARG H 58 Details of bonding type rmsd hydrogen bonds : bond 0.03839 ( 1524) hydrogen bonds : angle 3.82008 ( 4512) covalent geometry : bond 0.00373 (20052) covalent geometry : angle 0.63827 (27243) *********************** 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 623 residues out of total 2167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 518 time to evaluate : 2.421 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 16 PHE cc_start: 0.8575 (OUTLIER) cc_final: 0.7504 (t80) REVERT: A 47 TYR cc_start: 0.9345 (OUTLIER) cc_final: 0.9042 (t80) REVERT: A 66 LYS cc_start: 0.8917 (tmmt) cc_final: 0.8473 (tptp) REVERT: A 72 ASP cc_start: 0.8544 (OUTLIER) cc_final: 0.8227 (t0) REVERT: A 78 ASN cc_start: 0.7597 (m-40) cc_final: 0.7239 (m110) REVERT: B 16 PHE cc_start: 0.7797 (OUTLIER) cc_final: 0.7334 (m-80) REVERT: B 63 ASN cc_start: 0.9006 (m-40) cc_final: 0.8724 (m-40) REVERT: C 33 LYS cc_start: 0.9178 (mmtm) cc_final: 0.8693 (mmtm) REVERT: C 34 LEU cc_start: 0.8775 (tp) cc_final: 0.8416 (tt) REVERT: C 53 GLU cc_start: 0.8438 (mt-10) cc_final: 0.8050 (mm-30) REVERT: C 54 TYR cc_start: 0.9073 (t80) cc_final: 0.8752 (t80) REVERT: C 66 LYS cc_start: 0.8979 (tptp) cc_final: 0.8265 (tppt) REVERT: C 70 ASP cc_start: 0.7788 (m-30) cc_final: 0.7205 (m-30) REVERT: D 31 LEU cc_start: 0.9508 (tp) cc_final: 0.9275 (tp) REVERT: D 69 LYS cc_start: 0.8928 (tptt) cc_final: 0.8202 (tppp) REVERT: D 75 ILE cc_start: 0.9172 (mm) cc_final: 0.8900 (tp) REVERT: E 11 ASP cc_start: 0.8869 (OUTLIER) cc_final: 0.8040 (m-30) REVERT: E 53 GLU cc_start: 0.8412 (tm-30) cc_final: 0.7887 (tm-30) REVERT: E 63 ASN cc_start: 0.8398 (t0) cc_final: 0.7928 (t0) REVERT: E 77 GLN cc_start: 0.8740 (tp40) cc_final: 0.8501 (tp40) REVERT: F 198 LEU cc_start: 0.6016 (mm) cc_final: 0.5569 (mm) REVERT: F 215 PHE cc_start: 0.7696 (t80) cc_final: 0.7260 (t80) REVERT: F 318 LEU cc_start: 0.7633 (OUTLIER) cc_final: 0.7196 (tt) REVERT: G 24 GLN cc_start: 0.8719 (mm-40) cc_final: 0.7910 (tp40) REVERT: G 63 ASN cc_start: 0.8503 (t0) cc_final: 0.8154 (t0) REVERT: G 69 LYS cc_start: 0.8740 (tmtt) cc_final: 0.8399 (tptm) REVERT: G 70 ASP cc_start: 0.8565 (m-30) cc_final: 0.8039 (m-30) REVERT: H 57 TYR cc_start: 0.8521 (OUTLIER) cc_final: 0.8087 (m-10) REVERT: I 21 ASP cc_start: 0.6797 (p0) cc_final: 0.6519 (p0) REVERT: J 57 TYR cc_start: 0.7773 (t80) cc_final: 0.6906 (t80) REVERT: J 59 ASN cc_start: 0.8913 (m-40) cc_final: 0.8263 (m110) REVERT: J 66 LYS cc_start: 0.8721 (tptm) cc_final: 0.7087 (tppt) REVERT: J 69 LYS cc_start: 0.9162 (tmtt) cc_final: 0.8522 (tppt) REVERT: J 70 ASP cc_start: 0.7386 (m-30) cc_final: 0.6783 (m-30) REVERT: J 77 GLN cc_start: 0.8333 (pp30) cc_final: 0.8021 (tm-30) REVERT: K 10 ASP cc_start: 0.8264 (m-30) cc_final: 0.6863 (t0) REVERT: K 61 GLN cc_start: 0.9240 (OUTLIER) cc_final: 0.8982 (tp40) REVERT: L 16 PHE cc_start: 0.8052 (OUTLIER) cc_final: 0.7471 (m-10) REVERT: L 25 THR cc_start: 0.9073 (OUTLIER) cc_final: 0.8632 (p) REVERT: L 34 LEU cc_start: 0.9465 (tp) cc_final: 0.9219 (tt) REVERT: L 69 LYS cc_start: 0.9146 (tttt) cc_final: 0.8939 (ttmt) REVERT: M 8 TYR cc_start: 0.7879 (t80) cc_final: 0.6465 (m-80) REVERT: M 21 ASP cc_start: 0.8159 (OUTLIER) cc_final: 0.7459 (p0) REVERT: M 23 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8614 (mp) REVERT: M 77 GLN cc_start: 0.9158 (tm-30) cc_final: 0.8792 (tm-30) REVERT: N 5 TRP cc_start: 0.4730 (t60) cc_final: 0.3907 (p90) REVERT: N 17 ASP cc_start: 0.8179 (m-30) cc_final: 0.7923 (m-30) REVERT: N 43 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.7981 (tt) REVERT: N 66 LYS cc_start: 0.8231 (tmtt) cc_final: 0.7926 (tmtt) REVERT: O 294 PHE cc_start: 0.7058 (OUTLIER) cc_final: 0.5637 (t80) REVERT: O 316 ASN cc_start: 0.8670 (m-40) cc_final: 0.8396 (m-40) REVERT: O 340 PHE cc_start: 0.7015 (m-80) cc_final: 0.6771 (m-80) REVERT: P 21 ASP cc_start: 0.8768 (OUTLIER) cc_final: 0.8045 (p0) REVERT: P 48 GLN cc_start: 0.8610 (pp30) cc_final: 0.8131 (pp30) REVERT: P 66 LYS cc_start: 0.8572 (tptm) cc_final: 0.8068 (tptt) REVERT: Q 17 ASP cc_start: 0.7548 (t0) cc_final: 0.7214 (t0) REVERT: T 23 LEU cc_start: 0.8133 (mp) cc_final: 0.7865 (mt) REVERT: T 29 GLU cc_start: 0.8289 (tp30) cc_final: 0.7863 (tm-30) REVERT: T 31 LEU cc_start: 0.8638 (tp) cc_final: 0.8347 (tp) REVERT: U 15 LYS cc_start: 0.8009 (tptp) cc_final: 0.7386 (tmtt) REVERT: U 16 PHE cc_start: 0.8653 (OUTLIER) cc_final: 0.7877 (t80) REVERT: V 150 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8074 (mp) REVERT: V 300 ASN cc_start: 0.8442 (OUTLIER) cc_final: 0.7932 (t0) REVERT: V 314 ASN cc_start: 0.7889 (m-40) cc_final: 0.7278 (t0) REVERT: W 50 LYS cc_start: 0.8429 (mtpt) cc_final: 0.8008 (mtmt) REVERT: X 149 TYR cc_start: 0.8083 (t80) cc_final: 0.7739 (t80) REVERT: X 161 THR cc_start: 0.8429 (m) cc_final: 0.8146 (p) REVERT: X 298 GLU cc_start: 0.8071 (tm-30) cc_final: 0.7565 (tm-30) outliers start: 105 outliers final: 58 residues processed: 585 average time/residue: 0.2793 time to fit residues: 259.2308 Evaluate side-chains 554 residues out of total 2167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 478 time to evaluate : 2.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 PHE 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 C residue 51 LEU Chi-restraints excluded: chain C residue 79 PHE 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 56 LEU Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 238 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 20 VAL Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 27 VAL Chi-restraints excluded: chain H residue 57 TYR Chi-restraints excluded: chain I residue 51 LEU Chi-restraints excluded: chain I residue 79 PHE Chi-restraints excluded: chain K residue 47 TYR Chi-restraints excluded: chain K residue 61 GLN Chi-restraints excluded: chain K residue 62 SER Chi-restraints excluded: chain K residue 75 ILE 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 57 TYR Chi-restraints excluded: chain M residue 21 ASP Chi-restraints excluded: chain M residue 23 LEU Chi-restraints excluded: chain M residue 44 LEU Chi-restraints excluded: chain M residue 65 VAL Chi-restraints excluded: chain M residue 71 ILE Chi-restraints excluded: chain N residue 16 PHE Chi-restraints excluded: chain N residue 43 LEU Chi-restraints excluded: chain O residue 136 ASP Chi-restraints excluded: chain O residue 157 VAL Chi-restraints excluded: chain O residue 161 THR Chi-restraints excluded: chain O residue 294 PHE Chi-restraints excluded: chain O residue 303 THR Chi-restraints excluded: chain O residue 306 GLN Chi-restraints excluded: chain O residue 323 VAL Chi-restraints excluded: chain P residue 21 ASP Chi-restraints excluded: chain P residue 77 GLN 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 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 21 ASP Chi-restraints excluded: chain U residue 34 LEU 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 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 291 GLN Chi-restraints excluded: chain V residue 300 ASN Chi-restraints excluded: chain V residue 301 MET Chi-restraints excluded: chain W residue 79 PHE Chi-restraints excluded: chain X residue 137 MET Chi-restraints excluded: chain X residue 154 GLU Chi-restraints excluded: chain X residue 268 ILE Chi-restraints excluded: chain X residue 291 GLN Chi-restraints excluded: chain X residue 295 LYS Chi-restraints excluded: chain X residue 322 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 61 optimal weight: 0.6980 chunk 13 optimal weight: 0.7980 chunk 163 optimal weight: 8.9990 chunk 97 optimal weight: 0.6980 chunk 201 optimal weight: 0.6980 chunk 53 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 159 optimal weight: 7.9990 chunk 44 optimal weight: 0.0040 chunk 102 optimal weight: 1.9990 chunk 204 optimal weight: 10.0000 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 48 GLN F 233 GLN ** H 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 48 GLN ** J 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 55 ASN K 61 GLN O 288 GLN ** O 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 78 ASN ** V 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 300 ASN ** 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 = 0.3672 r_free = 0.3672 target = 0.087245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.076150 restraints weight = 63862.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.078073 restraints weight = 35456.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.079386 restraints weight = 22635.060| |-----------------------------------------------------------------------------| r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.7428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20052 Z= 0.131 Angle : 0.642 10.825 27243 Z= 0.326 Chirality : 0.041 0.190 3119 Planarity : 0.003 0.056 3524 Dihedral : 4.187 27.844 2693 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 3.89 % Allowed : 27.12 % Favored : 68.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.17), residues: 2487 helix: 1.62 (0.12), residues: 1931 sheet: -1.53 (0.77), residues: 50 loop : -1.53 (0.27), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP F 234 PHE 0.016 0.001 PHE R 215 TYR 0.029 0.002 TYR P 47 ARG 0.003 0.000 ARG H 58 Details of bonding type rmsd hydrogen bonds : bond 0.03645 ( 1524) hydrogen bonds : angle 3.80058 ( 4512) covalent geometry : bond 0.00289 (20052) covalent geometry : angle 0.64190 (27243) *********************** 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 606 residues out of total 2167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 522 time to evaluate : 4.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 PHE cc_start: 0.8504 (OUTLIER) cc_final: 0.7545 (t80) REVERT: A 66 LYS cc_start: 0.8858 (tmmt) cc_final: 0.8419 (tptp) REVERT: A 72 ASP cc_start: 0.8550 (OUTLIER) cc_final: 0.8338 (t0) REVERT: A 78 ASN cc_start: 0.7568 (m-40) cc_final: 0.7184 (m110) REVERT: B 16 PHE cc_start: 0.7727 (OUTLIER) cc_final: 0.7232 (m-80) REVERT: B 29 GLU cc_start: 0.8085 (mm-30) cc_final: 0.7576 (mt-10) REVERT: B 63 ASN cc_start: 0.8979 (m-40) cc_final: 0.8716 (m-40) REVERT: C 10 ASP cc_start: 0.7904 (t0) cc_final: 0.7562 (t0) REVERT: C 33 LYS cc_start: 0.8917 (mmtm) cc_final: 0.8552 (mmtm) REVERT: C 34 LEU cc_start: 0.8759 (tp) cc_final: 0.8382 (tt) REVERT: C 53 GLU cc_start: 0.8360 (mt-10) cc_final: 0.7957 (tt0) REVERT: C 54 TYR cc_start: 0.9030 (t80) cc_final: 0.8653 (t80) REVERT: C 66 LYS cc_start: 0.8895 (tptp) cc_final: 0.8185 (tppt) REVERT: C 70 ASP cc_start: 0.7734 (m-30) cc_final: 0.7211 (m-30) REVERT: D 31 LEU cc_start: 0.9468 (tp) cc_final: 0.9229 (tp) REVERT: D 69 LYS cc_start: 0.8958 (tptt) cc_final: 0.8642 (ttmt) REVERT: D 75 ILE cc_start: 0.9101 (mm) cc_final: 0.8853 (tp) REVERT: E 11 ASP cc_start: 0.8767 (OUTLIER) cc_final: 0.7903 (m-30) REVERT: E 53 GLU cc_start: 0.8381 (tm-30) cc_final: 0.7768 (tm-30) REVERT: E 76 ILE cc_start: 0.8878 (pt) cc_final: 0.8541 (mm) REVERT: E 77 GLN cc_start: 0.8677 (tp40) cc_final: 0.8358 (tp40) REVERT: F 198 LEU cc_start: 0.6020 (mm) cc_final: 0.5615 (mm) REVERT: F 264 MET cc_start: 0.8792 (tmm) cc_final: 0.8521 (mtp) REVERT: F 318 LEU cc_start: 0.7824 (OUTLIER) cc_final: 0.7401 (tt) REVERT: G 24 GLN cc_start: 0.8882 (mm-40) cc_final: 0.8219 (tp40) REVERT: G 63 ASN cc_start: 0.8293 (t0) cc_final: 0.7911 (t0) REVERT: G 69 LYS cc_start: 0.8809 (tmtt) cc_final: 0.8259 (tptm) REVERT: G 70 ASP cc_start: 0.8466 (m-30) cc_final: 0.7985 (m-30) REVERT: H 57 TYR cc_start: 0.8456 (OUTLIER) cc_final: 0.7990 (m-10) REVERT: I 11 ASP cc_start: 0.7652 (p0) cc_final: 0.7446 (p0) REVERT: I 75 ILE cc_start: 0.9126 (mm) cc_final: 0.8924 (mm) REVERT: J 29 GLU cc_start: 0.8657 (mt-10) cc_final: 0.8268 (mp0) REVERT: J 34 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8761 (mm) REVERT: J 57 TYR cc_start: 0.7607 (t80) cc_final: 0.7067 (t80) REVERT: J 59 ASN cc_start: 0.8848 (m-40) cc_final: 0.8156 (m110) REVERT: J 66 LYS cc_start: 0.8704 (tptm) cc_final: 0.7426 (tppt) REVERT: J 69 LYS cc_start: 0.9072 (tmtt) cc_final: 0.8375 (tppt) REVERT: J 70 ASP cc_start: 0.7497 (m-30) cc_final: 0.6707 (m-30) REVERT: K 10 ASP cc_start: 0.8379 (m-30) cc_final: 0.7089 (t0) REVERT: L 16 PHE cc_start: 0.8248 (OUTLIER) cc_final: 0.7546 (m-10) REVERT: L 17 ASP cc_start: 0.8278 (m-30) cc_final: 0.7939 (m-30) REVERT: L 25 THR cc_start: 0.9096 (m) cc_final: 0.8626 (p) REVERT: L 34 LEU cc_start: 0.9425 (tp) cc_final: 0.9152 (tt) REVERT: M 8 TYR cc_start: 0.7804 (t80) cc_final: 0.6469 (m-80) REVERT: M 21 ASP cc_start: 0.8125 (OUTLIER) cc_final: 0.7456 (p0) REVERT: M 65 VAL cc_start: 0.8805 (t) cc_final: 0.8504 (p) REVERT: M 66 LYS cc_start: 0.8651 (tppp) cc_final: 0.8195 (tppt) REVERT: M 77 GLN cc_start: 0.8974 (tm-30) cc_final: 0.8566 (tm-30) REVERT: N 5 TRP cc_start: 0.4749 (t60) cc_final: 0.3922 (p90) REVERT: N 9 LEU cc_start: 0.7560 (OUTLIER) cc_final: 0.7312 (mt) REVERT: N 17 ASP cc_start: 0.8173 (m-30) cc_final: 0.7949 (m-30) REVERT: N 24 GLN cc_start: 0.7862 (pm20) cc_final: 0.7608 (pp30) REVERT: N 66 LYS cc_start: 0.8054 (tmtt) cc_final: 0.7738 (tmtt) REVERT: O 153 TYR cc_start: 0.6010 (t80) cc_final: 0.5632 (t80) REVERT: O 169 ASP cc_start: 0.7082 (t70) cc_final: 0.6811 (m-30) REVERT: O 294 PHE cc_start: 0.7044 (OUTLIER) cc_final: 0.5916 (t80) REVERT: O 312 TYR cc_start: 0.5578 (m-10) cc_final: 0.5213 (m-10) REVERT: O 340 PHE cc_start: 0.6983 (m-80) cc_final: 0.6779 (m-80) REVERT: P 21 ASP cc_start: 0.8705 (OUTLIER) cc_final: 0.7974 (p0) REVERT: P 48 GLN cc_start: 0.8623 (pp30) cc_final: 0.8090 (pp30) REVERT: P 54 TYR cc_start: 0.8465 (t80) cc_final: 0.8032 (t80) REVERT: P 66 LYS cc_start: 0.8627 (tptm) cc_final: 0.8198 (tptt) REVERT: Q 37 LYS cc_start: 0.8362 (mmtm) cc_final: 0.8107 (mmtm) REVERT: R 142 ILE cc_start: 0.8515 (tp) cc_final: 0.8296 (tp) REVERT: R 160 TYR cc_start: 0.5153 (t80) cc_final: 0.4882 (t80) REVERT: R 264 MET cc_start: 0.5888 (tpp) cc_final: 0.5682 (tpp) REVERT: T 23 LEU cc_start: 0.8075 (mp) cc_final: 0.7796 (mt) REVERT: T 29 GLU cc_start: 0.8245 (tp30) cc_final: 0.7889 (tm-30) REVERT: T 31 LEU cc_start: 0.8645 (tp) cc_final: 0.8254 (tp) REVERT: U 15 LYS cc_start: 0.8017 (tptp) cc_final: 0.7378 (tmtt) REVERT: U 16 PHE cc_start: 0.8599 (OUTLIER) cc_final: 0.7826 (t80) REVERT: U 33 LYS cc_start: 0.8911 (ttpt) cc_final: 0.8606 (tttp) REVERT: V 150 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8235 (mp) REVERT: V 300 ASN cc_start: 0.8296 (OUTLIER) cc_final: 0.7439 (t0) REVERT: V 314 ASN cc_start: 0.7783 (m-40) cc_final: 0.7140 (t0) REVERT: W 50 LYS cc_start: 0.8473 (mtpt) cc_final: 0.8028 (mtmt) REVERT: X 161 THR cc_start: 0.8403 (m) cc_final: 0.8116 (p) REVERT: X 264 MET cc_start: 0.8444 (tpp) cc_final: 0.8172 (tpp) REVERT: X 298 GLU cc_start: 0.8068 (tm-30) cc_final: 0.7643 (tp30) outliers start: 84 outliers final: 50 residues processed: 572 average time/residue: 0.3790 time to fit residues: 351.9613 Evaluate side-chains 561 residues out of total 2167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 496 time to evaluate : 2.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 PHE Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 77 GLN Chi-restraints excluded: chain B residue 16 PHE 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 11 ASP Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain F residue 238 LEU 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 H residue 25 THR Chi-restraints excluded: chain H residue 57 TYR 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 47 TYR 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 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 9 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 161 THR Chi-restraints excluded: chain O residue 294 PHE Chi-restraints excluded: chain O residue 303 THR Chi-restraints excluded: chain O residue 306 GLN Chi-restraints excluded: chain O residue 323 VAL Chi-restraints excluded: chain P residue 21 ASP Chi-restraints excluded: chain P residue 77 GLN Chi-restraints excluded: chain Q residue 62 SER Chi-restraints excluded: chain R residue 167 PHE Chi-restraints excluded: chain R residue 221 SER Chi-restraints excluded: chain R residue 227 THR Chi-restraints excluded: chain R residue 323 VAL Chi-restraints excluded: chain S residue 16 PHE Chi-restraints excluded: chain S residue 79 PHE Chi-restraints excluded: chain T residue 75 ILE Chi-restraints excluded: chain U residue 12 VAL Chi-restraints excluded: chain U residue 16 PHE Chi-restraints excluded: chain U residue 21 ASP Chi-restraints excluded: chain U residue 43 LEU 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 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 300 ASN Chi-restraints excluded: chain W residue 79 PHE Chi-restraints excluded: chain X residue 177 TRP Chi-restraints excluded: chain X residue 268 ILE Chi-restraints excluded: chain X residue 322 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 162 optimal weight: 4.9990 chunk 139 optimal weight: 2.9990 chunk 24 optimal weight: 6.9990 chunk 64 optimal weight: 0.9980 chunk 126 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 151 optimal weight: 1.9990 chunk 179 optimal weight: 0.9980 chunk 84 optimal weight: 8.9990 chunk 102 optimal weight: 0.7980 chunk 228 optimal weight: 4.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 48 GLN ** H 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 59 ASN J 24 GLN ** J 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 61 GLN ** O 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 61 GLN ** 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 V 314 ASN ** X 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 316 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.085153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.074089 restraints weight = 65389.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.075954 restraints weight = 36485.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.077239 restraints weight = 23407.892| |-----------------------------------------------------------------------------| r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.8124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 20052 Z= 0.169 Angle : 0.671 10.938 27243 Z= 0.351 Chirality : 0.043 0.272 3119 Planarity : 0.004 0.056 3524 Dihedral : 4.323 31.152 2693 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 3.94 % Allowed : 27.58 % Favored : 68.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.17), residues: 2487 helix: 1.55 (0.12), residues: 1931 sheet: None (None), residues: 0 loop : -1.55 (0.25), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP F 234 PHE 0.024 0.002 PHE F 215 TYR 0.025 0.002 TYR S 47 ARG 0.005 0.001 ARG K 80 Details of bonding type rmsd hydrogen bonds : bond 0.03980 ( 1524) hydrogen bonds : angle 3.94019 ( 4512) covalent geometry : bond 0.00387 (20052) covalent geometry : angle 0.67071 (27243) *********************** 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 599 residues out of total 2167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 514 time to evaluate : 2.544 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: 0.8476 (OUTLIER) cc_final: 0.7362 (t80) REVERT: A 66 LYS cc_start: 0.8747 (tmmt) cc_final: 0.8458 (tptp) REVERT: A 72 ASP cc_start: 0.8528 (OUTLIER) cc_final: 0.8316 (t0) REVERT: B 16 PHE cc_start: 0.8084 (OUTLIER) cc_final: 0.7665 (m-80) REVERT: B 29 GLU cc_start: 0.8211 (mm-30) cc_final: 0.7875 (mt-10) REVERT: B 63 ASN cc_start: 0.9108 (m-40) cc_final: 0.8853 (m-40) REVERT: C 9 LEU cc_start: 0.8742 (mt) cc_final: 0.8488 (mt) REVERT: C 10 ASP cc_start: 0.8336 (t0) cc_final: 0.7790 (t0) REVERT: C 33 LYS cc_start: 0.8992 (mmtm) cc_final: 0.8591 (mmtm) REVERT: C 34 LEU cc_start: 0.8828 (tp) cc_final: 0.8398 (tt) REVERT: C 53 GLU cc_start: 0.8460 (mt-10) cc_final: 0.7887 (tt0) REVERT: C 54 TYR cc_start: 0.9059 (t80) cc_final: 0.8692 (t80) REVERT: C 66 LYS cc_start: 0.8927 (tptp) cc_final: 0.7954 (tppt) REVERT: C 70 ASP cc_start: 0.7684 (m-30) cc_final: 0.7170 (m-30) REVERT: D 31 LEU cc_start: 0.9481 (tp) cc_final: 0.9222 (tt) REVERT: D 44 LEU cc_start: 0.8668 (tt) cc_final: 0.8465 (tt) REVERT: D 69 LYS cc_start: 0.9027 (tptt) cc_final: 0.8731 (ttmt) REVERT: D 72 ASP cc_start: 0.8831 (m-30) cc_final: 0.8617 (m-30) REVERT: E 11 ASP cc_start: 0.8844 (OUTLIER) cc_final: 0.7909 (m-30) REVERT: E 34 LEU cc_start: 0.8554 (tt) cc_final: 0.8014 (tp) REVERT: E 53 GLU cc_start: 0.8567 (tm-30) cc_final: 0.7969 (tm-30) REVERT: E 63 ASN cc_start: 0.8503 (t0) cc_final: 0.8034 (t0) REVERT: F 198 LEU cc_start: 0.6161 (mm) cc_final: 0.5757 (mm) REVERT: F 215 PHE cc_start: 0.8105 (t80) cc_final: 0.7665 (t80) REVERT: F 318 LEU cc_start: 0.7947 (OUTLIER) cc_final: 0.7578 (tt) REVERT: G 24 GLN cc_start: 0.8951 (mm-40) cc_final: 0.8325 (tp40) REVERT: G 69 LYS cc_start: 0.8820 (tmtt) cc_final: 0.8308 (tptm) REVERT: G 70 ASP cc_start: 0.8479 (m-30) cc_final: 0.8025 (m-30) REVERT: H 57 TYR cc_start: 0.8466 (OUTLIER) cc_final: 0.8148 (m-10) REVERT: I 11 ASP cc_start: 0.7990 (p0) cc_final: 0.7719 (p0) REVERT: I 75 ILE cc_start: 0.9235 (mm) cc_final: 0.8963 (mm) REVERT: J 29 GLU cc_start: 0.8666 (mt-10) cc_final: 0.8340 (mp0) REVERT: J 34 LEU cc_start: 0.9159 (OUTLIER) cc_final: 0.8777 (mm) REVERT: J 57 TYR cc_start: 0.7869 (t80) cc_final: 0.7144 (t80) REVERT: J 59 ASN cc_start: 0.8911 (m-40) cc_final: 0.8341 (m110) REVERT: J 66 LYS cc_start: 0.8759 (tptm) cc_final: 0.7435 (tppt) REVERT: J 69 LYS cc_start: 0.9138 (tmtt) cc_final: 0.8467 (tppt) REVERT: J 70 ASP cc_start: 0.7624 (m-30) cc_final: 0.6864 (m-30) REVERT: K 10 ASP cc_start: 0.8318 (m-30) cc_final: 0.7322 (t0) REVERT: K 61 GLN cc_start: 0.9282 (OUTLIER) cc_final: 0.9066 (tp40) REVERT: L 16 PHE cc_start: 0.8238 (OUTLIER) cc_final: 0.7867 (m-10) REVERT: L 17 ASP cc_start: 0.8440 (m-30) cc_final: 0.8068 (m-30) REVERT: L 25 THR cc_start: 0.9353 (m) cc_final: 0.8931 (p) REVERT: L 34 LEU cc_start: 0.9466 (tp) cc_final: 0.9218 (tt) REVERT: M 8 TYR cc_start: 0.7909 (t80) cc_final: 0.6556 (m-80) REVERT: M 65 VAL cc_start: 0.8900 (t) cc_final: 0.8618 (p) REVERT: M 66 LYS cc_start: 0.8733 (tppp) cc_final: 0.8160 (tppt) REVERT: M 77 GLN cc_start: 0.9023 (tm-30) cc_final: 0.8556 (tm-30) REVERT: N 5 TRP cc_start: 0.4515 (t60) cc_final: 0.4012 (p90) REVERT: N 9 LEU cc_start: 0.8280 (OUTLIER) cc_final: 0.8019 (mt) REVERT: N 24 GLN cc_start: 0.7958 (pm20) cc_final: 0.7728 (pp30) REVERT: N 66 LYS cc_start: 0.8159 (tmtt) cc_final: 0.7913 (tmtt) REVERT: O 340 PHE cc_start: 0.7215 (m-80) cc_final: 0.6941 (m-80) REVERT: P 21 ASP cc_start: 0.8812 (OUTLIER) cc_final: 0.8217 (p0) REVERT: P 54 TYR cc_start: 0.8461 (t80) cc_final: 0.8174 (t80) REVERT: P 66 LYS cc_start: 0.8802 (tptm) cc_final: 0.8349 (tptt) REVERT: Q 37 LYS cc_start: 0.8662 (mmtm) cc_final: 0.8370 (mmtm) REVERT: R 160 TYR cc_start: 0.5238 (t80) cc_final: 0.4847 (t80) REVERT: R 264 MET cc_start: 0.6060 (tpp) cc_final: 0.5808 (tpp) REVERT: S 54 TYR cc_start: 0.9103 (t80) cc_final: 0.8831 (t80) REVERT: T 10 ASP cc_start: 0.8578 (m-30) cc_final: 0.8324 (m-30) REVERT: T 29 GLU cc_start: 0.8371 (tp30) cc_final: 0.7997 (tm-30) REVERT: U 15 LYS cc_start: 0.8073 (tptp) cc_final: 0.7404 (tmtt) REVERT: U 16 PHE cc_start: 0.8744 (OUTLIER) cc_final: 0.7930 (t80) REVERT: V 300 ASN cc_start: 0.8419 (OUTLIER) cc_final: 0.8036 (t0) REVERT: V 314 ASN cc_start: 0.8046 (m110) cc_final: 0.7312 (t0) REVERT: X 149 TYR cc_start: 0.7992 (t80) cc_final: 0.7742 (t80) REVERT: X 161 THR cc_start: 0.8553 (m) cc_final: 0.8287 (p) REVERT: X 264 MET cc_start: 0.8231 (tpp) cc_final: 0.8003 (tpp) REVERT: X 298 GLU cc_start: 0.8145 (tm-30) cc_final: 0.7631 (tm-30) REVERT: X 314 ASN cc_start: 0.8618 (m-40) cc_final: 0.8321 (m-40) outliers start: 85 outliers final: 56 residues processed: 567 average time/residue: 0.2841 time to fit residues: 254.2351 Evaluate side-chains 545 residues out of total 2167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 476 time to evaluate : 2.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 PHE Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 77 GLN 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 39 SER Chi-restraints excluded: chain E residue 11 ASP Chi-restraints excluded: chain E residue 48 GLN Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 238 LEU 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 H residue 18 THR Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 27 VAL Chi-restraints excluded: chain H residue 57 TYR 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 25 THR Chi-restraints excluded: chain K residue 43 LEU 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 57 TYR Chi-restraints excluded: chain M residue 44 LEU Chi-restraints excluded: chain N residue 9 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 161 THR Chi-restraints excluded: chain O residue 303 THR Chi-restraints excluded: chain O residue 306 GLN Chi-restraints excluded: chain O residue 323 VAL Chi-restraints excluded: chain P residue 21 ASP Chi-restraints excluded: chain P residue 77 GLN Chi-restraints excluded: chain Q residue 44 LEU Chi-restraints excluded: chain Q residue 62 SER Chi-restraints excluded: chain R residue 227 THR Chi-restraints excluded: chain R residue 309 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 21 ASP 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 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 300 ASN Chi-restraints excluded: chain W residue 79 PHE Chi-restraints excluded: chain X residue 150 LEU Chi-restraints excluded: chain X residue 157 VAL Chi-restraints excluded: chain X residue 268 ILE Chi-restraints excluded: chain X residue 295 LYS Chi-restraints excluded: chain X residue 322 LEU Chi-restraints excluded: chain X residue 334 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 112 optimal weight: 0.0970 chunk 141 optimal weight: 1.9990 chunk 7 optimal weight: 10.0000 chunk 226 optimal weight: 6.9990 chunk 187 optimal weight: 3.9990 chunk 236 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 171 optimal weight: 8.9990 chunk 155 optimal weight: 0.6980 chunk 183 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 61 GLN ** E 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 22 ASN U 63 ASN ** V 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 300 ASN V 314 ASN ** X 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 316 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.085097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.074123 restraints weight = 66622.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.076072 restraints weight = 36254.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.077409 restraints weight = 22681.328| |-----------------------------------------------------------------------------| r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.8445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 20052 Z= 0.156 Angle : 0.677 11.057 27243 Z= 0.354 Chirality : 0.042 0.253 3119 Planarity : 0.004 0.059 3524 Dihedral : 4.322 32.899 2693 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 3.76 % Allowed : 28.42 % Favored : 67.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.17), residues: 2487 helix: 1.52 (0.12), residues: 1936 sheet: None (None), residues: 0 loop : -1.52 (0.26), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP F 234 PHE 0.029 0.002 PHE F 215 TYR 0.040 0.002 TYR P 47 ARG 0.002 0.000 ARG H 58 Details of bonding type rmsd hydrogen bonds : bond 0.03912 ( 1524) hydrogen bonds : angle 3.97364 ( 4512) covalent geometry : bond 0.00354 (20052) covalent geometry : angle 0.67653 (27243) *********************** 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 585 residues out of total 2167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 504 time to evaluate : 3.171 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 16 PHE cc_start: 0.8591 (OUTLIER) cc_final: 0.7498 (t80) REVERT: A 66 LYS cc_start: 0.8747 (tmmt) cc_final: 0.8447 (tptp) REVERT: A 72 ASP cc_start: 0.8696 (OUTLIER) cc_final: 0.8392 (t0) REVERT: B 16 PHE cc_start: 0.8149 (OUTLIER) cc_final: 0.7713 (m-80) REVERT: B 63 ASN cc_start: 0.9173 (m-40) cc_final: 0.8859 (m-40) REVERT: C 9 LEU cc_start: 0.8824 (mt) cc_final: 0.8556 (mt) REVERT: C 10 ASP cc_start: 0.8337 (t0) cc_final: 0.7896 (t0) REVERT: C 18 THR cc_start: 0.8493 (m) cc_final: 0.8288 (t) REVERT: C 33 LYS cc_start: 0.9031 (mmtm) cc_final: 0.8579 (mmtm) REVERT: C 34 LEU cc_start: 0.9055 (tp) cc_final: 0.8775 (tt) REVERT: C 53 GLU cc_start: 0.8692 (mt-10) cc_final: 0.8404 (mm-30) REVERT: C 66 LYS cc_start: 0.9010 (tptp) cc_final: 0.8020 (tppt) REVERT: C 70 ASP cc_start: 0.7949 (m-30) cc_final: 0.7365 (m-30) REVERT: D 31 LEU cc_start: 0.9527 (tp) cc_final: 0.9323 (tt) REVERT: D 69 LYS cc_start: 0.9103 (tptt) cc_final: 0.8876 (ttmt) REVERT: D 72 ASP cc_start: 0.8836 (m-30) cc_final: 0.8534 (m-30) REVERT: E 11 ASP cc_start: 0.8751 (OUTLIER) cc_final: 0.7671 (m-30) REVERT: E 53 GLU cc_start: 0.8596 (tm-30) cc_final: 0.7987 (tm-30) REVERT: F 318 LEU cc_start: 0.8140 (OUTLIER) cc_final: 0.7795 (tt) REVERT: G 24 GLN cc_start: 0.8997 (mm-40) cc_final: 0.8268 (tp40) REVERT: G 69 LYS cc_start: 0.9004 (tmtt) cc_final: 0.8526 (tptm) REVERT: G 70 ASP cc_start: 0.8487 (m-30) cc_final: 0.8248 (m-30) REVERT: H 21 ASP cc_start: 0.7244 (m-30) cc_final: 0.6869 (m-30) REVERT: I 11 ASP cc_start: 0.8068 (p0) cc_final: 0.7778 (p0) REVERT: I 75 ILE cc_start: 0.9190 (mm) cc_final: 0.8925 (mm) REVERT: J 29 GLU cc_start: 0.8737 (mt-10) cc_final: 0.8314 (mp0) REVERT: J 34 LEU cc_start: 0.9043 (OUTLIER) cc_final: 0.8547 (mm) REVERT: J 59 ASN cc_start: 0.8928 (m-40) cc_final: 0.8185 (m110) REVERT: J 69 LYS cc_start: 0.9184 (tmtt) cc_final: 0.8880 (tptp) REVERT: K 10 ASP cc_start: 0.8479 (m-30) cc_final: 0.7380 (t0) REVERT: K 11 ASP cc_start: 0.8683 (t0) cc_final: 0.8445 (t0) REVERT: K 32 ASP cc_start: 0.7938 (OUTLIER) cc_final: 0.7222 (p0) REVERT: L 16 PHE cc_start: 0.8264 (OUTLIER) cc_final: 0.7881 (m-10) REVERT: L 17 ASP cc_start: 0.8578 (m-30) cc_final: 0.8222 (m-30) REVERT: L 25 THR cc_start: 0.9233 (m) cc_final: 0.8762 (p) REVERT: M 8 TYR cc_start: 0.7949 (t80) cc_final: 0.6593 (m-80) REVERT: M 65 VAL cc_start: 0.8884 (t) cc_final: 0.8619 (p) REVERT: M 66 LYS cc_start: 0.8718 (tppp) cc_final: 0.8241 (tppp) REVERT: M 77 GLN cc_start: 0.9086 (tm-30) cc_final: 0.8638 (tm-30) REVERT: N 5 TRP cc_start: 0.4540 (t60) cc_final: 0.4026 (p90) REVERT: N 24 GLN cc_start: 0.7847 (pm20) cc_final: 0.7577 (pp30) REVERT: N 66 LYS cc_start: 0.8186 (tmtt) cc_final: 0.7931 (tmtt) REVERT: O 169 ASP cc_start: 0.8175 (t0) cc_final: 0.7601 (m-30) REVERT: O 340 PHE cc_start: 0.7118 (m-80) cc_final: 0.6899 (m-80) REVERT: P 21 ASP cc_start: 0.8927 (OUTLIER) cc_final: 0.8313 (p0) REVERT: P 34 LEU cc_start: 0.9240 (OUTLIER) cc_final: 0.9016 (mm) REVERT: P 48 GLN cc_start: 0.8732 (pp30) cc_final: 0.8228 (pp30) REVERT: P 66 LYS cc_start: 0.8699 (tptm) cc_final: 0.8354 (tptm) REVERT: R 264 MET cc_start: 0.5636 (tpp) cc_final: 0.5405 (tpp) REVERT: S 54 TYR cc_start: 0.9095 (t80) cc_final: 0.8822 (t80) REVERT: T 29 GLU cc_start: 0.8461 (tp30) cc_final: 0.8132 (tm-30) REVERT: T 31 LEU cc_start: 0.8538 (tp) cc_final: 0.8272 (tp) REVERT: U 15 LYS cc_start: 0.8098 (tptp) cc_final: 0.7448 (tmtt) REVERT: U 16 PHE cc_start: 0.8837 (OUTLIER) cc_final: 0.8024 (t80) REVERT: V 150 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8192 (mp) REVERT: V 300 ASN cc_start: 0.8488 (OUTLIER) cc_final: 0.7894 (t0) REVERT: V 314 ASN cc_start: 0.7999 (m-40) cc_final: 0.7179 (t0) REVERT: V 340 PHE cc_start: 0.7305 (m-10) cc_final: 0.7002 (m-80) REVERT: X 161 THR cc_start: 0.8466 (m) cc_final: 0.8211 (p) REVERT: X 298 GLU cc_start: 0.8215 (tm-30) cc_final: 0.7662 (tm-30) outliers start: 81 outliers final: 55 residues processed: 558 average time/residue: 0.2801 time to fit residues: 247.4783 Evaluate side-chains 551 residues out of total 2167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 483 time to evaluate : 3.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 PHE Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 77 GLN Chi-restraints excluded: chain B residue 16 PHE Chi-restraints excluded: chain B residue 47 TYR Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 79 PHE Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain E residue 11 ASP Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 238 LEU Chi-restraints excluded: chain F residue 240 LEU 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 H residue 18 THR Chi-restraints excluded: chain H residue 25 THR 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 K residue 20 VAL Chi-restraints excluded: chain K residue 25 THR Chi-restraints excluded: chain K residue 32 ASP Chi-restraints excluded: chain L residue 8 TYR Chi-restraints excluded: chain L residue 16 PHE Chi-restraints excluded: chain L residue 57 TYR Chi-restraints excluded: chain M residue 44 LEU Chi-restraints excluded: chain N residue 16 PHE Chi-restraints excluded: chain N residue 57 TYR Chi-restraints excluded: chain O residue 136 ASP Chi-restraints excluded: chain O residue 157 VAL Chi-restraints excluded: chain O residue 161 THR Chi-restraints excluded: chain O residue 303 THR Chi-restraints excluded: chain O residue 306 GLN Chi-restraints excluded: chain O residue 323 VAL Chi-restraints excluded: chain P residue 21 ASP Chi-restraints excluded: chain P residue 34 LEU Chi-restraints excluded: chain P residue 77 GLN Chi-restraints excluded: chain Q residue 44 LEU Chi-restraints excluded: chain Q residue 62 SER 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 21 ASP 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 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 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 157 VAL Chi-restraints excluded: chain X residue 268 ILE Chi-restraints excluded: chain X residue 295 LYS Chi-restraints excluded: chain X residue 322 LEU Chi-restraints excluded: chain X residue 334 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 6 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 93 optimal weight: 0.9990 chunk 170 optimal weight: 3.9990 chunk 201 optimal weight: 0.5980 chunk 150 optimal weight: 1.9990 chunk 230 optimal weight: 0.7980 chunk 224 optimal weight: 5.9990 chunk 58 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 61 GLN E 48 GLN ** H 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 22 ASN U 63 ASN ** V 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 300 ASN ** X 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.086262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.075208 restraints weight = 66081.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.077122 restraints weight = 36449.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.078425 restraints weight = 23128.758| |-----------------------------------------------------------------------------| r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.8666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 20052 Z= 0.145 Angle : 0.685 11.891 27243 Z= 0.356 Chirality : 0.042 0.248 3119 Planarity : 0.004 0.055 3524 Dihedral : 4.312 37.490 2693 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 3.52 % Allowed : 29.16 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.17), residues: 2487 helix: 1.59 (0.12), residues: 1926 sheet: None (None), residues: 0 loop : -1.50 (0.25), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP F 234 PHE 0.048 0.001 PHE F 215 TYR 0.034 0.002 TYR P 47 ARG 0.004 0.000 ARG H 58 Details of bonding type rmsd hydrogen bonds : bond 0.03827 ( 1524) hydrogen bonds : angle 3.95638 ( 4512) covalent geometry : bond 0.00326 (20052) covalent geometry : angle 0.68478 (27243) ********************** 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 576 residues out of total 2167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 500 time to evaluate : 2.215 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: 0.8499 (OUTLIER) cc_final: 0.7420 (t80) REVERT: A 66 LYS cc_start: 0.8707 (tmmt) cc_final: 0.8436 (tptp) REVERT: A 72 ASP cc_start: 0.8628 (OUTLIER) cc_final: 0.8318 (t0) REVERT: B 16 PHE cc_start: 0.7970 (OUTLIER) cc_final: 0.7440 (m-80) REVERT: B 29 GLU cc_start: 0.8028 (mm-30) cc_final: 0.7706 (mm-30) REVERT: B 63 ASN cc_start: 0.9126 (m-40) cc_final: 0.8809 (m-40) REVERT: C 9 LEU cc_start: 0.8805 (mt) cc_final: 0.8566 (mt) REVERT: C 33 LYS cc_start: 0.9056 (mmtm) cc_final: 0.8588 (mmtm) REVERT: C 34 LEU cc_start: 0.9018 (tp) cc_final: 0.8752 (tt) REVERT: C 53 GLU cc_start: 0.8295 (mt-10) cc_final: 0.7751 (mm-30) REVERT: C 66 LYS cc_start: 0.8956 (tptp) cc_final: 0.7921 (tppt) REVERT: C 70 ASP cc_start: 0.7873 (m-30) cc_final: 0.7329 (m-30) REVERT: D 31 LEU cc_start: 0.9489 (tp) cc_final: 0.9267 (tt) REVERT: D 61 GLN cc_start: 0.8639 (OUTLIER) cc_final: 0.8344 (pp30) REVERT: D 68 PHE cc_start: 0.8754 (m-80) cc_final: 0.8402 (m-80) REVERT: D 72 ASP cc_start: 0.8373 (m-30) cc_final: 0.8082 (m-30) REVERT: E 11 ASP cc_start: 0.8793 (OUTLIER) cc_final: 0.7552 (m-30) REVERT: E 34 LEU cc_start: 0.8463 (tt) cc_final: 0.7983 (tp) REVERT: E 53 GLU cc_start: 0.8550 (tm-30) cc_final: 0.7919 (tm-30) REVERT: F 318 LEU cc_start: 0.8177 (OUTLIER) cc_final: 0.7848 (tt) REVERT: G 24 GLN cc_start: 0.8944 (mm-40) cc_final: 0.8252 (tp40) REVERT: G 63 ASN cc_start: 0.8580 (t0) cc_final: 0.8186 (t0) REVERT: G 69 LYS cc_start: 0.8977 (tmtt) cc_final: 0.8528 (tptm) REVERT: G 70 ASP cc_start: 0.8364 (m-30) cc_final: 0.8083 (m-30) REVERT: H 21 ASP cc_start: 0.7177 (m-30) cc_final: 0.6819 (m-30) REVERT: I 11 ASP cc_start: 0.7991 (p0) cc_final: 0.7704 (p0) REVERT: I 63 ASN cc_start: 0.9040 (t0) cc_final: 0.8479 (t0) REVERT: J 17 ASP cc_start: 0.8218 (m-30) cc_final: 0.7949 (m-30) REVERT: J 29 GLU cc_start: 0.8694 (mt-10) cc_final: 0.8282 (mp0) REVERT: J 34 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8619 (mm) REVERT: J 59 ASN cc_start: 0.8874 (m-40) cc_final: 0.8175 (m110) REVERT: J 69 LYS cc_start: 0.9102 (tmtt) cc_final: 0.8869 (tptp) REVERT: K 10 ASP cc_start: 0.8345 (m-30) cc_final: 0.7372 (t0) REVERT: K 11 ASP cc_start: 0.8595 (t0) cc_final: 0.8330 (t0) REVERT: K 32 ASP cc_start: 0.7857 (OUTLIER) cc_final: 0.7108 (p0) REVERT: K 80 ARG cc_start: 0.6942 (mtm110) cc_final: 0.6672 (mtm180) REVERT: L 16 PHE cc_start: 0.8181 (OUTLIER) cc_final: 0.7826 (m-10) REVERT: L 17 ASP cc_start: 0.8517 (m-30) cc_final: 0.8160 (m-30) REVERT: L 25 THR cc_start: 0.9240 (m) cc_final: 0.8762 (p) REVERT: L 34 LEU cc_start: 0.9468 (tp) cc_final: 0.9199 (tt) REVERT: M 8 TYR cc_start: 0.7929 (t80) cc_final: 0.6566 (m-80) REVERT: M 65 VAL cc_start: 0.8868 (t) cc_final: 0.8606 (p) REVERT: M 66 LYS cc_start: 0.8664 (tppp) cc_final: 0.8234 (tppp) REVERT: M 77 GLN cc_start: 0.9063 (tm-30) cc_final: 0.8601 (tm-30) REVERT: N 5 TRP cc_start: 0.4517 (t60) cc_final: 0.4032 (p90) REVERT: N 9 LEU cc_start: 0.8111 (OUTLIER) cc_final: 0.7832 (mt) REVERT: N 24 GLN cc_start: 0.7609 (pm20) cc_final: 0.7278 (pp30) REVERT: N 66 LYS cc_start: 0.8161 (tmtt) cc_final: 0.7941 (tmtt) REVERT: O 153 TYR cc_start: 0.5977 (t80) cc_final: 0.5705 (t80) REVERT: O 169 ASP cc_start: 0.8291 (t0) cc_final: 0.7805 (m-30) REVERT: O 294 PHE cc_start: 0.7417 (OUTLIER) cc_final: 0.6522 (t80) REVERT: P 21 ASP cc_start: 0.8830 (OUTLIER) cc_final: 0.8249 (p0) REVERT: P 66 LYS cc_start: 0.8722 (tptm) cc_final: 0.8359 (tptm) REVERT: Q 33 LYS cc_start: 0.8867 (mmpt) cc_final: 0.8635 (mmmt) REVERT: R 160 TYR cc_start: 0.5514 (t80) cc_final: 0.4786 (t80) REVERT: R 334 LEU cc_start: 0.8632 (mm) cc_final: 0.8251 (mm) REVERT: T 11 ASP cc_start: 0.8212 (m-30) cc_final: 0.7997 (p0) REVERT: T 29 GLU cc_start: 0.8446 (tp30) cc_final: 0.8163 (tm-30) REVERT: T 31 LEU cc_start: 0.8638 (tp) cc_final: 0.8372 (tp) REVERT: U 15 LYS cc_start: 0.8147 (tptp) cc_final: 0.7535 (tmtt) REVERT: U 16 PHE cc_start: 0.8783 (OUTLIER) cc_final: 0.7919 (t80) REVERT: V 150 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8193 (mp) REVERT: V 300 ASN cc_start: 0.8531 (OUTLIER) cc_final: 0.7820 (t0) REVERT: V 314 ASN cc_start: 0.7799 (m-40) cc_final: 0.7364 (t0) REVERT: V 340 PHE cc_start: 0.6684 (m-10) cc_final: 0.6426 (m-80) REVERT: W 29 GLU cc_start: 0.8706 (tm-30) cc_final: 0.8453 (tp30) REVERT: X 161 THR cc_start: 0.8486 (m) cc_final: 0.8237 (p) REVERT: X 298 GLU cc_start: 0.8175 (tm-30) cc_final: 0.7666 (tm-30) outliers start: 76 outliers final: 52 residues processed: 548 average time/residue: 0.3065 time to fit residues: 262.8070 Evaluate side-chains 549 residues out of total 2167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 482 time to evaluate : 2.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 PHE Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 77 GLN Chi-restraints excluded: chain B residue 16 PHE Chi-restraints excluded: chain B residue 47 TYR Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 79 PHE 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 56 LEU Chi-restraints excluded: chain F residue 238 LEU 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 H residue 25 THR Chi-restraints excluded: chain H residue 43 LEU 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 K residue 20 VAL Chi-restraints excluded: chain K residue 25 THR Chi-restraints excluded: chain K residue 32 ASP Chi-restraints excluded: chain L residue 8 TYR Chi-restraints excluded: chain L residue 16 PHE Chi-restraints excluded: chain L residue 57 TYR Chi-restraints excluded: chain M residue 44 LEU Chi-restraints excluded: chain N residue 9 LEU Chi-restraints excluded: chain N residue 16 PHE Chi-restraints excluded: chain N residue 57 TYR Chi-restraints excluded: chain O residue 136 ASP Chi-restraints excluded: chain O residue 157 VAL Chi-restraints excluded: chain O residue 161 THR Chi-restraints excluded: chain O residue 294 PHE Chi-restraints excluded: chain O residue 303 THR Chi-restraints excluded: chain O residue 306 GLN Chi-restraints excluded: chain O residue 323 VAL Chi-restraints excluded: chain P residue 21 ASP Chi-restraints excluded: chain P residue 77 GLN Chi-restraints excluded: chain Q residue 44 LEU Chi-restraints excluded: chain Q residue 62 SER Chi-restraints excluded: chain R residue 227 THR Chi-restraints excluded: chain R residue 323 VAL Chi-restraints excluded: chain S residue 16 PHE 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 57 TYR Chi-restraints excluded: chain U residue 79 PHE Chi-restraints excluded: chain U residue 80 ARG Chi-restraints excluded: chain V residue 150 LEU Chi-restraints excluded: chain V residue 157 VAL Chi-restraints excluded: chain V residue 170 ILE Chi-restraints excluded: chain V residue 237 GLU Chi-restraints excluded: chain V residue 264 MET Chi-restraints excluded: chain V residue 300 ASN Chi-restraints excluded: chain W residue 79 PHE Chi-restraints excluded: chain X residue 150 LEU Chi-restraints excluded: chain X residue 157 VAL Chi-restraints excluded: chain X residue 268 ILE Chi-restraints excluded: chain X residue 295 LYS Chi-restraints excluded: chain X residue 322 LEU Chi-restraints excluded: chain X residue 334 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 223 optimal weight: 1.9990 chunk 41 optimal weight: 5.9990 chunk 171 optimal weight: 5.9990 chunk 186 optimal weight: 0.7980 chunk 217 optimal weight: 2.9990 chunk 56 optimal weight: 0.0170 chunk 128 optimal weight: 0.8980 chunk 157 optimal weight: 1.9990 chunk 147 optimal weight: 2.9990 chunk 190 optimal weight: 0.7980 chunk 117 optimal weight: 9.9990 overall best weight: 0.9020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 61 GLN E 48 GLN ** H 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 61 GLN ** O 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 22 ASN U 63 ASN ** V 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.085776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.074951 restraints weight = 66353.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.076888 restraints weight = 36306.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.078198 restraints weight = 22869.440| |-----------------------------------------------------------------------------| r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.8670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.132 20052 Z= 0.191 Angle : 0.828 59.200 27243 Z= 0.463 Chirality : 0.043 0.535 3119 Planarity : 0.004 0.089 3524 Dihedral : 4.321 37.503 2693 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 15.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 3.66 % Allowed : 29.25 % Favored : 67.08 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.17), residues: 2487 helix: 1.57 (0.12), residues: 1926 sheet: None (None), residues: 0 loop : -1.50 (0.25), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP F 234 PHE 0.031 0.001 PHE X 215 TYR 0.028 0.002 TYR P 47 ARG 0.003 0.000 ARG H 58 Details of bonding type rmsd hydrogen bonds : bond 0.03893 ( 1524) hydrogen bonds : angle 3.96543 ( 4512) covalent geometry : bond 0.00422 (20052) covalent geometry : angle 0.82826 (27243) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7440.75 seconds wall clock time: 135 minutes 39.10 seconds (8139.10 seconds total)