Starting phenix.real_space_refine on Tue Aug 26 15:32:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8f39_28835/08_2025/8f39_28835.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f39_28835/08_2025/8f39_28835.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8f39_28835/08_2025/8f39_28835.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f39_28835/08_2025/8f39_28835.map" model { file = "/net/cci-nas-00/data/ceres_data/8f39_28835/08_2025/8f39_28835.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f39_28835/08_2025/8f39_28835.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 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: 6 Type Number sf(0) Gaussians P 10 5.49 5 Mg 4 5.21 5 S 100 5.16 5 C 24788 2.51 5 N 6540 2.21 5 O 7325 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 78 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 38767 Number of models: 1 Model: "" Number of chains: 32 Chain: "G" Number of atoms: 2032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2032 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 9, 'TRANS': 251} Chain breaks: 1 Chain: "Z" Number of atoms: 1232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1232 Classifications: {'peptide': 155} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 152} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "7" Number of atoms: 1363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1363 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 165} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "6" Number of atoms: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 710 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 8, 'TRANS': 80} Chain: "U" Number of atoms: 639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 639 Classifications: {'peptide': 85} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 7, 'TRANS': 77} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 12 Chain: "S" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 533 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 2, 'TRANS': 71} Chain: "T" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 533 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 2, 'TRANS': 71} Chain: "K" Number of atoms: 537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 537 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "L" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 533 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 2, 'TRANS': 71} Chain: "M" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 533 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 2, 'TRANS': 71} Chain: "N" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 533 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 2, 'TRANS': 71} Chain: "O" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 533 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 2, 'TRANS': 71} Chain: "P" Number of atoms: 537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 537 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "Q" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 533 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 2, 'TRANS': 71} Chain: "R" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 533 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 2, 'TRANS': 71} Chain: "8" Number of atoms: 356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 356 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 1, 'TRANS': 39} Chain: "X" Number of atoms: 1772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1772 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 7, 'TRANS': 216} Chain: "J" Number of atoms: 292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 292 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 3, 'TRANS': 33} Chain: "Y" Number of atoms: 1254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1254 Classifications: {'peptide': 166} Link IDs: {'PTRANS': 7, 'TRANS': 158} Chain: "A" Number of atoms: 3858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 3858 Classifications: {'peptide': 507} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 486} Chain: "B" Number of atoms: 3846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 506, 3846 Classifications: {'peptide': 506} Link IDs: {'PTRANS': 20, 'TRANS': 485} Chain: "C" Number of atoms: 3844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 505, 3844 Classifications: {'peptide': 505} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 484} Chain: "D" Number of atoms: 3572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 473, 3572 Classifications: {'peptide': 473} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 449} Chain: "E" Number of atoms: 3572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 473, 3572 Classifications: {'peptide': 473} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 449} Chain: "F" Number of atoms: 3566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 3566 Classifications: {'peptide': 472} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 448} Chain: "H" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 990 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 125} Chain: "I" Number of atoms: 392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 392 Classifications: {'peptide': 59} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 2, 'TRANS': 56} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ARG:plan': 1, 'GLN:plan1': 1, 'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 9.10, per 1000 atoms: 0.23 Number of scatterers: 38767 At special positions: 0 Unit cell: (130, 149, 237, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 100 16.00 P 10 15.00 Mg 4 11.99 O 7325 8.00 N 6540 7.00 C 24788 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 Atom "HETATM38737 O5' ADP E 501 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.57 Conformation dependent library (CDL) restraints added in 1.7 seconds Enol-peptide restraints added in 1.2 microseconds 10084 Ramachandran restraints generated. 5042 Oldfield, 0 Emsley, 5042 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9318 Finding SS restraints... Secondary structure from input PDB file: 205 helices and 30 sheets defined 59.0% alpha, 8.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain 'G' and resid 5 through 55 removed outlier: 5.250A pdb=" N LYS G 36 " --> pdb=" O SER G 32 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N ALA G 37 " --> pdb=" O LYS G 33 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N SER G 40 " --> pdb=" O LYS G 36 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N PHE G 51 " --> pdb=" O ALA G 47 " (cutoff:3.500A) Processing helix chain 'G' and resid 86 through 102 removed outlier: 3.540A pdb=" N GLN G 90 " --> pdb=" O SER G 86 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LEU G 91 " --> pdb=" O ILE G 87 " (cutoff:3.500A) Processing helix chain 'G' and resid 112 through 119 Processing helix chain 'G' and resid 122 through 126 removed outlier: 4.087A pdb=" N ASN G 125 " --> pdb=" O HIS G 122 " (cutoff:3.500A) Processing helix chain 'G' and resid 139 through 153 removed outlier: 4.031A pdb=" N SER G 143 " --> pdb=" O THR G 139 " (cutoff:3.500A) Processing helix chain 'G' and resid 155 through 159 removed outlier: 3.622A pdb=" N TYR G 159 " --> pdb=" O ALA G 156 " (cutoff:3.500A) Processing helix chain 'G' and resid 184 through 189 Processing helix chain 'G' and resid 204 through 274 Processing helix chain 'Z' and resid 55 through 111 removed outlier: 3.516A pdb=" N LEU Z 59 " --> pdb=" O GLU Z 55 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU Z 63 " --> pdb=" O LEU Z 59 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLY Z 64 " --> pdb=" O LEU Z 60 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ALA Z 74 " --> pdb=" O ALA Z 70 " (cutoff:3.500A) Proline residue: Z 75 - end of helix removed outlier: 3.566A pdb=" N ARG Z 84 " --> pdb=" O PHE Z 80 " (cutoff:3.500A) Processing helix chain 'Z' and resid 112 through 114 No H-bonds generated for 'chain 'Z' and resid 112 through 114' Processing helix chain 'Z' and resid 115 through 133 removed outlier: 3.729A pdb=" N THR Z 119 " --> pdb=" O ASN Z 115 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N VAL Z 122 " --> pdb=" O GLU Z 118 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS Z 128 " --> pdb=" O PHE Z 124 " (cutoff:3.500A) Processing helix chain 'Z' and resid 134 through 186 removed outlier: 3.737A pdb=" N GLN Z 142 " --> pdb=" O PHE Z 138 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LYS Z 143 " --> pdb=" O GLU Z 139 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ILE Z 177 " --> pdb=" O ALA Z 173 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N SER Z 178 " --> pdb=" O LYS Z 174 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU Z 183 " --> pdb=" O ARG Z 179 " (cutoff:3.500A) Processing helix chain 'Z' and resid 190 through 207 removed outlier: 3.683A pdb=" N SER Z 206 " --> pdb=" O GLU Z 202 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LYS Z 207 " --> pdb=" O GLN Z 203 " (cutoff:3.500A) Processing helix chain '7' and resid 4 through 18 Processing helix chain '7' and resid 26 through 48 Processing helix chain '7' and resid 67 through 78 Processing helix chain '7' and resid 90 through 127 removed outlier: 3.979A pdb=" N SER 7 126 " --> pdb=" O ASP 7 122 " (cutoff:3.500A) Processing helix chain '7' and resid 134 through 142 Processing helix chain '7' and resid 142 through 156 removed outlier: 4.094A pdb=" N ASP 7 146 " --> pdb=" O LYS 7 142 " (cutoff:3.500A) Processing helix chain '6' and resid 5 through 17 removed outlier: 3.768A pdb=" N ARG 6 9 " --> pdb=" O ASP 6 5 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N GLU 6 10 " --> pdb=" O LEU 6 6 " (cutoff:3.500A) Processing helix chain '6' and resid 45 through 51 Processing helix chain '6' and resid 75 through 90 removed outlier: 3.768A pdb=" N GLU 6 90 " --> pdb=" O GLU 6 86 " (cutoff:3.500A) Processing helix chain 'U' and resid 17 through 28 removed outlier: 4.029A pdb=" N ALA U 21 " --> pdb=" O SER U 17 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LYS U 22 " --> pdb=" O ALA U 18 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ILE U 24 " --> pdb=" O ASN U 20 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N VAL U 28 " --> pdb=" O ILE U 24 " (cutoff:3.500A) Processing helix chain 'U' and resid 48 through 55 Processing helix chain 'U' and resid 63 through 85 removed outlier: 4.195A pdb=" N SER U 79 " --> pdb=" O ALA U 75 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N MET U 80 " --> pdb=" O PHE U 76 " (cutoff:3.500A) Processing helix chain 'S' and resid 2 through 16 Processing helix chain 'S' and resid 17 through 40 removed outlier: 4.238A pdb=" N GLY S 21 " --> pdb=" O ILE S 17 " (cutoff:3.500A) Processing helix chain 'S' and resid 43 through 74 Proline residue: S 49 - end of helix removed outlier: 3.725A pdb=" N GLY S 62 " --> pdb=" O SER S 58 " (cutoff:3.500A) Processing helix chain 'T' and resid 2 through 17 removed outlier: 3.627A pdb=" N ILE T 17 " --> pdb=" O GLY T 13 " (cutoff:3.500A) Processing helix chain 'T' and resid 18 through 40 removed outlier: 3.969A pdb=" N ALA T 22 " --> pdb=" O GLY T 18 " (cutoff:3.500A) Processing helix chain 'T' and resid 43 through 74 Proline residue: T 49 - end of helix Processing helix chain 'K' and resid 2 through 16 Processing helix chain 'K' and resid 17 through 40 removed outlier: 4.255A pdb=" N GLY K 21 " --> pdb=" O ILE K 17 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ALA K 22 " --> pdb=" O GLY K 18 " (cutoff:3.500A) Processing helix chain 'K' and resid 43 through 75 Proline residue: K 49 - end of helix removed outlier: 3.851A pdb=" N CYS K 65 " --> pdb=" O THR K 61 " (cutoff:3.500A) Processing helix chain 'L' and resid 2 through 15 Processing helix chain 'L' and resid 17 through 40 removed outlier: 4.185A pdb=" N GLY L 21 " --> pdb=" O ILE L 17 " (cutoff:3.500A) Processing helix chain 'L' and resid 43 through 74 Proline residue: L 49 - end of helix removed outlier: 4.112A pdb=" N THR L 61 " --> pdb=" O LEU L 57 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLY L 62 " --> pdb=" O SER L 58 " (cutoff:3.500A) Processing helix chain 'M' and resid 2 through 16 Processing helix chain 'M' and resid 18 through 40 removed outlier: 3.724A pdb=" N ALA M 22 " --> pdb=" O GLY M 18 " (cutoff:3.500A) Processing helix chain 'M' and resid 43 through 74 Proline residue: M 49 - end of helix removed outlier: 3.946A pdb=" N THR M 61 " --> pdb=" O LEU M 57 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLY M 62 " --> pdb=" O SER M 58 " (cutoff:3.500A) Processing helix chain 'N' and resid 2 through 16 Processing helix chain 'N' and resid 17 through 40 removed outlier: 4.110A pdb=" N GLY N 21 " --> pdb=" O ILE N 17 " (cutoff:3.500A) Processing helix chain 'N' and resid 42 through 72 removed outlier: 4.474A pdb=" N THR N 46 " --> pdb=" O SER N 42 " (cutoff:3.500A) Proline residue: N 49 - end of helix removed outlier: 3.711A pdb=" N THR N 61 " --> pdb=" O LEU N 57 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLY N 62 " --> pdb=" O SER N 58 " (cutoff:3.500A) Processing helix chain 'O' and resid 2 through 15 Processing helix chain 'O' and resid 18 through 40 removed outlier: 3.654A pdb=" N ALA O 22 " --> pdb=" O GLY O 18 " (cutoff:3.500A) Processing helix chain 'O' and resid 43 through 72 Proline residue: O 49 - end of helix removed outlier: 3.622A pdb=" N CYS O 65 " --> pdb=" O THR O 61 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 16 Processing helix chain 'P' and resid 17 through 40 removed outlier: 3.857A pdb=" N GLY P 21 " --> pdb=" O ILE P 17 " (cutoff:3.500A) Processing helix chain 'P' and resid 43 through 75 Proline residue: P 49 - end of helix Processing helix chain 'Q' and resid 2 through 17 Processing helix chain 'Q' and resid 18 through 40 removed outlier: 3.823A pdb=" N ALA Q 22 " --> pdb=" O GLY Q 18 " (cutoff:3.500A) Processing helix chain 'Q' and resid 43 through 72 Proline residue: Q 49 - end of helix removed outlier: 3.670A pdb=" N LEU Q 72 " --> pdb=" O VAL Q 68 " (cutoff:3.500A) Processing helix chain 'R' and resid 2 through 16 removed outlier: 3.615A pdb=" N THR R 16 " --> pdb=" O ALA R 12 " (cutoff:3.500A) Processing helix chain 'R' and resid 18 through 40 removed outlier: 3.685A pdb=" N ALA R 22 " --> pdb=" O GLY R 18 " (cutoff:3.500A) Processing helix chain 'R' and resid 43 through 74 Proline residue: R 49 - end of helix Processing helix chain '8' and resid 12 through 47 removed outlier: 4.995A pdb=" N LEU 8 32 " --> pdb=" O SER 8 28 " (cutoff:3.500A) Proline residue: 8 33 - end of helix Processing helix chain 'X' and resid 27 through 46 removed outlier: 3.748A pdb=" N TYR X 44 " --> pdb=" O ILE X 40 " (cutoff:3.500A) Processing helix chain 'X' and resid 56 through 78 Processing helix chain 'X' and resid 81 through 102 removed outlier: 3.774A pdb=" N TYR X 85 " --> pdb=" O ASN X 81 " (cutoff:3.500A) Proline residue: X 87 - end of helix Processing helix chain 'X' and resid 110 through 114 removed outlier: 4.034A pdb=" N HIS X 114 " --> pdb=" O LEU X 111 " (cutoff:3.500A) Processing helix chain 'X' and resid 115 through 137 removed outlier: 3.834A pdb=" N ILE X 119 " --> pdb=" O LEU X 115 " (cutoff:3.500A) Processing helix chain 'X' and resid 138 through 146 Processing helix chain 'X' and resid 151 through 153 No H-bonds generated for 'chain 'X' and resid 151 through 153' Processing helix chain 'X' and resid 154 through 173 removed outlier: 3.645A pdb=" N ILE X 171 " --> pdb=" O PHE X 167 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N LEU X 173 " --> pdb=" O ARG X 169 " (cutoff:3.500A) Processing helix chain 'X' and resid 173 through 195 removed outlier: 5.799A pdb=" N SER X 179 " --> pdb=" O LEU X 175 " (cutoff:3.500A) Processing helix chain 'X' and resid 206 through 247 Proline residue: X 212 - end of helix Processing helix chain 'J' and resid 13 through 32 removed outlier: 4.391A pdb=" N ASP J 32 " --> pdb=" O SER J 28 " (cutoff:3.500A) Processing helix chain 'Y' and resid 17 through 31 removed outlier: 3.533A pdb=" N THR Y 21 " --> pdb=" O GLY Y 17 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ASN Y 30 " --> pdb=" O ALA Y 26 " (cutoff:3.500A) Processing helix chain 'Y' and resid 34 through 50 removed outlier: 3.604A pdb=" N ASN Y 50 " --> pdb=" O THR Y 46 " (cutoff:3.500A) Processing helix chain 'Y' and resid 50 through 55 Processing helix chain 'Y' and resid 63 through 75 removed outlier: 3.512A pdb=" N VAL Y 75 " --> pdb=" O ILE Y 71 " (cutoff:3.500A) Processing helix chain 'Y' and resid 84 through 94 removed outlier: 3.668A pdb=" N GLU Y 94 " --> pdb=" O LYS Y 90 " (cutoff:3.500A) Processing helix chain 'Y' and resid 100 through 115 Processing helix chain 'Y' and resid 137 through 149 removed outlier: 3.657A pdb=" N LEU Y 141 " --> pdb=" O ILE Y 137 " (cutoff:3.500A) Processing helix chain 'Y' and resid 159 through 172 removed outlier: 3.737A pdb=" N ILE Y 163 " --> pdb=" O VAL Y 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 5 through 15 Processing helix chain 'A' and resid 18 through 22 removed outlier: 3.652A pdb=" N VAL A 21 " --> pdb=" O ILE A 18 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N SER A 22 " --> pdb=" O LYS A 19 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 18 through 22' Processing helix chain 'A' and resid 24 through 28 removed outlier: 4.439A pdb=" N LEU A 27 " --> pdb=" O GLU A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 84 removed outlier: 3.630A pdb=" N LEU A 83 " --> pdb=" O SER A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 106 removed outlier: 3.746A pdb=" N LEU A 105 " --> pdb=" O GLY A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 157 Processing helix chain 'A' and resid 177 through 188 removed outlier: 3.509A pdb=" N ALA A 181 " --> pdb=" O LYS A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 193 Processing helix chain 'A' and resid 211 through 225 Processing helix chain 'A' and resid 241 through 262 Proline residue: A 249 - end of helix removed outlier: 3.691A pdb=" N PHE A 259 " --> pdb=" O ILE A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 287 Processing helix chain 'A' and resid 292 through 296 removed outlier: 4.284A pdb=" N ALA A 295 " --> pdb=" O GLY A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 309 Processing helix chain 'A' and resid 315 through 319 Processing helix chain 'A' and resid 338 through 348 Processing helix chain 'A' and resid 355 through 362 Processing helix chain 'A' and resid 376 through 381 removed outlier: 3.594A pdb=" N ALA A 380 " --> pdb=" O VAL A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 390 Processing helix chain 'A' and resid 391 through 403 Processing helix chain 'A' and resid 404 through 406 No H-bonds generated for 'chain 'A' and resid 404 through 406' Processing helix chain 'A' and resid 413 through 431 removed outlier: 4.338A pdb=" N ARG A 425 " --> pdb=" O VAL A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 453 Proline residue: A 445 - end of helix Processing helix chain 'A' and resid 459 through 461 No H-bonds generated for 'chain 'A' and resid 459 through 461' Processing helix chain 'A' and resid 462 through 477 Processing helix chain 'A' and resid 478 through 489 removed outlier: 4.377A pdb=" N LEU A 482 " --> pdb=" O HIS A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 508 Processing helix chain 'B' and resid 5 through 24 Processing helix chain 'B' and resid 102 through 106 removed outlier: 3.697A pdb=" N LEU B 105 " --> pdb=" O GLY B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 159 Processing helix chain 'B' and resid 176 through 188 removed outlier: 3.996A pdb=" N GLN B 188 " --> pdb=" O THR B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 193 Processing helix chain 'B' and resid 211 through 225 Processing helix chain 'B' and resid 241 through 262 Proline residue: B 249 - end of helix removed outlier: 3.546A pdb=" N PHE B 259 " --> pdb=" O ILE B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 287 Processing helix chain 'B' and resid 297 through 299 No H-bonds generated for 'chain 'B' and resid 297 through 299' Processing helix chain 'B' and resid 300 through 310 removed outlier: 3.899A pdb=" N ARG B 310 " --> pdb=" O ARG B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 319 Processing helix chain 'B' and resid 338 through 348 Processing helix chain 'B' and resid 355 through 362 Processing helix chain 'B' and resid 382 through 387 removed outlier: 4.353A pdb=" N GLN B 387 " --> pdb=" O LYS B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 405 Processing helix chain 'B' and resid 413 through 430 Processing helix chain 'B' and resid 439 through 450 Proline residue: B 445 - end of helix Processing helix chain 'B' and resid 462 through 476 removed outlier: 3.687A pdb=" N SER B 468 " --> pdb=" O GLY B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 488 Processing helix chain 'B' and resid 492 through 509 Processing helix chain 'C' and resid 80 through 84 removed outlier: 3.703A pdb=" N LEU C 83 " --> pdb=" O SER C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 106 removed outlier: 3.681A pdb=" N LEU C 105 " --> pdb=" O GLY C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 159 Processing helix chain 'C' and resid 176 through 188 Processing helix chain 'C' and resid 188 through 193 Processing helix chain 'C' and resid 211 through 225 Processing helix chain 'C' and resid 227 through 229 No H-bonds generated for 'chain 'C' and resid 227 through 229' Processing helix chain 'C' and resid 241 through 262 Proline residue: C 249 - end of helix removed outlier: 3.695A pdb=" N PHE C 259 " --> pdb=" O ILE C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 287 Processing helix chain 'C' and resid 292 through 296 Processing helix chain 'C' and resid 299 through 310 removed outlier: 3.811A pdb=" N ARG C 310 " --> pdb=" O ARG C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 319 Processing helix chain 'C' and resid 338 through 348 Processing helix chain 'C' and resid 355 through 361 Processing helix chain 'C' and resid 376 through 381 removed outlier: 3.682A pdb=" N ALA C 379 " --> pdb=" O VAL C 376 " (cutoff:3.500A) Processing helix chain 'C' and resid 382 through 403 removed outlier: 3.987A pdb=" N GLY C 390 " --> pdb=" O LYS C 386 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N SER C 391 " --> pdb=" O GLN C 387 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU C 392 " --> pdb=" O VAL C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 408 removed outlier: 3.734A pdb=" N GLN C 407 " --> pdb=" O ALA C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 431 removed outlier: 3.527A pdb=" N LYS C 417 " --> pdb=" O ASP C 413 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 452 Proline residue: C 445 - end of helix Processing helix chain 'C' and resid 459 through 461 No H-bonds generated for 'chain 'C' and resid 459 through 461' Processing helix chain 'C' and resid 462 through 477 Processing helix chain 'C' and resid 478 through 489 Processing helix chain 'C' and resid 492 through 509 removed outlier: 3.706A pdb=" N THR C 509 " --> pdb=" O SER C 505 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 92 Processing helix chain 'D' and resid 140 through 145 removed outlier: 3.916A pdb=" N LEU D 144 " --> pdb=" O VAL D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 162 through 178 Processing helix chain 'D' and resid 192 through 204 Processing helix chain 'D' and resid 227 through 248 removed outlier: 4.359A pdb=" N ALA D 233 " --> pdb=" O ARG D 229 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N LEU D 234 " --> pdb=" O ALA D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 270 Processing helix chain 'D' and resid 284 through 295 removed outlier: 4.084A pdb=" N ARG D 295 " --> pdb=" O LEU D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 312 through 316 Processing helix chain 'D' and resid 319 through 327 Processing helix chain 'D' and resid 364 through 391 removed outlier: 4.518A pdb=" N ASP D 386 " --> pdb=" O LYS D 382 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N ILE D 387 " --> pdb=" O SER D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 397 through 415 removed outlier: 4.059A pdb=" N SER D 415 " --> pdb=" O GLN D 411 " (cutoff:3.500A) Processing helix chain 'D' and resid 418 through 420 No H-bonds generated for 'chain 'D' and resid 418 through 420' Processing helix chain 'D' and resid 421 through 426 Processing helix chain 'D' and resid 433 through 446 Processing helix chain 'D' and resid 453 through 458 Processing helix chain 'D' and resid 462 through 478 Processing helix chain 'E' and resid 138 through 144 Processing helix chain 'E' and resid 162 through 175 Processing helix chain 'E' and resid 176 through 178 No H-bonds generated for 'chain 'E' and resid 176 through 178' Processing helix chain 'E' and resid 190 through 204 Processing helix chain 'E' and resid 225 through 246 removed outlier: 4.593A pdb=" N ALA E 233 " --> pdb=" O ARG E 229 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N LEU E 234 " --> pdb=" O ALA E 230 " (cutoff:3.500A) Processing helix chain 'E' and resid 258 through 272 removed outlier: 4.014A pdb=" N THR E 262 " --> pdb=" O ILE E 258 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU E 271 " --> pdb=" O GLU E 267 " (cutoff:3.500A) Processing helix chain 'E' and resid 277 through 281 Processing helix chain 'E' and resid 282 through 283 No H-bonds generated for 'chain 'E' and resid 282 through 283' Processing helix chain 'E' and resid 284 through 295 removed outlier: 3.764A pdb=" N ARG E 295 " --> pdb=" O LEU E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 313 through 316 Processing helix chain 'E' and resid 319 through 328 removed outlier: 4.321A pdb=" N ALA E 327 " --> pdb=" O ALA E 323 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N HIS E 328 " --> pdb=" O THR E 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 336 through 343 removed outlier: 3.592A pdb=" N LEU E 342 " --> pdb=" O GLY E 338 " (cutoff:3.500A) Processing helix chain 'E' and resid 359 through 364 Processing helix chain 'E' and resid 366 through 391 removed outlier: 4.642A pdb=" N ASP E 386 " --> pdb=" O LYS E 382 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N ILE E 387 " --> pdb=" O SER E 383 " (cutoff:3.500A) Processing helix chain 'E' and resid 397 through 414 Processing helix chain 'E' and resid 418 through 420 No H-bonds generated for 'chain 'E' and resid 418 through 420' Processing helix chain 'E' and resid 421 through 426 Processing helix chain 'E' and resid 433 through 446 Processing helix chain 'E' and resid 453 through 458 Processing helix chain 'E' and resid 462 through 476 Processing helix chain 'F' and resid 88 through 92 Processing helix chain 'F' and resid 138 through 144 Processing helix chain 'F' and resid 162 through 178 removed outlier: 4.302A pdb=" N LYS F 176 " --> pdb=" O ASN F 172 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ALA F 177 " --> pdb=" O ASN F 173 " (cutoff:3.500A) Processing helix chain 'F' and resid 190 through 205 Processing helix chain 'F' and resid 225 through 246 removed outlier: 4.491A pdb=" N ALA F 233 " --> pdb=" O ARG F 229 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N LEU F 234 " --> pdb=" O ALA F 230 " (cutoff:3.500A) Processing helix chain 'F' and resid 258 through 272 removed outlier: 4.147A pdb=" N THR F 262 " --> pdb=" O ILE F 258 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA F 270 " --> pdb=" O SER F 266 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N LEU F 271 " --> pdb=" O GLU F 267 " (cutoff:3.500A) Processing helix chain 'F' and resid 277 through 281 Processing helix chain 'F' and resid 284 through 296 removed outlier: 3.881A pdb=" N ARG F 295 " --> pdb=" O LEU F 291 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ILE F 296 " --> pdb=" O LEU F 292 " (cutoff:3.500A) Processing helix chain 'F' and resid 313 through 316 Processing helix chain 'F' and resid 319 through 327 removed outlier: 4.288A pdb=" N ALA F 327 " --> pdb=" O ALA F 323 " (cutoff:3.500A) Processing helix chain 'F' and resid 336 through 342 removed outlier: 3.603A pdb=" N SER F 340 " --> pdb=" O SER F 336 " (cutoff:3.500A) Processing helix chain 'F' and resid 364 through 384 Processing helix chain 'F' and resid 384 through 391 Processing helix chain 'F' and resid 392 through 396 Processing helix chain 'F' and resid 397 through 415 removed outlier: 4.015A pdb=" N SER F 415 " --> pdb=" O GLN F 411 " (cutoff:3.500A) Processing helix chain 'F' and resid 418 through 422 removed outlier: 3.701A pdb=" N GLU F 422 " --> pdb=" O ALA F 419 " (cutoff:3.500A) Processing helix chain 'F' and resid 433 through 446 Processing helix chain 'F' and resid 453 through 458 Processing helix chain 'F' and resid 462 through 478 Processing helix chain 'H' and resid 98 through 112 removed outlier: 3.928A pdb=" N LYS H 102 " --> pdb=" O GLN H 98 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ASN H 111 " --> pdb=" O GLU H 107 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N VAL H 112 " --> pdb=" O ALA H 108 " (cutoff:3.500A) Processing helix chain 'H' and resid 113 through 115 No H-bonds generated for 'chain 'H' and resid 113 through 115' Processing helix chain 'H' and resid 116 through 138 removed outlier: 3.628A pdb=" N ALA H 124 " --> pdb=" O ALA H 120 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE H 125 " --> pdb=" O ALA H 121 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N LYS H 138 " --> pdb=" O GLN H 134 " (cutoff:3.500A) Processing helix chain 'I' and resid 9 through 24 removed outlier: 3.803A pdb=" N ILE I 21 " --> pdb=" O ALA I 17 " (cutoff:3.500A) Processing helix chain 'I' and resid 31 through 39 Processing helix chain 'I' and resid 47 through 52 Processing sheet with id=AA1, first strand: chain 'G' and resid 75 through 76 removed outlier: 7.181A pdb=" N VAL G 75 " --> pdb=" O PHE G 165 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 30 through 36 removed outlier: 4.731A pdb=" N VAL A 33 " --> pdb=" O PHE A 44 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N PHE A 44 " --> pdb=" O VAL A 33 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N VAL A 76 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N ALA A 65 " --> pdb=" O VAL A 76 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N PHE A 78 " --> pdb=" O GLY A 63 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N GLY A 63 " --> pdb=" O PHE A 78 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N GLU A 53 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N LEU A 54 " --> pdb=" O THR A 93 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 98 through 101 Processing sheet with id=AA4, first strand: chain 'A' and resid 108 through 110 removed outlier: 3.607A pdb=" N ASP A 271 " --> pdb=" O VAL A 206 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N VAL A 208 " --> pdb=" O ASP A 271 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 328 through 330 removed outlier: 6.641A pdb=" N ILE A 169 " --> pdb=" O ILE A 329 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 31 through 36 removed outlier: 5.353A pdb=" N VAL B 33 " --> pdb=" O PHE B 44 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N PHE B 44 " --> pdb=" O VAL B 33 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 40 through 44 current: chain 'B' and resid 62 through 68 removed outlier: 5.690A pdb=" N ALA B 65 " --> pdb=" O VAL B 76 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N VAL B 76 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ASN B 67 " --> pdb=" O GLY B 74 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 72 through 77 current: chain 'C' and resid 40 through 45 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 40 through 45 current: chain 'C' and resid 62 through 67 removed outlier: 5.472A pdb=" N ALA C 65 " --> pdb=" O VAL C 76 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N VAL C 76 " --> pdb=" O ALA C 65 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 72 through 77 current: chain 'F' and resid 20 through 25 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 20 through 25 current: chain 'F' and resid 44 through 53 removed outlier: 5.565A pdb=" N VAL F 50 " --> pdb=" O ILE F 62 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N ILE F 62 " --> pdb=" O VAL F 50 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 98 through 101 Processing sheet with id=AA8, first strand: chain 'B' and resid 109 through 110 removed outlier: 6.512A pdb=" N TYR B 202 " --> pdb=" O LEU B 267 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N VAL B 269 " --> pdb=" O TYR B 202 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N VAL B 204 " --> pdb=" O VAL B 269 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ALA B 266 " --> pdb=" O THR B 324 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 147 through 148 removed outlier: 4.562A pdb=" N ILE B 161 " --> pdb=" O VAL B 148 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 328 through 330 removed outlier: 6.378A pdb=" N LEU B 168 " --> pdb=" O ILE B 352 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N LEU B 354 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ILE B 170 " --> pdb=" O LEU B 354 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 98 through 101 Processing sheet with id=AB3, first strand: chain 'C' and resid 108 through 110 removed outlier: 4.017A pdb=" N ARG C 108 " --> pdb=" O SER C 231 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N TYR C 202 " --> pdb=" O LEU C 267 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N VAL C 269 " --> pdb=" O TYR C 202 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N VAL C 204 " --> pdb=" O VAL C 269 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ASP C 271 " --> pdb=" O VAL C 204 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N VAL C 206 " --> pdb=" O ASP C 271 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N TYR C 270 " --> pdb=" O LEU C 326 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N VAL C 328 " --> pdb=" O TYR C 270 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASP C 272 " --> pdb=" O VAL C 328 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N GLU C 330 " --> pdb=" O ASP C 272 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 147 through 148 removed outlier: 4.432A pdb=" N ILE C 161 " --> pdb=" O VAL C 148 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 350 through 351 Processing sheet with id=AB6, first strand: chain 'D' and resid 10 through 17 removed outlier: 5.584A pdb=" N VAL D 13 " --> pdb=" O HIS D 24 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N HIS D 24 " --> pdb=" O VAL D 13 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N THR D 58 " --> pdb=" O HIS D 53 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N HIS D 53 " --> pdb=" O THR D 58 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ARG D 60 " --> pdb=" O ALA D 51 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LEU D 46 " --> pdb=" O ILE D 39 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ASN D 35 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ALA D 36 " --> pdb=" O THR D 79 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N LYS D 40 " --> pdb=" O LYS D 75 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N LYS D 75 " --> pdb=" O LYS D 40 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 84 through 87 removed outlier: 3.509A pdb=" N LYS D 115 " --> pdb=" O VAL D 85 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N LEU D 113 " --> pdb=" O VAL D 87 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 95 through 96 Processing sheet with id=AB9, first strand: chain 'D' and resid 133 through 134 removed outlier: 4.160A pdb=" N TYR D 147 " --> pdb=" O LEU D 134 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 183 through 185 removed outlier: 7.905A pdb=" N THR D 333 " --> pdb=" O LYS D 152 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N GLY D 154 " --> pdb=" O THR D 333 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 10 through 17 removed outlier: 5.578A pdb=" N VAL E 13 " --> pdb=" O HIS E 24 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N HIS E 24 " --> pdb=" O VAL E 13 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N THR E 58 " --> pdb=" O LEU E 54 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ILE E 62 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N VAL E 50 " --> pdb=" O ILE E 62 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 84 through 87 removed outlier: 4.546A pdb=" N LEU E 113 " --> pdb=" O VAL E 87 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 95 through 96 removed outlier: 6.318A pdb=" N SER E 182 " --> pdb=" O ALA E 216 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N VAL E 218 " --> pdb=" O SER E 182 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N PHE E 184 " --> pdb=" O VAL E 218 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 133 through 134 removed outlier: 4.341A pdb=" N TYR E 147 " --> pdb=" O LEU E 134 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 156 through 157 Processing sheet with id=AC7, first strand: chain 'F' and resid 84 through 87 removed outlier: 4.314A pdb=" N LEU F 113 " --> pdb=" O VAL F 87 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 95 through 96 removed outlier: 7.146A pdb=" N SER F 182 " --> pdb=" O ALA F 216 " (cutoff:3.500A) removed outlier: 8.370A pdb=" N VAL F 218 " --> pdb=" O SER F 182 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N PHE F 184 " --> pdb=" O VAL F 218 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N GLY F 220 " --> pdb=" O PHE F 184 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N GLY F 186 " --> pdb=" O GLY F 220 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL F 187 " --> pdb=" O ASP F 256 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N LEU F 253 " --> pdb=" O VAL F 307 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N ALA F 309 " --> pdb=" O LEU F 253 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N ILE F 255 " --> pdb=" O ALA F 309 " (cutoff:3.500A) removed outlier: 8.512A pdb=" N TYR F 311 " --> pdb=" O ILE F 255 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N ILE F 153 " --> pdb=" O GLN F 308 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N VAL F 310 " --> pdb=" O ILE F 153 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N LEU F 155 " --> pdb=" O VAL F 310 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N LYS F 152 " --> pdb=" O ALA F 331 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N THR F 333 " --> pdb=" O LYS F 152 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N GLY F 154 " --> pdb=" O THR F 333 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N LEU F 335 " --> pdb=" O GLY F 154 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N PHE F 156 " --> pdb=" O LEU F 335 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 133 through 134 removed outlier: 4.336A pdb=" N TYR F 147 " --> pdb=" O LEU F 134 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 25 through 27 removed outlier: 3.741A pdb=" N SER H 25 " --> pdb=" O LEU H 12 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA H 15 " --> pdb=" O VAL H 85 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N CYS H 84 " --> pdb=" O THR H 76 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N THR H 76 " --> pdb=" O CYS H 84 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N THR H 86 " --> pdb=" O PHE H 74 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N PHE H 74 " --> pdb=" O THR H 86 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N GLY H 73 " --> pdb=" O LEU H 52 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 56 through 60 removed outlier: 3.611A pdb=" N LYS H 66 " --> pdb=" O VAL H 59 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 43 through 44 2203 hydrogen bonds defined for protein. 6411 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: 7.15 Time building geometry restraints manager: 4.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 10966 1.33 - 1.46: 6357 1.46 - 1.58: 21867 1.58 - 1.70: 19 1.70 - 1.82: 184 Bond restraints: 39393 Sorted by residual: bond pdb=" CG PRO G 123 " pdb=" CD PRO G 123 " ideal model delta sigma weight residual 1.503 1.319 0.184 3.40e-02 8.65e+02 2.91e+01 bond pdb=" CB PRO G 123 " pdb=" CG PRO G 123 " ideal model delta sigma weight residual 1.492 1.639 -0.147 5.00e-02 4.00e+02 8.59e+00 bond pdb=" N PRO G 123 " pdb=" CA PRO G 123 " ideal model delta sigma weight residual 1.473 1.435 0.037 1.33e-02 5.65e+03 7.87e+00 bond pdb=" N PRO G 123 " pdb=" CD PRO G 123 " ideal model delta sigma weight residual 1.473 1.505 -0.032 1.40e-02 5.10e+03 5.28e+00 bond pdb=" CB GLU A 294 " pdb=" CG GLU A 294 " ideal model delta sigma weight residual 1.520 1.584 -0.064 3.00e-02 1.11e+03 4.58e+00 ... (remaining 39388 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.83: 53008 3.83 - 7.67: 324 7.67 - 11.50: 32 11.50 - 15.33: 3 15.33 - 19.16: 3 Bond angle restraints: 53370 Sorted by residual: angle pdb=" CA PRO G 123 " pdb=" N PRO G 123 " pdb=" CD PRO G 123 " ideal model delta sigma weight residual 112.00 92.84 19.16 1.40e+00 5.10e-01 1.87e+02 angle pdb=" CA MET X 72 " pdb=" CB MET X 72 " pdb=" CG MET X 72 " ideal model delta sigma weight residual 114.10 132.11 -18.01 2.00e+00 2.50e-01 8.11e+01 angle pdb=" N PRO G 123 " pdb=" CD PRO G 123 " pdb=" CG PRO G 123 " ideal model delta sigma weight residual 103.20 92.51 10.69 1.50e+00 4.44e-01 5.08e+01 angle pdb=" CA PRO 6 40 " pdb=" N PRO 6 40 " pdb=" CD PRO 6 40 " ideal model delta sigma weight residual 112.00 102.67 9.33 1.40e+00 5.10e-01 4.44e+01 angle pdb=" C SER E 123 " pdb=" CA SER E 123 " pdb=" CB SER E 123 " ideal model delta sigma weight residual 116.63 110.47 6.16 1.16e+00 7.43e-01 2.82e+01 ... (remaining 53365 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.81: 23049 32.81 - 65.63: 652 65.63 - 98.44: 68 98.44 - 131.26: 2 131.26 - 164.07: 3 Dihedral angle restraints: 23774 sinusoidal: 9258 harmonic: 14516 Sorted by residual: dihedral pdb=" C5' ADP E 501 " pdb=" O5' ADP E 501 " pdb=" PA ADP E 501 " pdb=" O2A ADP E 501 " ideal model delta sinusoidal sigma weight residual -60.00 104.07 -164.07 1 2.00e+01 2.50e-03 4.71e+01 dihedral pdb=" C2' ADP B 601 " pdb=" C1' ADP B 601 " pdb=" N9 ADP B 601 " pdb=" C4 ADP B 601 " ideal model delta sinusoidal sigma weight residual 91.55 -108.81 -159.65 1 2.00e+01 2.50e-03 4.65e+01 dihedral pdb=" O1B ADP B 601 " pdb=" O3A ADP B 601 " pdb=" PB ADP B 601 " pdb=" PA ADP B 601 " ideal model delta sinusoidal sigma weight residual -60.00 77.10 -137.10 1 2.00e+01 2.50e-03 4.16e+01 ... (remaining 23771 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 5583 0.069 - 0.137: 708 0.137 - 0.206: 24 0.206 - 0.274: 5 0.274 - 0.343: 2 Chirality restraints: 6322 Sorted by residual: chirality pdb=" C1' ADP E 501 " pdb=" C2' ADP E 501 " pdb=" N9 ADP E 501 " pdb=" O4' ADP E 501 " both_signs ideal model delta sigma weight residual False 2.48 2.14 0.34 2.00e-01 2.50e+01 2.94e+00 chirality pdb=" CG LEU 7 114 " pdb=" CB LEU 7 114 " pdb=" CD1 LEU 7 114 " pdb=" CD2 LEU 7 114 " both_signs ideal model delta sigma weight residual False -2.59 -2.27 -0.32 2.00e-01 2.50e+01 2.57e+00 chirality pdb=" CB ILE C 345 " pdb=" CA ILE C 345 " pdb=" CG1 ILE C 345 " pdb=" CG2 ILE C 345 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.47e+00 ... (remaining 6319 not shown) Planarity restraints: 6814 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS G 122 " -0.120 5.00e-02 4.00e+02 1.65e-01 4.35e+01 pdb=" N PRO G 123 " 0.284 5.00e-02 4.00e+02 pdb=" CA PRO G 123 " -0.084 5.00e-02 4.00e+02 pdb=" CD PRO G 123 " -0.080 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU 6 39 " -0.083 5.00e-02 4.00e+02 1.19e-01 2.28e+01 pdb=" N PRO 6 40 " 0.206 5.00e-02 4.00e+02 pdb=" CA PRO 6 40 " -0.059 5.00e-02 4.00e+02 pdb=" CD PRO 6 40 " -0.064 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN Q 40 " -0.078 5.00e-02 4.00e+02 1.15e-01 2.13e+01 pdb=" N PRO Q 41 " 0.199 5.00e-02 4.00e+02 pdb=" CA PRO Q 41 " -0.059 5.00e-02 4.00e+02 pdb=" CD PRO Q 41 " -0.062 5.00e-02 4.00e+02 ... (remaining 6811 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.54: 384 2.54 - 3.13: 32486 3.13 - 3.72: 68316 3.72 - 4.31: 90562 4.31 - 4.90: 147484 Nonbonded interactions: 339232 Sorted by model distance: nonbonded pdb=" O2B ADP B 601 " pdb="MG MG B 602 " model vdw 1.955 2.170 nonbonded pdb=" O3B ADP A 601 " pdb="MG MG A 602 " model vdw 2.006 2.170 nonbonded pdb=" OG1 THR B 30 " pdb=" O VAL B 90 " model vdw 2.031 3.040 nonbonded pdb=" O3B ADP C 601 " pdb="MG MG C 602 " model vdw 2.036 2.170 nonbonded pdb=" O ALA 7 39 " pdb=" NE2 GLN 7 42 " model vdw 2.074 3.120 ... (remaining 339227 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 6 through 509 or resid 601 through 602)) selection = (chain 'B' and resid 6 through 602) selection = (chain 'C' and (resid 6 through 509 or resid 601 through 602)) } ncs_group { reference = (chain 'D' and resid 7 through 478) selection = (chain 'E' and resid 7 through 478) selection = (chain 'F' and resid 7 through 478) } ncs_group { reference = (chain 'K' and resid 1 through 74) selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = (chain 'P' and resid 1 through 74) selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } 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: 1.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 33.190 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6988 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 0.184 39393 Z= 0.151 Angle : 0.741 19.162 53370 Z= 0.379 Chirality : 0.044 0.343 6322 Planarity : 0.005 0.165 6814 Dihedral : 15.477 164.071 14456 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 14.72 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.16 % Favored : 94.63 % Rotamer: Outliers : 0.22 % Allowed : 16.09 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.30 (0.12), residues: 5042 helix: 1.22 (0.10), residues: 2613 sheet: -0.74 (0.25), residues: 454 loop : -0.91 (0.15), residues: 1975 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 375 TYR 0.049 0.001 TYR 7 58 PHE 0.042 0.001 PHE 7 32 TRP 0.014 0.001 TRP X 234 HIS 0.010 0.001 HIS D 328 Details of bonding type rmsd covalent geometry : bond 0.00341 (39393) covalent geometry : angle 0.74069 (53370) hydrogen bonds : bond 0.13241 ( 2203) hydrogen bonds : angle 6.13134 ( 6411) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10084 Ramachandran restraints generated. 5042 Oldfield, 0 Emsley, 5042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10084 Ramachandran restraints generated. 5042 Oldfield, 0 Emsley, 5042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 600 residues out of total 4147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 591 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 136 ASP cc_start: 0.7715 (m-30) cc_final: 0.7513 (m-30) REVERT: Z 128 LYS cc_start: 0.2761 (mmmt) cc_final: 0.2141 (mmtt) REVERT: K 39 ARG cc_start: 0.7869 (ptm160) cc_final: 0.7365 (ptm-80) REVERT: Y 81 LEU cc_start: 0.9410 (mm) cc_final: 0.9105 (mp) REVERT: A 52 GLU cc_start: 0.8319 (mm-30) cc_final: 0.8020 (mm-30) REVERT: A 294 GLU cc_start: 0.8698 (tm-30) cc_final: 0.8308 (tm-30) REVERT: B 335 ASP cc_start: 0.8742 (t0) cc_final: 0.8536 (t0) REVERT: C 396 LEU cc_start: 0.9730 (OUTLIER) cc_final: 0.9508 (mm) REVERT: D 291 LEU cc_start: 0.9385 (mm) cc_final: 0.9166 (mm) REVERT: E 420 VAL cc_start: 0.9410 (m) cc_final: 0.9134 (p) REVERT: E 458 TYR cc_start: 0.8502 (t80) cc_final: 0.8278 (t80) REVERT: F 200 GLU cc_start: 0.9046 (tt0) cc_final: 0.8800 (tm-30) REVERT: F 201 MET cc_start: 0.9331 (mtt) cc_final: 0.9113 (mtm) outliers start: 9 outliers final: 6 residues processed: 596 average time/residue: 0.2259 time to fit residues: 223.5868 Evaluate side-chains 508 residues out of total 4147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 501 time to evaluate : 1.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 8 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain D residue 308 GLN Chi-restraints excluded: chain D residue 375 GLN Chi-restraints excluded: chain F residue 291 LEU Chi-restraints excluded: chain F residue 385 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 432 optimal weight: 9.9990 chunk 197 optimal weight: 10.0000 chunk 388 optimal weight: 0.0020 chunk 455 optimal weight: 0.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 30.0000 chunk 132 optimal weight: 50.0000 chunk 494 optimal weight: 20.0000 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 5.9990 overall best weight: 3.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 265 ASN ** Z 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 56 GLN U 68 HIS ** M 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 35 ASN P 40 ASN Y 68 ASN ** Y 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 332 GLN A 478 HIS ** D 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 29 GLN ** I 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 19 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.136754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.085038 restraints weight = 116487.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.086245 restraints weight = 56030.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.087379 restraints weight = 33947.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.088138 restraints weight = 24553.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.088615 restraints weight = 19876.582| |-----------------------------------------------------------------------------| r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.1142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 39393 Z= 0.189 Angle : 0.663 12.852 53370 Z= 0.332 Chirality : 0.044 0.259 6322 Planarity : 0.005 0.077 6814 Dihedral : 6.301 157.974 5480 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.04 % Favored : 94.74 % Rotamer: Outliers : 2.48 % Allowed : 14.80 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.34 (0.12), residues: 5042 helix: 1.23 (0.10), residues: 2639 sheet: -0.81 (0.23), residues: 513 loop : -0.85 (0.15), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 375 TYR 0.028 0.002 TYR G 226 PHE 0.030 0.002 PHE 7 32 TRP 0.021 0.002 TRP Z 157 HIS 0.008 0.001 HIS E 118 Details of bonding type rmsd covalent geometry : bond 0.00416 (39393) covalent geometry : angle 0.66326 (53370) hydrogen bonds : bond 0.04132 ( 2203) hydrogen bonds : angle 5.08229 ( 6411) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10084 Ramachandran restraints generated. 5042 Oldfield, 0 Emsley, 5042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10084 Ramachandran restraints generated. 5042 Oldfield, 0 Emsley, 5042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 634 residues out of total 4147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 532 time to evaluate : 1.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 237 MET cc_start: 0.6460 (mmt) cc_final: 0.5912 (mmt) REVERT: G 250 ARG cc_start: 0.8833 (ttp-110) cc_final: 0.8372 (ptp-170) REVERT: Z 128 LYS cc_start: 0.2015 (mmmt) cc_final: 0.1757 (mmtt) REVERT: Z 166 GLN cc_start: 0.9152 (mm-40) cc_final: 0.8897 (mm-40) REVERT: U 4 LEU cc_start: 0.6760 (OUTLIER) cc_final: 0.6054 (tt) REVERT: K 1 MET cc_start: 0.4801 (ptt) cc_final: 0.4506 (tpp) REVERT: K 39 ARG cc_start: 0.7959 (ptm160) cc_final: 0.7372 (ttp80) REVERT: X 70 MET cc_start: 0.4128 (OUTLIER) cc_final: 0.3909 (tmm) REVERT: Y 68 ASN cc_start: 0.9528 (m-40) cc_final: 0.9251 (m110) REVERT: Y 81 LEU cc_start: 0.9116 (mm) cc_final: 0.8908 (mp) REVERT: Y 107 ASP cc_start: 0.9070 (m-30) cc_final: 0.8770 (m-30) REVERT: Y 116 ASN cc_start: 0.8525 (t0) cc_final: 0.8275 (t0) REVERT: A 89 LEU cc_start: 0.9032 (tp) cc_final: 0.8815 (tp) REVERT: A 294 GLU cc_start: 0.8555 (tm-30) cc_final: 0.8346 (tm-30) REVERT: A 351 GLN cc_start: 0.8770 (pm20) cc_final: 0.8318 (pm20) REVERT: A 375 ARG cc_start: 0.7698 (mmt180) cc_final: 0.7473 (mmt180) REVERT: B 82 ARG cc_start: 0.8298 (mtt-85) cc_final: 0.7957 (mtt180) REVERT: B 355 GLU cc_start: 0.8248 (pm20) cc_final: 0.7904 (pm20) REVERT: B 357 GLU cc_start: 0.8918 (tp30) cc_final: 0.8704 (tp30) REVERT: B 375 ARG cc_start: 0.7939 (tpp-160) cc_final: 0.7602 (mmt90) REVERT: B 442 GLU cc_start: 0.9132 (OUTLIER) cc_final: 0.8751 (mp0) REVERT: C 90 VAL cc_start: 0.9569 (OUTLIER) cc_final: 0.9353 (p) REVERT: C 396 LEU cc_start: 0.9784 (OUTLIER) cc_final: 0.9534 (mm) REVERT: D 257 ASN cc_start: 0.8698 (t0) cc_final: 0.8115 (t0) REVERT: D 291 LEU cc_start: 0.9466 (mm) cc_final: 0.9053 (mm) REVERT: D 316 ASP cc_start: 0.8472 (t0) cc_final: 0.8268 (t0) REVERT: D 375 GLN cc_start: 0.9122 (OUTLIER) cc_final: 0.8787 (mm-40) REVERT: E 287 THR cc_start: 0.9540 (m) cc_final: 0.9288 (p) REVERT: E 339 ILE cc_start: 0.9541 (mt) cc_final: 0.9022 (mt) REVERT: E 342 LEU cc_start: 0.9670 (mt) cc_final: 0.9428 (pp) REVERT: E 369 ASP cc_start: 0.9196 (m-30) cc_final: 0.8916 (m-30) REVERT: F 200 GLU cc_start: 0.8964 (tt0) cc_final: 0.8744 (tm-30) REVERT: F 201 MET cc_start: 0.9316 (mtt) cc_final: 0.9070 (mtt) REVERT: F 256 ASP cc_start: 0.8524 (t0) cc_final: 0.8293 (t0) REVERT: F 257 ASN cc_start: 0.8223 (t0) cc_final: 0.7568 (t0) REVERT: F 400 ASP cc_start: 0.8886 (m-30) cc_final: 0.8656 (m-30) outliers start: 102 outliers final: 46 residues processed: 603 average time/residue: 0.2184 time to fit residues: 220.1935 Evaluate side-chains 523 residues out of total 4147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 471 time to evaluate : 1.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 126 ILE Chi-restraints excluded: chain G residue 165 PHE Chi-restraints excluded: chain 7 residue 43 LEU Chi-restraints excluded: chain 7 residue 55 PHE Chi-restraints excluded: chain 7 residue 74 TYR Chi-restraints excluded: chain 7 residue 173 MET Chi-restraints excluded: chain 6 residue 8 LEU Chi-restraints excluded: chain 6 residue 42 LEU Chi-restraints excluded: chain 6 residue 60 THR Chi-restraints excluded: chain U residue 3 THR Chi-restraints excluded: chain U residue 4 LEU Chi-restraints excluded: chain S residue 57 LEU Chi-restraints excluded: chain N residue 24 ILE Chi-restraints excluded: chain Q residue 40 ASN Chi-restraints excluded: chain X residue 70 MET Chi-restraints excluded: chain X residue 88 MET Chi-restraints excluded: chain Y residue 21 THR Chi-restraints excluded: chain Y residue 38 GLN Chi-restraints excluded: chain Y residue 66 ASP Chi-restraints excluded: chain Y residue 111 LEU Chi-restraints excluded: chain Y residue 115 HIS Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 442 GLU Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 401 GLU Chi-restraints excluded: chain C residue 440 THR Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 375 GLN Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 207 ILE Chi-restraints excluded: chain E residue 297 THR Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 396 LEU Chi-restraints excluded: chain F residue 348 VAL Chi-restraints excluded: chain H residue 22 TYR Chi-restraints excluded: chain I residue 15 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 142 optimal weight: 50.0000 chunk 385 optimal weight: 9.9990 chunk 436 optimal weight: 8.9990 chunk 4 optimal weight: 50.0000 chunk 282 optimal weight: 7.9990 chunk 94 optimal weight: 40.0000 chunk 298 optimal weight: 1.9990 chunk 79 optimal weight: 40.0000 chunk 307 optimal weight: 3.9990 chunk 320 optimal weight: 5.9990 chunk 469 optimal weight: 4.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 196 GLN ** M 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 35 ASN ** Y 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 116 ASN ** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 26 ASN B 188 GLN ** C 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 52 GLN F 173 ASN ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 132 ASN ** I 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 19 GLN ** 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 = 0.4078 r_free = 0.4078 target = 0.132306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.079704 restraints weight = 113189.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.081343 restraints weight = 54630.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.082320 restraints weight = 32695.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.082819 restraints weight = 24037.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.083274 restraints weight = 20282.081| |-----------------------------------------------------------------------------| r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.1672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.095 39393 Z= 0.246 Angle : 0.675 10.589 53370 Z= 0.336 Chirality : 0.044 0.236 6322 Planarity : 0.004 0.056 6814 Dihedral : 6.153 158.444 5472 Min Nonbonded Distance : 1.773 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.98 % Favored : 94.80 % Rotamer: Outliers : 3.11 % Allowed : 15.43 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.28 (0.12), residues: 5042 helix: 1.25 (0.10), residues: 2633 sheet: -0.94 (0.23), residues: 520 loop : -0.93 (0.15), residues: 1889 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG Z 170 TYR 0.026 0.002 TYR G 226 PHE 0.029 0.002 PHE S 55 TRP 0.038 0.002 TRP X 82 HIS 0.010 0.001 HIS Z 148 Details of bonding type rmsd covalent geometry : bond 0.00534 (39393) covalent geometry : angle 0.67469 (53370) hydrogen bonds : bond 0.04038 ( 2203) hydrogen bonds : angle 4.94423 ( 6411) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10084 Ramachandran restraints generated. 5042 Oldfield, 0 Emsley, 5042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10084 Ramachandran restraints generated. 5042 Oldfield, 0 Emsley, 5042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 625 residues out of total 4147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 497 time to evaluate : 0.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 116 MET cc_start: 0.8606 (mpp) cc_final: 0.8308 (mpp) REVERT: G 250 ARG cc_start: 0.8891 (ttp-110) cc_final: 0.8574 (ttp-110) REVERT: Z 128 LYS cc_start: 0.2030 (mmmt) cc_final: 0.1767 (mmtt) REVERT: Z 166 GLN cc_start: 0.9074 (mm-40) cc_final: 0.8854 (mm-40) REVERT: Z 186 ASN cc_start: 0.7483 (t0) cc_final: 0.7196 (p0) REVERT: Z 203 GLN cc_start: 0.8876 (OUTLIER) cc_final: 0.8487 (tp-100) REVERT: U 4 LEU cc_start: 0.6627 (OUTLIER) cc_final: 0.6036 (tt) REVERT: K 1 MET cc_start: 0.4767 (ptt) cc_final: 0.4455 (tpp) REVERT: K 39 ARG cc_start: 0.7992 (ptm160) cc_final: 0.7411 (ttp80) REVERT: M 30 PHE cc_start: 0.4339 (m-80) cc_final: 0.3961 (m-80) REVERT: Q 66 LEU cc_start: 0.3801 (OUTLIER) cc_final: 0.3422 (mp) REVERT: X 82 TRP cc_start: 0.5557 (p-90) cc_final: 0.5130 (p-90) REVERT: X 199 MET cc_start: 0.2378 (mpp) cc_final: 0.2080 (pmm) REVERT: Y 68 ASN cc_start: 0.9558 (m-40) cc_final: 0.9299 (m110) REVERT: Y 81 LEU cc_start: 0.9131 (mm) cc_final: 0.8922 (mp) REVERT: Y 90 LYS cc_start: 0.9527 (OUTLIER) cc_final: 0.9094 (mttt) REVERT: Y 107 ASP cc_start: 0.9086 (m-30) cc_final: 0.8686 (m-30) REVERT: A 52 GLU cc_start: 0.8364 (mm-30) cc_final: 0.8111 (mm-30) REVERT: A 89 LEU cc_start: 0.9147 (tp) cc_final: 0.8932 (tp) REVERT: A 272 ASP cc_start: 0.8196 (m-30) cc_final: 0.7690 (m-30) REVERT: A 294 GLU cc_start: 0.8588 (tm-30) cc_final: 0.8169 (tm-30) REVERT: A 355 GLU cc_start: 0.7934 (mm-30) cc_final: 0.7691 (mm-30) REVERT: B 82 ARG cc_start: 0.8313 (mtt-85) cc_final: 0.8003 (ttm110) REVERT: B 271 ASP cc_start: 0.8789 (t70) cc_final: 0.8436 (t0) REVERT: B 351 GLN cc_start: 0.9087 (pm20) cc_final: 0.8662 (pm20) REVERT: B 355 GLU cc_start: 0.8349 (pm20) cc_final: 0.7885 (pm20) REVERT: B 357 GLU cc_start: 0.8984 (tp30) cc_final: 0.8734 (tp30) REVERT: B 375 ARG cc_start: 0.7989 (tpp-160) cc_final: 0.7586 (mmt90) REVERT: B 442 GLU cc_start: 0.9227 (OUTLIER) cc_final: 0.8889 (mp0) REVERT: C 90 VAL cc_start: 0.9594 (OUTLIER) cc_final: 0.9361 (p) REVERT: C 173 ARG cc_start: 0.9542 (OUTLIER) cc_final: 0.8722 (ptp90) REVERT: C 396 LEU cc_start: 0.9802 (OUTLIER) cc_final: 0.9570 (mm) REVERT: D 191 THR cc_start: 0.8590 (OUTLIER) cc_final: 0.8234 (p) REVERT: D 257 ASN cc_start: 0.8772 (t0) cc_final: 0.8249 (t0) REVERT: D 281 TYR cc_start: 0.8213 (m-80) cc_final: 0.7826 (m-80) REVERT: D 291 LEU cc_start: 0.9457 (mm) cc_final: 0.9007 (mm) REVERT: D 316 ASP cc_start: 0.8478 (t0) cc_final: 0.8275 (t70) REVERT: D 375 GLN cc_start: 0.9177 (OUTLIER) cc_final: 0.8882 (mm-40) REVERT: E 256 ASP cc_start: 0.7825 (t0) cc_final: 0.7619 (t0) REVERT: E 287 THR cc_start: 0.9515 (m) cc_final: 0.9259 (p) REVERT: E 324 THR cc_start: 0.9707 (m) cc_final: 0.9370 (p) REVERT: E 458 TYR cc_start: 0.8972 (t80) cc_final: 0.8648 (t80) REVERT: F 17 ILE cc_start: 0.9559 (mm) cc_final: 0.9358 (mm) REVERT: F 189 GLU cc_start: 0.8139 (mm-30) cc_final: 0.7834 (tp30) REVERT: F 201 MET cc_start: 0.9419 (mtt) cc_final: 0.9187 (mtt) REVERT: F 400 ASP cc_start: 0.8945 (m-30) cc_final: 0.8658 (m-30) outliers start: 128 outliers final: 64 residues processed: 589 average time/residue: 0.2019 time to fit residues: 200.3418 Evaluate side-chains 514 residues out of total 4147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 440 time to evaluate : 1.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 126 ILE Chi-restraints excluded: chain G residue 165 PHE Chi-restraints excluded: chain Z residue 203 GLN Chi-restraints excluded: chain 7 residue 43 LEU Chi-restraints excluded: chain 7 residue 55 PHE Chi-restraints excluded: chain 7 residue 95 PHE Chi-restraints excluded: chain 7 residue 173 MET Chi-restraints excluded: chain 6 residue 42 LEU Chi-restraints excluded: chain 6 residue 60 THR Chi-restraints excluded: chain U residue 3 THR Chi-restraints excluded: chain U residue 4 LEU Chi-restraints excluded: chain S residue 57 LEU Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain M residue 48 PHE Chi-restraints excluded: chain N residue 24 ILE Chi-restraints excluded: chain Q residue 40 ASN Chi-restraints excluded: chain Q residue 66 LEU Chi-restraints excluded: chain R residue 16 THR Chi-restraints excluded: chain X residue 88 MET Chi-restraints excluded: chain Y residue 21 THR Chi-restraints excluded: chain Y residue 38 GLN Chi-restraints excluded: chain Y residue 66 ASP Chi-restraints excluded: chain Y residue 90 LYS Chi-restraints excluded: chain Y residue 111 LEU Chi-restraints excluded: chain Y residue 115 HIS Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 272 ASP Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 442 GLU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 173 ARG Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 340 ILE Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 401 GLU Chi-restraints excluded: chain C residue 415 SER Chi-restraints excluded: chain C residue 440 THR Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 263 GLN Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 317 LEU Chi-restraints excluded: chain D residue 375 GLN Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 207 ILE Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 297 THR Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 396 LEU Chi-restraints excluded: chain F residue 140 VAL Chi-restraints excluded: chain F residue 291 LEU Chi-restraints excluded: chain F residue 348 VAL Chi-restraints excluded: chain F residue 357 LEU Chi-restraints excluded: chain H residue 22 TYR Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain I residue 15 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 497 optimal weight: 5.9990 chunk 350 optimal weight: 0.9990 chunk 35 optimal weight: 7.9990 chunk 486 optimal weight: 20.0000 chunk 282 optimal weight: 9.9990 chunk 199 optimal weight: 0.9980 chunk 44 optimal weight: 7.9990 chunk 219 optimal weight: 0.8980 chunk 244 optimal weight: 0.9980 chunk 303 optimal weight: 5.9990 chunk 213 optimal weight: 0.0070 overall best weight: 0.7800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 80 ASN ** Y 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 411 GLN F 195 ASN ** H 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 132 ASN ** I 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 19 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.135347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.083633 restraints weight = 111405.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.086311 restraints weight = 53551.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.085948 restraints weight = 28719.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.086928 restraints weight = 23390.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.086797 restraints weight = 19290.182| |-----------------------------------------------------------------------------| r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 39393 Z= 0.127 Angle : 0.634 11.687 53370 Z= 0.313 Chirality : 0.043 0.221 6322 Planarity : 0.004 0.054 6814 Dihedral : 6.021 157.573 5470 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.12 % Favored : 94.63 % Rotamer: Outliers : 2.92 % Allowed : 16.62 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.25 (0.12), residues: 5042 helix: 1.20 (0.10), residues: 2641 sheet: -1.17 (0.22), residues: 527 loop : -0.86 (0.15), residues: 1874 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 141 TYR 0.026 0.002 TYR G 226 PHE 0.029 0.001 PHE K 48 TRP 0.025 0.001 TRP X 82 HIS 0.007 0.001 HIS E 367 Details of bonding type rmsd covalent geometry : bond 0.00274 (39393) covalent geometry : angle 0.63402 (53370) hydrogen bonds : bond 0.03781 ( 2203) hydrogen bonds : angle 4.77165 ( 6411) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10084 Ramachandran restraints generated. 5042 Oldfield, 0 Emsley, 5042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10084 Ramachandran restraints generated. 5042 Oldfield, 0 Emsley, 5042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 678 residues out of total 4147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 558 time to evaluate : 1.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 250 ARG cc_start: 0.8906 (ttp-110) cc_final: 0.8553 (ttp-110) REVERT: G 262 VAL cc_start: 0.8679 (p) cc_final: 0.8353 (p) REVERT: Z 128 LYS cc_start: 0.2068 (mmmt) cc_final: 0.1785 (mmtt) REVERT: Z 166 GLN cc_start: 0.9084 (mm-40) cc_final: 0.8828 (mm-40) REVERT: Z 186 ASN cc_start: 0.7360 (t0) cc_final: 0.7048 (p0) REVERT: Z 203 GLN cc_start: 0.9004 (OUTLIER) cc_final: 0.8332 (tp-100) REVERT: U 4 LEU cc_start: 0.6548 (OUTLIER) cc_final: 0.5954 (tt) REVERT: K 1 MET cc_start: 0.4896 (ptt) cc_final: 0.4558 (tpp) REVERT: K 39 ARG cc_start: 0.8054 (ptm160) cc_final: 0.7434 (ttp80) REVERT: X 82 TRP cc_start: 0.6135 (p-90) cc_final: 0.5860 (p-90) REVERT: Y 81 LEU cc_start: 0.9189 (mm) cc_final: 0.8982 (mp) REVERT: Y 107 ASP cc_start: 0.9111 (m-30) cc_final: 0.8695 (m-30) REVERT: Y 116 ASN cc_start: 0.8499 (t0) cc_final: 0.8281 (t0) REVERT: A 52 GLU cc_start: 0.8349 (mm-30) cc_final: 0.8052 (mm-30) REVERT: A 275 LYS cc_start: 0.9217 (mttm) cc_final: 0.9004 (mtmm) REVERT: A 294 GLU cc_start: 0.8538 (tm-30) cc_final: 0.8149 (tm-30) REVERT: A 355 GLU cc_start: 0.7888 (mm-30) cc_final: 0.7666 (mm-30) REVERT: B 82 ARG cc_start: 0.8196 (mtt-85) cc_final: 0.7939 (ttm110) REVERT: B 271 ASP cc_start: 0.8658 (t70) cc_final: 0.8321 (t70) REVERT: B 294 GLU cc_start: 0.8663 (pm20) cc_final: 0.8441 (pm20) REVERT: B 351 GLN cc_start: 0.9080 (pm20) cc_final: 0.8851 (pm20) REVERT: B 355 GLU cc_start: 0.8282 (pm20) cc_final: 0.7739 (pm20) REVERT: B 357 GLU cc_start: 0.8973 (tp30) cc_final: 0.8663 (tp30) REVERT: B 375 ARG cc_start: 0.7684 (tpp-160) cc_final: 0.7369 (mmt90) REVERT: B 471 LEU cc_start: 0.9606 (mm) cc_final: 0.9384 (mm) REVERT: C 90 VAL cc_start: 0.9614 (OUTLIER) cc_final: 0.9394 (p) REVERT: C 173 ARG cc_start: 0.9546 (OUTLIER) cc_final: 0.8624 (ptp90) REVERT: C 178 THR cc_start: 0.9105 (OUTLIER) cc_final: 0.8754 (m) REVERT: C 217 GLN cc_start: 0.8780 (mm110) cc_final: 0.8500 (tp40) REVERT: C 331 THR cc_start: 0.9673 (OUTLIER) cc_final: 0.9383 (t) REVERT: D 191 THR cc_start: 0.8442 (OUTLIER) cc_final: 0.8097 (p) REVERT: D 281 TYR cc_start: 0.7948 (m-80) cc_final: 0.7628 (m-80) REVERT: D 291 LEU cc_start: 0.9430 (mm) cc_final: 0.8951 (mm) REVERT: D 352 ASP cc_start: 0.9190 (m-30) cc_final: 0.8880 (p0) REVERT: D 375 GLN cc_start: 0.9168 (OUTLIER) cc_final: 0.8842 (mm-40) REVERT: D 449 TYR cc_start: 0.9159 (m-80) cc_final: 0.8844 (m-80) REVERT: E 287 THR cc_start: 0.9486 (m) cc_final: 0.9256 (p) REVERT: E 324 THR cc_start: 0.9645 (m) cc_final: 0.9357 (p) REVERT: F 257 ASN cc_start: 0.8530 (t0) cc_final: 0.7408 (t0) REVERT: F 311 TYR cc_start: 0.8934 (t80) cc_final: 0.8541 (t80) REVERT: F 400 ASP cc_start: 0.8941 (m-30) cc_final: 0.8672 (m-30) outliers start: 120 outliers final: 65 residues processed: 640 average time/residue: 0.2191 time to fit residues: 234.5376 Evaluate side-chains 557 residues out of total 4147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 484 time to evaluate : 1.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 126 ILE Chi-restraints excluded: chain G residue 164 ILE Chi-restraints excluded: chain G residue 165 PHE Chi-restraints excluded: chain Z residue 203 GLN Chi-restraints excluded: chain 7 residue 43 LEU Chi-restraints excluded: chain 7 residue 55 PHE Chi-restraints excluded: chain 7 residue 65 THR Chi-restraints excluded: chain 7 residue 95 PHE Chi-restraints excluded: chain 7 residue 173 MET Chi-restraints excluded: chain 6 residue 8 LEU Chi-restraints excluded: chain 6 residue 42 LEU Chi-restraints excluded: chain 6 residue 58 VAL Chi-restraints excluded: chain 6 residue 60 THR Chi-restraints excluded: chain U residue 3 THR Chi-restraints excluded: chain U residue 4 LEU Chi-restraints excluded: chain S residue 57 LEU Chi-restraints excluded: chain M residue 48 PHE Chi-restraints excluded: chain N residue 24 ILE Chi-restraints excluded: chain N residue 30 PHE Chi-restraints excluded: chain N residue 55 PHE Chi-restraints excluded: chain Q residue 40 ASN Chi-restraints excluded: chain X residue 88 MET Chi-restraints excluded: chain Y residue 23 LEU Chi-restraints excluded: chain Y residue 38 GLN Chi-restraints excluded: chain Y residue 66 ASP Chi-restraints excluded: chain Y residue 90 LYS Chi-restraints excluded: chain Y residue 115 HIS Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 375 ARG Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 173 ARG Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 246 TYR Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 401 GLU Chi-restraints excluded: chain C residue 440 THR Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 182 SER Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 263 GLN Chi-restraints excluded: chain D residue 375 GLN Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 207 ILE Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain E residue 271 LEU Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 396 LEU Chi-restraints excluded: chain E residue 411 GLN Chi-restraints excluded: chain F residue 267 GLU Chi-restraints excluded: chain F residue 284 THR Chi-restraints excluded: chain F residue 291 LEU Chi-restraints excluded: chain F residue 348 VAL Chi-restraints excluded: chain H residue 22 TYR Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain I residue 15 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 195 optimal weight: 0.8980 chunk 366 optimal weight: 2.9990 chunk 5 optimal weight: 10.0000 chunk 426 optimal weight: 3.9990 chunk 83 optimal weight: 10.0000 chunk 465 optimal weight: 10.0000 chunk 194 optimal weight: 0.8980 chunk 497 optimal weight: 7.9990 chunk 212 optimal weight: 3.9990 chunk 175 optimal weight: 10.0000 chunk 208 optimal weight: 7.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 122 HIS G 260 GLN ** M 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 68 ASN ** Y 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 116 ASN ** C 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 328 HIS F 195 ASN ** H 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.133867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.081694 restraints weight = 111886.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.083333 restraints weight = 53063.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.084192 restraints weight = 32344.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.084938 restraints weight = 24251.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.085303 restraints weight = 19949.564| |-----------------------------------------------------------------------------| r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 39393 Z= 0.162 Angle : 0.650 13.344 53370 Z= 0.320 Chirality : 0.043 0.208 6322 Planarity : 0.004 0.054 6814 Dihedral : 5.924 157.272 5468 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.30 % Favored : 94.45 % Rotamer: Outliers : 2.84 % Allowed : 17.98 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.21 (0.12), residues: 5042 helix: 1.17 (0.10), residues: 2680 sheet: -1.21 (0.22), residues: 515 loop : -0.91 (0.15), residues: 1847 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG S 39 TYR 0.032 0.002 TYR K 9 PHE 0.049 0.001 PHE M 30 TRP 0.012 0.001 TRP X 82 HIS 0.011 0.001 HIS E 178 Details of bonding type rmsd covalent geometry : bond 0.00358 (39393) covalent geometry : angle 0.64954 (53370) hydrogen bonds : bond 0.03786 ( 2203) hydrogen bonds : angle 4.78300 ( 6411) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10084 Ramachandran restraints generated. 5042 Oldfield, 0 Emsley, 5042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10084 Ramachandran restraints generated. 5042 Oldfield, 0 Emsley, 5042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 631 residues out of total 4147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 514 time to evaluate : 1.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 250 ARG cc_start: 0.8920 (ttp-110) cc_final: 0.8545 (ttp-110) REVERT: G 262 VAL cc_start: 0.8812 (p) cc_final: 0.8500 (p) REVERT: Z 151 LYS cc_start: 0.8762 (ptpp) cc_final: 0.8446 (mmtt) REVERT: Z 166 GLN cc_start: 0.9049 (mm-40) cc_final: 0.8834 (mm-40) REVERT: Z 203 GLN cc_start: 0.9016 (OUTLIER) cc_final: 0.8231 (tp-100) REVERT: 7 58 TYR cc_start: 0.5649 (t80) cc_final: 0.5320 (t80) REVERT: 6 7 TYR cc_start: 0.6007 (t80) cc_final: 0.5718 (t80) REVERT: U 4 LEU cc_start: 0.6399 (OUTLIER) cc_final: 0.5861 (tt) REVERT: K 1 MET cc_start: 0.4895 (ptt) cc_final: 0.4620 (tpp) REVERT: K 39 ARG cc_start: 0.7968 (ptm160) cc_final: 0.7410 (ttp80) REVERT: L 50 MET cc_start: -0.2954 (mmm) cc_final: -0.3170 (mmt) REVERT: Q 67 MET cc_start: -0.3120 (tpt) cc_final: -0.3630 (mmt) REVERT: Y 68 ASN cc_start: 0.9505 (m-40) cc_final: 0.9289 (m110) REVERT: Y 107 ASP cc_start: 0.9136 (m-30) cc_final: 0.8680 (m-30) REVERT: A 52 GLU cc_start: 0.8342 (mm-30) cc_final: 0.8017 (mm-30) REVERT: A 275 LYS cc_start: 0.9242 (mttm) cc_final: 0.9011 (mtmm) REVERT: A 294 GLU cc_start: 0.8489 (tm-30) cc_final: 0.8096 (tm-30) REVERT: A 375 ARG cc_start: 0.7706 (OUTLIER) cc_final: 0.7336 (mmp-170) REVERT: B 82 ARG cc_start: 0.8212 (mtt-85) cc_final: 0.7891 (ttm110) REVERT: B 271 ASP cc_start: 0.8715 (t70) cc_final: 0.8264 (t70) REVERT: B 299 ASP cc_start: 0.8825 (OUTLIER) cc_final: 0.8483 (p0) REVERT: B 351 GLN cc_start: 0.9087 (pm20) cc_final: 0.8521 (pm20) REVERT: B 355 GLU cc_start: 0.8310 (pm20) cc_final: 0.7706 (pm20) REVERT: B 357 GLU cc_start: 0.8964 (tp30) cc_final: 0.8653 (tp30) REVERT: B 375 ARG cc_start: 0.7803 (tpp-160) cc_final: 0.7404 (mmt90) REVERT: B 442 GLU cc_start: 0.9174 (mt-10) cc_final: 0.8801 (mp0) REVERT: B 455 LEU cc_start: 0.9295 (OUTLIER) cc_final: 0.9044 (pp) REVERT: B 471 LEU cc_start: 0.9636 (mm) cc_final: 0.9430 (mm) REVERT: C 172 ASP cc_start: 0.9033 (t0) cc_final: 0.8818 (t0) REVERT: C 173 ARG cc_start: 0.9556 (OUTLIER) cc_final: 0.8515 (ptp90) REVERT: C 217 GLN cc_start: 0.8794 (mm110) cc_final: 0.8517 (tp40) REVERT: C 269 VAL cc_start: 0.9710 (t) cc_final: 0.9485 (p) REVERT: C 270 TYR cc_start: 0.8779 (m-10) cc_final: 0.8400 (m-80) REVERT: C 331 THR cc_start: 0.9669 (OUTLIER) cc_final: 0.9386 (t) REVERT: C 396 LEU cc_start: 0.9777 (OUTLIER) cc_final: 0.9336 (mm) REVERT: D 191 THR cc_start: 0.8530 (OUTLIER) cc_final: 0.8178 (p) REVERT: D 257 ASN cc_start: 0.8802 (t0) cc_final: 0.8426 (t0) REVERT: D 281 TYR cc_start: 0.8226 (m-80) cc_final: 0.7855 (m-80) REVERT: D 291 LEU cc_start: 0.9488 (mm) cc_final: 0.9001 (mm) REVERT: D 311 TYR cc_start: 0.9079 (t80) cc_final: 0.8592 (t80) REVERT: D 352 ASP cc_start: 0.9196 (m-30) cc_final: 0.8852 (p0) REVERT: D 375 GLN cc_start: 0.9180 (OUTLIER) cc_final: 0.8868 (mm-40) REVERT: D 459 MET cc_start: 0.8647 (tpt) cc_final: 0.8090 (mmm) REVERT: E 287 THR cc_start: 0.9485 (m) cc_final: 0.9211 (p) REVERT: E 324 THR cc_start: 0.9691 (m) cc_final: 0.9427 (p) REVERT: F 353 SER cc_start: 0.9619 (m) cc_final: 0.9381 (m) REVERT: F 400 ASP cc_start: 0.8941 (m-30) cc_final: 0.8671 (m-30) outliers start: 117 outliers final: 74 residues processed: 595 average time/residue: 0.2134 time to fit residues: 211.9719 Evaluate side-chains 559 residues out of total 4147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 475 time to evaluate : 1.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 126 ILE Chi-restraints excluded: chain G residue 164 ILE Chi-restraints excluded: chain G residue 165 PHE Chi-restraints excluded: chain Z residue 203 GLN Chi-restraints excluded: chain 7 residue 43 LEU Chi-restraints excluded: chain 7 residue 55 PHE Chi-restraints excluded: chain 7 residue 65 THR Chi-restraints excluded: chain 7 residue 95 PHE Chi-restraints excluded: chain 7 residue 100 MET Chi-restraints excluded: chain 7 residue 173 MET Chi-restraints excluded: chain 6 residue 8 LEU Chi-restraints excluded: chain 6 residue 42 LEU Chi-restraints excluded: chain 6 residue 58 VAL Chi-restraints excluded: chain 6 residue 60 THR Chi-restraints excluded: chain U residue 3 THR Chi-restraints excluded: chain U residue 4 LEU Chi-restraints excluded: chain S residue 57 LEU Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain N residue 24 ILE Chi-restraints excluded: chain N residue 55 PHE Chi-restraints excluded: chain P residue 50 MET Chi-restraints excluded: chain Q residue 40 ASN Chi-restraints excluded: chain X residue 88 MET Chi-restraints excluded: chain Y residue 23 LEU Chi-restraints excluded: chain Y residue 38 GLN Chi-restraints excluded: chain Y residue 66 ASP Chi-restraints excluded: chain Y residue 90 LYS Chi-restraints excluded: chain Y residue 111 LEU Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 375 ARG Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 272 ASP Chi-restraints excluded: chain B residue 299 ASP Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 173 ARG Chi-restraints excluded: chain C residue 246 TYR Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 401 GLU Chi-restraints excluded: chain C residue 440 THR Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 182 SER Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 263 GLN Chi-restraints excluded: chain D residue 375 GLN Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 207 ILE Chi-restraints excluded: chain E residue 213 SER Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain E residue 271 LEU Chi-restraints excluded: chain E residue 297 THR Chi-restraints excluded: chain E residue 299 THR Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 396 LEU Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 129 THR Chi-restraints excluded: chain F residue 140 VAL Chi-restraints excluded: chain F residue 284 THR Chi-restraints excluded: chain F residue 291 LEU Chi-restraints excluded: chain F residue 348 VAL Chi-restraints excluded: chain F residue 357 LEU Chi-restraints excluded: chain H residue 22 TYR Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain I residue 15 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 83 optimal weight: 50.0000 chunk 190 optimal weight: 3.9990 chunk 184 optimal weight: 7.9990 chunk 160 optimal weight: 30.0000 chunk 250 optimal weight: 0.5980 chunk 229 optimal weight: 20.0000 chunk 34 optimal weight: 30.0000 chunk 55 optimal weight: 20.0000 chunk 212 optimal weight: 0.9980 chunk 342 optimal weight: 0.9980 chunk 18 optimal weight: 8.9990 overall best weight: 2.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 210 GLN ** D 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 411 GLN H 18 HIS ** H 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 132 ASN ** I 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 19 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.133314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 99)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.080564 restraints weight = 112406.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.082693 restraints weight = 53521.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.083711 restraints weight = 32971.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.084511 restraints weight = 24802.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.085050 restraints weight = 20796.121| |-----------------------------------------------------------------------------| r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 39393 Z= 0.172 Angle : 0.655 11.430 53370 Z= 0.323 Chirality : 0.043 0.200 6322 Planarity : 0.004 0.055 6814 Dihedral : 5.927 156.511 5468 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.55 % Favored : 94.19 % Rotamer: Outliers : 3.40 % Allowed : 18.35 % Favored : 78.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.26 (0.12), residues: 5042 helix: 1.20 (0.10), residues: 2694 sheet: -1.25 (0.22), residues: 536 loop : -0.87 (0.15), residues: 1812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 130 TYR 0.022 0.002 TYR G 226 PHE 0.027 0.001 PHE S 55 TRP 0.021 0.002 TRP 6 79 HIS 0.012 0.001 HIS E 178 Details of bonding type rmsd covalent geometry : bond 0.00380 (39393) covalent geometry : angle 0.65476 (53370) hydrogen bonds : bond 0.03757 ( 2203) hydrogen bonds : angle 4.75384 ( 6411) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10084 Ramachandran restraints generated. 5042 Oldfield, 0 Emsley, 5042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10084 Ramachandran restraints generated. 5042 Oldfield, 0 Emsley, 5042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 636 residues out of total 4147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 496 time to evaluate : 1.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 250 ARG cc_start: 0.8957 (ttp-110) cc_final: 0.8564 (ttp-110) REVERT: Z 166 GLN cc_start: 0.9055 (mm-40) cc_final: 0.8835 (mm-40) REVERT: U 4 LEU cc_start: 0.6704 (OUTLIER) cc_final: 0.6160 (tt) REVERT: S 47 VAL cc_start: 0.2346 (OUTLIER) cc_final: 0.1979 (t) REVERT: K 1 MET cc_start: 0.4824 (ptt) cc_final: 0.4571 (tpp) REVERT: K 39 ARG cc_start: 0.7998 (ptm160) cc_final: 0.7420 (ttp80) REVERT: L 50 MET cc_start: -0.2912 (mmm) cc_final: -0.3149 (mmt) REVERT: Q 66 LEU cc_start: 0.3937 (OUTLIER) cc_final: 0.3593 (mp) REVERT: Q 67 MET cc_start: -0.3053 (tpt) cc_final: -0.3674 (mmt) REVERT: Y 68 ASN cc_start: 0.9551 (m-40) cc_final: 0.9338 (m110) REVERT: Y 107 ASP cc_start: 0.9147 (m-30) cc_final: 0.8680 (m-30) REVERT: A 52 GLU cc_start: 0.8370 (mm-30) cc_final: 0.8093 (mm-30) REVERT: A 217 GLN cc_start: 0.9113 (OUTLIER) cc_final: 0.8857 (mt0) REVERT: A 275 LYS cc_start: 0.9245 (mttm) cc_final: 0.9005 (mtmm) REVERT: A 294 GLU cc_start: 0.8488 (tm-30) cc_final: 0.8088 (tm-30) REVERT: A 375 ARG cc_start: 0.7776 (OUTLIER) cc_final: 0.7477 (mmp-170) REVERT: B 82 ARG cc_start: 0.8246 (mtt-85) cc_final: 0.7932 (ttm110) REVERT: B 217 GLN cc_start: 0.9121 (mm110) cc_final: 0.8775 (mm-40) REVERT: B 240 GLU cc_start: 0.8688 (mt-10) cc_final: 0.8376 (mt-10) REVERT: B 271 ASP cc_start: 0.8794 (t70) cc_final: 0.8343 (t0) REVERT: B 294 GLU cc_start: 0.8817 (pm20) cc_final: 0.8581 (pm20) REVERT: B 299 ASP cc_start: 0.8865 (OUTLIER) cc_final: 0.8512 (p0) REVERT: B 351 GLN cc_start: 0.9096 (pm20) cc_final: 0.8522 (pm20) REVERT: B 355 GLU cc_start: 0.8381 (pm20) cc_final: 0.7701 (pm20) REVERT: B 357 GLU cc_start: 0.8962 (tp30) cc_final: 0.8623 (tp30) REVERT: B 375 ARG cc_start: 0.7848 (tpp-160) cc_final: 0.7377 (mmt90) REVERT: B 455 LEU cc_start: 0.9310 (OUTLIER) cc_final: 0.9070 (pp) REVERT: B 471 LEU cc_start: 0.9616 (mm) cc_final: 0.9399 (mm) REVERT: C 178 THR cc_start: 0.9255 (OUTLIER) cc_final: 0.8928 (m) REVERT: C 217 GLN cc_start: 0.8787 (mm110) cc_final: 0.8504 (tp40) REVERT: C 270 TYR cc_start: 0.8797 (m-10) cc_final: 0.8371 (m-80) REVERT: C 396 LEU cc_start: 0.9766 (OUTLIER) cc_final: 0.9401 (mm) REVERT: D 68 GLU cc_start: 0.8229 (mp0) cc_final: 0.7990 (mp0) REVERT: D 191 THR cc_start: 0.8575 (OUTLIER) cc_final: 0.8261 (p) REVERT: D 200 GLU cc_start: 0.8966 (mm-30) cc_final: 0.8674 (mm-30) REVERT: D 257 ASN cc_start: 0.8839 (t0) cc_final: 0.8436 (t0) REVERT: D 281 TYR cc_start: 0.8287 (m-80) cc_final: 0.7946 (m-80) REVERT: D 311 TYR cc_start: 0.9069 (t80) cc_final: 0.8620 (t80) REVERT: D 352 ASP cc_start: 0.9233 (m-30) cc_final: 0.8874 (p0) REVERT: D 375 GLN cc_start: 0.9195 (OUTLIER) cc_final: 0.8879 (mm-40) REVERT: D 459 MET cc_start: 0.8775 (tpt) cc_final: 0.8267 (mmm) REVERT: E 287 THR cc_start: 0.9472 (m) cc_final: 0.9186 (p) REVERT: E 324 THR cc_start: 0.9713 (m) cc_final: 0.9421 (p) REVERT: F 141 VAL cc_start: 0.9440 (t) cc_final: 0.9185 (p) REVERT: F 353 SER cc_start: 0.9616 (m) cc_final: 0.9395 (m) REVERT: F 400 ASP cc_start: 0.8927 (m-30) cc_final: 0.8641 (m-30) outliers start: 140 outliers final: 90 residues processed: 595 average time/residue: 0.2182 time to fit residues: 219.3837 Evaluate side-chains 574 residues out of total 4147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 473 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 126 ILE Chi-restraints excluded: chain G residue 164 ILE Chi-restraints excluded: chain G residue 165 PHE Chi-restraints excluded: chain Z residue 126 VAL Chi-restraints excluded: chain 7 residue 29 LEU Chi-restraints excluded: chain 7 residue 43 LEU Chi-restraints excluded: chain 7 residue 44 LEU Chi-restraints excluded: chain 7 residue 55 PHE Chi-restraints excluded: chain 7 residue 65 THR Chi-restraints excluded: chain 7 residue 95 PHE Chi-restraints excluded: chain 7 residue 100 MET Chi-restraints excluded: chain 7 residue 173 MET Chi-restraints excluded: chain 6 residue 42 LEU Chi-restraints excluded: chain 6 residue 58 VAL Chi-restraints excluded: chain 6 residue 60 THR Chi-restraints excluded: chain U residue 3 THR Chi-restraints excluded: chain U residue 4 LEU Chi-restraints excluded: chain S residue 47 VAL Chi-restraints excluded: chain S residue 57 LEU Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain N residue 24 ILE Chi-restraints excluded: chain N residue 55 PHE Chi-restraints excluded: chain O residue 55 PHE Chi-restraints excluded: chain Q residue 40 ASN Chi-restraints excluded: chain Q residue 66 LEU Chi-restraints excluded: chain X residue 77 ILE Chi-restraints excluded: chain X residue 88 MET Chi-restraints excluded: chain Y residue 23 LEU Chi-restraints excluded: chain Y residue 38 GLN Chi-restraints excluded: chain Y residue 66 ASP Chi-restraints excluded: chain Y residue 81 LEU Chi-restraints excluded: chain Y residue 90 LYS Chi-restraints excluded: chain Y residue 163 ILE Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 217 GLN Chi-restraints excluded: chain A residue 375 ARG Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 272 ASP Chi-restraints excluded: chain B residue 299 ASP Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 349 ASP Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 246 TYR Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 400 ARG Chi-restraints excluded: chain C residue 401 GLU Chi-restraints excluded: chain C residue 440 THR Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 182 SER Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 263 GLN Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 317 LEU Chi-restraints excluded: chain D residue 375 GLN Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 207 ILE Chi-restraints excluded: chain E residue 213 SER Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain E residue 297 THR Chi-restraints excluded: chain E residue 299 THR Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 396 LEU Chi-restraints excluded: chain E residue 411 GLN Chi-restraints excluded: chain F residue 129 THR Chi-restraints excluded: chain F residue 140 VAL Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 279 VAL Chi-restraints excluded: chain F residue 284 THR Chi-restraints excluded: chain F residue 291 LEU Chi-restraints excluded: chain F residue 308 GLN Chi-restraints excluded: chain F residue 348 VAL Chi-restraints excluded: chain F residue 357 LEU Chi-restraints excluded: chain H residue 22 TYR Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain I residue 15 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 90 optimal weight: 30.0000 chunk 11 optimal weight: 8.9990 chunk 149 optimal weight: 9.9990 chunk 231 optimal weight: 5.9990 chunk 270 optimal weight: 5.9990 chunk 263 optimal weight: 1.9990 chunk 405 optimal weight: 0.7980 chunk 262 optimal weight: 0.9980 chunk 134 optimal weight: 8.9990 chunk 319 optimal weight: 0.9990 chunk 421 optimal weight: 4.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 6 57 ASN ** M 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 195 ASN ** H 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 132 ASN ** I 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.134029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.082173 restraints weight = 111877.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 70)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.083397 restraints weight = 53508.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.084401 restraints weight = 32656.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.085282 restraints weight = 24103.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 64)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.085757 restraints weight = 19826.179| |-----------------------------------------------------------------------------| r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 39393 Z= 0.147 Angle : 0.659 10.617 53370 Z= 0.324 Chirality : 0.043 0.199 6322 Planarity : 0.004 0.055 6814 Dihedral : 5.918 156.195 5468 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.24 % Favored : 94.51 % Rotamer: Outliers : 2.62 % Allowed : 19.44 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.24 (0.12), residues: 5042 helix: 1.19 (0.10), residues: 2673 sheet: -1.20 (0.22), residues: 523 loop : -0.88 (0.15), residues: 1846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 130 TYR 0.025 0.001 TYR D 242 PHE 0.027 0.001 PHE S 55 TRP 0.032 0.001 TRP 6 79 HIS 0.010 0.001 HIS E 178 Details of bonding type rmsd covalent geometry : bond 0.00326 (39393) covalent geometry : angle 0.65856 (53370) hydrogen bonds : bond 0.03734 ( 2203) hydrogen bonds : angle 4.73218 ( 6411) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10084 Ramachandran restraints generated. 5042 Oldfield, 0 Emsley, 5042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10084 Ramachandran restraints generated. 5042 Oldfield, 0 Emsley, 5042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 627 residues out of total 4147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 519 time to evaluate : 1.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 116 MET cc_start: 0.8724 (mpp) cc_final: 0.8415 (mpp) REVERT: G 250 ARG cc_start: 0.8979 (ttp-110) cc_final: 0.8369 (ptt-90) REVERT: G 262 VAL cc_start: 0.8763 (p) cc_final: 0.8518 (p) REVERT: G 265 ASN cc_start: 0.9103 (m110) cc_final: 0.8790 (m110) REVERT: Z 151 LYS cc_start: 0.8729 (ptpp) cc_final: 0.8368 (mmtt) REVERT: Z 200 GLU cc_start: 0.9721 (tp30) cc_final: 0.9479 (tp30) REVERT: 7 58 TYR cc_start: 0.5531 (t80) cc_final: 0.5113 (t80) REVERT: U 4 LEU cc_start: 0.6621 (OUTLIER) cc_final: 0.6096 (tt) REVERT: S 47 VAL cc_start: 0.2624 (OUTLIER) cc_final: 0.2258 (t) REVERT: K 1 MET cc_start: 0.4868 (ptt) cc_final: 0.4606 (tpp) REVERT: K 39 ARG cc_start: 0.8056 (ptm160) cc_final: 0.7422 (ttp80) REVERT: L 50 MET cc_start: -0.2718 (mmm) cc_final: -0.2948 (mmt) REVERT: Q 66 LEU cc_start: 0.3901 (OUTLIER) cc_final: 0.3559 (mp) REVERT: Q 67 MET cc_start: -0.3101 (tpt) cc_final: -0.3760 (mmt) REVERT: Y 68 ASN cc_start: 0.9525 (m-40) cc_final: 0.9292 (m110) REVERT: Y 107 ASP cc_start: 0.9138 (m-30) cc_final: 0.8667 (m-30) REVERT: A 34 LEU cc_start: 0.9528 (tp) cc_final: 0.9033 (mt) REVERT: A 217 GLN cc_start: 0.9093 (OUTLIER) cc_final: 0.8831 (mt0) REVERT: A 275 LYS cc_start: 0.9241 (mttm) cc_final: 0.8985 (mtmm) REVERT: A 294 GLU cc_start: 0.8476 (tm-30) cc_final: 0.8075 (tm-30) REVERT: B 82 ARG cc_start: 0.8226 (mtt-85) cc_final: 0.7909 (ttm110) REVERT: B 217 GLN cc_start: 0.9117 (mm110) cc_final: 0.8774 (mm-40) REVERT: B 271 ASP cc_start: 0.8652 (t70) cc_final: 0.8217 (t0) REVERT: B 299 ASP cc_start: 0.8854 (OUTLIER) cc_final: 0.8474 (p0) REVERT: B 351 GLN cc_start: 0.9090 (pm20) cc_final: 0.8522 (pm20) REVERT: B 355 GLU cc_start: 0.8352 (pm20) cc_final: 0.7689 (pm20) REVERT: B 357 GLU cc_start: 0.8936 (tp30) cc_final: 0.8574 (tp30) REVERT: B 375 ARG cc_start: 0.7732 (tpp-160) cc_final: 0.7223 (mmt90) REVERT: B 442 GLU cc_start: 0.9156 (mt-10) cc_final: 0.8789 (mp0) REVERT: B 455 LEU cc_start: 0.9275 (OUTLIER) cc_final: 0.9040 (pp) REVERT: B 471 LEU cc_start: 0.9613 (mm) cc_final: 0.9355 (mm) REVERT: C 178 THR cc_start: 0.9201 (OUTLIER) cc_final: 0.8880 (m) REVERT: C 217 GLN cc_start: 0.8758 (mm110) cc_final: 0.8429 (tp40) REVERT: C 270 TYR cc_start: 0.8778 (m-10) cc_final: 0.8235 (m-80) REVERT: C 396 LEU cc_start: 0.9778 (OUTLIER) cc_final: 0.9435 (mm) REVERT: D 191 THR cc_start: 0.8547 (OUTLIER) cc_final: 0.8236 (p) REVERT: D 200 GLU cc_start: 0.9010 (mm-30) cc_final: 0.8739 (mm-30) REVERT: D 281 TYR cc_start: 0.8278 (m-80) cc_final: 0.7927 (m-80) REVERT: D 311 TYR cc_start: 0.9078 (t80) cc_final: 0.8630 (t80) REVERT: D 352 ASP cc_start: 0.9212 (m-30) cc_final: 0.8871 (p0) REVERT: D 375 GLN cc_start: 0.9179 (OUTLIER) cc_final: 0.8853 (mm-40) REVERT: E 241 GLU cc_start: 0.8655 (mt-10) cc_final: 0.8247 (mt-10) REVERT: E 287 THR cc_start: 0.9433 (m) cc_final: 0.9158 (p) REVERT: E 324 THR cc_start: 0.9704 (m) cc_final: 0.9412 (p) REVERT: E 459 MET cc_start: 0.8557 (mmm) cc_final: 0.8014 (mmm) REVERT: F 141 VAL cc_start: 0.9436 (t) cc_final: 0.9213 (p) REVERT: F 353 SER cc_start: 0.9607 (m) cc_final: 0.9390 (m) REVERT: F 400 ASP cc_start: 0.8926 (m-30) cc_final: 0.8653 (m-30) outliers start: 108 outliers final: 77 residues processed: 594 average time/residue: 0.2158 time to fit residues: 214.5205 Evaluate side-chains 574 residues out of total 4147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 487 time to evaluate : 1.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 126 ILE Chi-restraints excluded: chain G residue 164 ILE Chi-restraints excluded: chain G residue 165 PHE Chi-restraints excluded: chain 7 residue 43 LEU Chi-restraints excluded: chain 7 residue 44 LEU Chi-restraints excluded: chain 7 residue 55 PHE Chi-restraints excluded: chain 7 residue 65 THR Chi-restraints excluded: chain 7 residue 95 PHE Chi-restraints excluded: chain 7 residue 100 MET Chi-restraints excluded: chain 7 residue 173 MET Chi-restraints excluded: chain 6 residue 42 LEU Chi-restraints excluded: chain 6 residue 58 VAL Chi-restraints excluded: chain 6 residue 60 THR Chi-restraints excluded: chain U residue 3 THR Chi-restraints excluded: chain U residue 4 LEU Chi-restraints excluded: chain S residue 47 VAL Chi-restraints excluded: chain S residue 57 LEU Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain N residue 24 ILE Chi-restraints excluded: chain N residue 55 PHE Chi-restraints excluded: chain O residue 55 PHE Chi-restraints excluded: chain Q residue 40 ASN Chi-restraints excluded: chain Q residue 66 LEU Chi-restraints excluded: chain R residue 53 LEU Chi-restraints excluded: chain X residue 88 MET Chi-restraints excluded: chain Y residue 23 LEU Chi-restraints excluded: chain Y residue 38 GLN Chi-restraints excluded: chain Y residue 66 ASP Chi-restraints excluded: chain Y residue 90 LYS Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 217 GLN Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 299 ASP Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 349 ASP Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 246 TYR Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 401 GLU Chi-restraints excluded: chain C residue 440 THR Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 182 SER Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 263 GLN Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 317 LEU Chi-restraints excluded: chain D residue 375 GLN Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 207 ILE Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain E residue 271 LEU Chi-restraints excluded: chain E residue 299 THR Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 396 LEU Chi-restraints excluded: chain F residue 129 THR Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 279 VAL Chi-restraints excluded: chain F residue 291 LEU Chi-restraints excluded: chain F residue 308 GLN Chi-restraints excluded: chain F residue 348 VAL Chi-restraints excluded: chain F residue 357 LEU Chi-restraints excluded: chain F residue 414 LEU Chi-restraints excluded: chain H residue 22 TYR Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain I residue 15 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 330 optimal weight: 0.9980 chunk 382 optimal weight: 6.9990 chunk 138 optimal weight: 5.9990 chunk 234 optimal weight: 7.9990 chunk 482 optimal weight: 8.9990 chunk 173 optimal weight: 2.9990 chunk 399 optimal weight: 3.9990 chunk 3 optimal weight: 7.9990 chunk 176 optimal weight: 6.9990 chunk 392 optimal weight: 5.9990 chunk 341 optimal weight: 6.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 217 GLN 6 57 ASN ** M 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 132 ASN ** I 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.132150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.079163 restraints weight = 112820.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.081146 restraints weight = 53104.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.082063 restraints weight = 32381.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.082935 restraints weight = 24537.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 71)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.083277 restraints weight = 20375.800| |-----------------------------------------------------------------------------| r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 39393 Z= 0.210 Angle : 0.695 13.473 53370 Z= 0.343 Chirality : 0.044 0.233 6322 Planarity : 0.004 0.056 6814 Dihedral : 5.991 155.579 5468 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 14.59 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.57 % Favored : 94.17 % Rotamer: Outliers : 2.82 % Allowed : 19.47 % Favored : 77.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.28 (0.12), residues: 5042 helix: 1.21 (0.10), residues: 2700 sheet: -1.24 (0.22), residues: 516 loop : -0.85 (0.15), residues: 1826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 130 TYR 0.021 0.002 TYR C 270 PHE 0.028 0.001 PHE S 55 TRP 0.031 0.002 TRP 6 79 HIS 0.010 0.001 HIS E 178 Details of bonding type rmsd covalent geometry : bond 0.00463 (39393) covalent geometry : angle 0.69461 (53370) hydrogen bonds : bond 0.03819 ( 2203) hydrogen bonds : angle 4.78166 ( 6411) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10084 Ramachandran restraints generated. 5042 Oldfield, 0 Emsley, 5042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10084 Ramachandran restraints generated. 5042 Oldfield, 0 Emsley, 5042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 609 residues out of total 4147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 493 time to evaluate : 1.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 8 MET cc_start: 0.9216 (ppp) cc_final: 0.8974 (ppp) REVERT: G 116 MET cc_start: 0.8818 (mpp) cc_final: 0.8443 (mpp) REVERT: G 250 ARG cc_start: 0.8967 (ttp-110) cc_final: 0.8374 (ptt-90) REVERT: 6 57 ASN cc_start: 0.4530 (OUTLIER) cc_final: 0.4312 (p0) REVERT: U 4 LEU cc_start: 0.6711 (OUTLIER) cc_final: 0.6158 (tt) REVERT: S 47 VAL cc_start: 0.2688 (OUTLIER) cc_final: 0.2299 (t) REVERT: K 1 MET cc_start: 0.4772 (ptt) cc_final: 0.4478 (tpp) REVERT: K 39 ARG cc_start: 0.7980 (ptm160) cc_final: 0.7379 (ttp80) REVERT: L 50 MET cc_start: -0.2858 (mmm) cc_final: -0.3071 (mmt) REVERT: Q 16 THR cc_start: -0.0208 (OUTLIER) cc_final: -0.0476 (p) REVERT: Q 66 LEU cc_start: 0.3903 (OUTLIER) cc_final: 0.3534 (mp) REVERT: Q 67 MET cc_start: -0.3151 (tpt) cc_final: -0.3718 (mmt) REVERT: Y 68 ASN cc_start: 0.9522 (m-40) cc_final: 0.9292 (m110) REVERT: Y 90 LYS cc_start: 0.9506 (OUTLIER) cc_final: 0.9043 (mttt) REVERT: Y 107 ASP cc_start: 0.9144 (m-30) cc_final: 0.8680 (m-30) REVERT: A 34 LEU cc_start: 0.9560 (tp) cc_final: 0.9053 (mt) REVERT: A 52 GLU cc_start: 0.8526 (mm-30) cc_final: 0.8082 (mm-30) REVERT: A 217 GLN cc_start: 0.9130 (OUTLIER) cc_final: 0.8859 (mt0) REVERT: A 294 GLU cc_start: 0.8474 (tm-30) cc_final: 0.8051 (tm-30) REVERT: B 82 ARG cc_start: 0.8263 (mtt-85) cc_final: 0.7935 (ttm110) REVERT: B 217 GLN cc_start: 0.9148 (mm110) cc_final: 0.8810 (mm-40) REVERT: B 271 ASP cc_start: 0.8669 (t70) cc_final: 0.8202 (t0) REVERT: B 294 GLU cc_start: 0.8845 (pm20) cc_final: 0.8637 (pm20) REVERT: B 299 ASP cc_start: 0.8904 (OUTLIER) cc_final: 0.8520 (p0) REVERT: B 349 ASP cc_start: 0.8946 (OUTLIER) cc_final: 0.7392 (m-30) REVERT: B 351 GLN cc_start: 0.9111 (pm20) cc_final: 0.8534 (pm20) REVERT: B 355 GLU cc_start: 0.8404 (pm20) cc_final: 0.7713 (pm20) REVERT: B 357 GLU cc_start: 0.8955 (tp30) cc_final: 0.8599 (tp30) REVERT: B 375 ARG cc_start: 0.7938 (tpp-160) cc_final: 0.7251 (mmt90) REVERT: C 178 THR cc_start: 0.9294 (OUTLIER) cc_final: 0.8965 (m) REVERT: C 217 GLN cc_start: 0.8787 (mm110) cc_final: 0.8502 (tp40) REVERT: C 270 TYR cc_start: 0.8893 (m-10) cc_final: 0.8245 (m-80) REVERT: C 331 THR cc_start: 0.9694 (OUTLIER) cc_final: 0.9433 (t) REVERT: C 375 ARG cc_start: 0.8902 (mmm-85) cc_final: 0.8411 (mmm-85) REVERT: C 396 LEU cc_start: 0.9771 (OUTLIER) cc_final: 0.9448 (mm) REVERT: D 38 GLU cc_start: 0.8676 (OUTLIER) cc_final: 0.8158 (mm-30) REVERT: D 191 THR cc_start: 0.8691 (OUTLIER) cc_final: 0.8388 (p) REVERT: D 200 GLU cc_start: 0.9072 (mm-30) cc_final: 0.8833 (mm-30) REVERT: D 257 ASN cc_start: 0.8778 (t0) cc_final: 0.8067 (t0) REVERT: D 281 TYR cc_start: 0.8406 (m-80) cc_final: 0.8099 (m-80) REVERT: D 311 TYR cc_start: 0.9131 (t80) cc_final: 0.8639 (t80) REVERT: D 352 ASP cc_start: 0.9222 (m-30) cc_final: 0.8873 (p0) REVERT: D 375 GLN cc_start: 0.9186 (OUTLIER) cc_final: 0.8878 (mm-40) REVERT: E 287 THR cc_start: 0.9404 (m) cc_final: 0.9110 (p) REVERT: E 324 THR cc_start: 0.9696 (m) cc_final: 0.9403 (p) REVERT: F 353 SER cc_start: 0.9633 (m) cc_final: 0.9393 (m) REVERT: F 400 ASP cc_start: 0.8901 (m-30) cc_final: 0.8634 (m-30) outliers start: 116 outliers final: 82 residues processed: 574 average time/residue: 0.2324 time to fit residues: 224.0843 Evaluate side-chains 564 residues out of total 4147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 467 time to evaluate : 1.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 126 ILE Chi-restraints excluded: chain G residue 165 PHE Chi-restraints excluded: chain Z residue 126 VAL Chi-restraints excluded: chain 7 residue 43 LEU Chi-restraints excluded: chain 7 residue 44 LEU Chi-restraints excluded: chain 7 residue 55 PHE Chi-restraints excluded: chain 7 residue 65 THR Chi-restraints excluded: chain 7 residue 95 PHE Chi-restraints excluded: chain 7 residue 100 MET Chi-restraints excluded: chain 7 residue 173 MET Chi-restraints excluded: chain 6 residue 42 LEU Chi-restraints excluded: chain 6 residue 57 ASN Chi-restraints excluded: chain 6 residue 58 VAL Chi-restraints excluded: chain 6 residue 60 THR Chi-restraints excluded: chain U residue 3 THR Chi-restraints excluded: chain U residue 4 LEU Chi-restraints excluded: chain S residue 47 VAL Chi-restraints excluded: chain S residue 57 LEU Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain N residue 24 ILE Chi-restraints excluded: chain N residue 55 PHE Chi-restraints excluded: chain O residue 55 PHE Chi-restraints excluded: chain Q residue 16 THR Chi-restraints excluded: chain Q residue 40 ASN Chi-restraints excluded: chain Q residue 66 LEU Chi-restraints excluded: chain R residue 53 LEU Chi-restraints excluded: chain X residue 77 ILE Chi-restraints excluded: chain X residue 88 MET Chi-restraints excluded: chain Y residue 23 LEU Chi-restraints excluded: chain Y residue 38 GLN Chi-restraints excluded: chain Y residue 66 ASP Chi-restraints excluded: chain Y residue 81 LEU Chi-restraints excluded: chain Y residue 90 LYS Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 217 GLN Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 246 TYR Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 272 ASP Chi-restraints excluded: chain B residue 299 ASP Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 349 ASP Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 246 TYR Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 401 GLU Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 38 GLU Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 182 SER Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 263 GLN Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 317 LEU Chi-restraints excluded: chain D residue 375 GLN Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 207 ILE Chi-restraints excluded: chain E residue 213 SER Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 297 THR Chi-restraints excluded: chain E residue 299 THR Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 396 LEU Chi-restraints excluded: chain F residue 129 THR Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 279 VAL Chi-restraints excluded: chain F residue 291 LEU Chi-restraints excluded: chain F residue 308 GLN Chi-restraints excluded: chain F residue 348 VAL Chi-restraints excluded: chain F residue 357 LEU Chi-restraints excluded: chain H residue 22 TYR Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain I residue 15 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 310 optimal weight: 3.9990 chunk 371 optimal weight: 4.9990 chunk 131 optimal weight: 6.9990 chunk 288 optimal weight: 10.0000 chunk 82 optimal weight: 0.3980 chunk 420 optimal weight: 1.9990 chunk 148 optimal weight: 3.9990 chunk 435 optimal weight: 0.9990 chunk 264 optimal weight: 1.9990 chunk 124 optimal weight: 20.0000 chunk 404 optimal weight: 3.9990 overall best weight: 1.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 260 GLN 6 57 ASN ** M 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 29 GLN ** Y 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 220 GLN E 411 GLN ** H 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 19 GLN ** 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 = 0.4098 r_free = 0.4098 target = 0.133688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.081084 restraints weight = 112205.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.083021 restraints weight = 53122.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.084256 restraints weight = 33108.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.084852 restraints weight = 24359.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.085135 restraints weight = 20602.168| |-----------------------------------------------------------------------------| r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.2570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 39393 Z= 0.147 Angle : 0.687 11.419 53370 Z= 0.338 Chirality : 0.044 0.243 6322 Planarity : 0.004 0.057 6814 Dihedral : 5.954 155.332 5468 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.32 % Favored : 94.43 % Rotamer: Outliers : 2.58 % Allowed : 19.95 % Favored : 77.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.27 (0.12), residues: 5042 helix: 1.21 (0.10), residues: 2691 sheet: -1.27 (0.22), residues: 529 loop : -0.83 (0.16), residues: 1822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 130 TYR 0.034 0.002 TYR F 345 PHE 0.027 0.001 PHE S 55 TRP 0.057 0.002 TRP 6 79 HIS 0.007 0.001 HIS E 367 Details of bonding type rmsd covalent geometry : bond 0.00326 (39393) covalent geometry : angle 0.68738 (53370) hydrogen bonds : bond 0.03731 ( 2203) hydrogen bonds : angle 4.73785 ( 6411) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10084 Ramachandran restraints generated. 5042 Oldfield, 0 Emsley, 5042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10084 Ramachandran restraints generated. 5042 Oldfield, 0 Emsley, 5042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 627 residues out of total 4147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 521 time to evaluate : 1.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 8 MET cc_start: 0.9245 (ppp) cc_final: 0.9018 (ppp) REVERT: G 250 ARG cc_start: 0.9020 (ttp-110) cc_final: 0.8582 (ttp-110) REVERT: G 265 ASN cc_start: 0.9096 (m110) cc_final: 0.8759 (m110) REVERT: Z 151 LYS cc_start: 0.8629 (ptpp) cc_final: 0.8182 (mmtt) REVERT: 7 58 TYR cc_start: 0.5175 (t80) cc_final: 0.4971 (t80) REVERT: 6 57 ASN cc_start: 0.4706 (OUTLIER) cc_final: 0.4454 (p0) REVERT: U 4 LEU cc_start: 0.6542 (OUTLIER) cc_final: 0.6063 (tt) REVERT: S 47 VAL cc_start: 0.2916 (OUTLIER) cc_final: 0.2466 (t) REVERT: K 1 MET cc_start: 0.4860 (ptt) cc_final: 0.4576 (tpp) REVERT: K 39 ARG cc_start: 0.8030 (ptm160) cc_final: 0.7363 (ttp80) REVERT: L 50 MET cc_start: -0.2609 (mmm) cc_final: -0.2928 (mmt) REVERT: Q 16 THR cc_start: -0.0325 (OUTLIER) cc_final: -0.0557 (p) REVERT: Q 66 LEU cc_start: 0.3851 (OUTLIER) cc_final: 0.3471 (mp) REVERT: Q 67 MET cc_start: -0.3432 (tpt) cc_final: -0.3961 (mmt) REVERT: Y 68 ASN cc_start: 0.9527 (m-40) cc_final: 0.9296 (m110) REVERT: Y 90 LYS cc_start: 0.9487 (OUTLIER) cc_final: 0.9014 (mttt) REVERT: Y 102 GLU cc_start: 0.8133 (pm20) cc_final: 0.7609 (pm20) REVERT: Y 107 ASP cc_start: 0.9126 (m-30) cc_final: 0.8657 (m-30) REVERT: A 34 LEU cc_start: 0.9546 (tp) cc_final: 0.9043 (mt) REVERT: A 52 GLU cc_start: 0.8513 (mm-30) cc_final: 0.8168 (mm-30) REVERT: A 217 GLN cc_start: 0.9093 (OUTLIER) cc_final: 0.8810 (mt0) REVERT: B 82 ARG cc_start: 0.8245 (mtt-85) cc_final: 0.7924 (ttm110) REVERT: B 217 GLN cc_start: 0.9143 (mm110) cc_final: 0.8733 (mm-40) REVERT: B 218 LEU cc_start: 0.9698 (tp) cc_final: 0.9437 (tt) REVERT: B 271 ASP cc_start: 0.8688 (t70) cc_final: 0.8288 (t0) REVERT: B 280 TYR cc_start: 0.9412 (t80) cc_final: 0.9171 (t80) REVERT: B 294 GLU cc_start: 0.8855 (pm20) cc_final: 0.8632 (pm20) REVERT: B 299 ASP cc_start: 0.8844 (OUTLIER) cc_final: 0.8227 (p0) REVERT: B 349 ASP cc_start: 0.8988 (OUTLIER) cc_final: 0.7443 (m-30) REVERT: B 351 GLN cc_start: 0.9091 (pm20) cc_final: 0.8504 (pm20) REVERT: B 355 GLU cc_start: 0.8366 (pm20) cc_final: 0.7690 (pm20) REVERT: B 357 GLU cc_start: 0.8941 (tp30) cc_final: 0.8545 (tp30) REVERT: B 375 ARG cc_start: 0.7809 (tpp-160) cc_final: 0.7169 (mmt90) REVERT: B 442 GLU cc_start: 0.9174 (mt-10) cc_final: 0.8869 (mp0) REVERT: C 178 THR cc_start: 0.9191 (OUTLIER) cc_final: 0.8834 (m) REVERT: C 217 GLN cc_start: 0.8746 (mm110) cc_final: 0.8412 (mm110) REVERT: C 270 TYR cc_start: 0.8816 (m-10) cc_final: 0.8166 (m-80) REVERT: C 331 THR cc_start: 0.9716 (OUTLIER) cc_final: 0.9432 (t) REVERT: C 375 ARG cc_start: 0.8887 (mmm-85) cc_final: 0.8412 (mmm-85) REVERT: C 396 LEU cc_start: 0.9771 (OUTLIER) cc_final: 0.9484 (mm) REVERT: D 38 GLU cc_start: 0.8694 (OUTLIER) cc_final: 0.8206 (mm-30) REVERT: D 191 THR cc_start: 0.8593 (OUTLIER) cc_final: 0.8291 (p) REVERT: D 200 GLU cc_start: 0.9089 (mm-30) cc_final: 0.8840 (mm-30) REVERT: D 257 ASN cc_start: 0.8739 (t0) cc_final: 0.8180 (t0) REVERT: D 281 TYR cc_start: 0.8311 (m-80) cc_final: 0.8028 (m-80) REVERT: D 311 TYR cc_start: 0.9116 (t80) cc_final: 0.8633 (t80) REVERT: D 352 ASP cc_start: 0.9194 (m-30) cc_final: 0.8887 (p0) REVERT: D 375 GLN cc_start: 0.9180 (OUTLIER) cc_final: 0.8837 (mm-40) REVERT: D 465 ASP cc_start: 0.8769 (t0) cc_final: 0.8527 (t0) REVERT: E 241 GLU cc_start: 0.8629 (mt-10) cc_final: 0.8235 (mt-10) REVERT: E 287 THR cc_start: 0.9379 (m) cc_final: 0.9075 (p) REVERT: E 324 THR cc_start: 0.9693 (m) cc_final: 0.9458 (p) REVERT: E 356 ARG cc_start: 0.8552 (tmm-80) cc_final: 0.8028 (tmm-80) REVERT: E 459 MET cc_start: 0.8593 (mmm) cc_final: 0.8038 (mmm) REVERT: F 353 SER cc_start: 0.9617 (m) cc_final: 0.9379 (m) REVERT: F 400 ASP cc_start: 0.8901 (m-30) cc_final: 0.8645 (m-30) REVERT: H 38 ARG cc_start: 0.7649 (mmt90) cc_final: 0.7398 (tpp80) outliers start: 106 outliers final: 81 residues processed: 592 average time/residue: 0.2529 time to fit residues: 248.5634 Evaluate side-chains 582 residues out of total 4147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 486 time to evaluate : 1.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 126 ILE Chi-restraints excluded: chain G residue 164 ILE Chi-restraints excluded: chain G residue 165 PHE Chi-restraints excluded: chain Z residue 126 VAL Chi-restraints excluded: chain 7 residue 29 LEU Chi-restraints excluded: chain 7 residue 43 LEU Chi-restraints excluded: chain 7 residue 44 LEU Chi-restraints excluded: chain 7 residue 55 PHE Chi-restraints excluded: chain 7 residue 65 THR Chi-restraints excluded: chain 7 residue 95 PHE Chi-restraints excluded: chain 7 residue 100 MET Chi-restraints excluded: chain 7 residue 173 MET Chi-restraints excluded: chain 6 residue 42 LEU Chi-restraints excluded: chain 6 residue 57 ASN Chi-restraints excluded: chain 6 residue 60 THR Chi-restraints excluded: chain U residue 3 THR Chi-restraints excluded: chain U residue 4 LEU Chi-restraints excluded: chain S residue 47 VAL Chi-restraints excluded: chain S residue 57 LEU Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain N residue 24 ILE Chi-restraints excluded: chain N residue 55 PHE Chi-restraints excluded: chain O residue 55 PHE Chi-restraints excluded: chain Q residue 16 THR Chi-restraints excluded: chain Q residue 40 ASN Chi-restraints excluded: chain Q residue 66 LEU Chi-restraints excluded: chain R residue 53 LEU Chi-restraints excluded: chain X residue 88 MET Chi-restraints excluded: chain Y residue 23 LEU Chi-restraints excluded: chain Y residue 38 GLN Chi-restraints excluded: chain Y residue 66 ASP Chi-restraints excluded: chain Y residue 90 LYS Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 217 GLN Chi-restraints excluded: chain A residue 375 ARG Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 246 TYR Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 299 ASP Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 349 ASP Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 467 GLU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 246 TYR Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 401 GLU Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 38 GLU Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 182 SER Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 263 GLN Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 317 LEU Chi-restraints excluded: chain D residue 375 GLN Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 207 ILE Chi-restraints excluded: chain E residue 213 SER Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain E residue 271 LEU Chi-restraints excluded: chain E residue 299 THR Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 396 LEU Chi-restraints excluded: chain E residue 411 GLN Chi-restraints excluded: chain F residue 129 THR Chi-restraints excluded: chain F residue 279 VAL Chi-restraints excluded: chain F residue 291 LEU Chi-restraints excluded: chain F residue 308 GLN Chi-restraints excluded: chain F residue 348 VAL Chi-restraints excluded: chain F residue 357 LEU Chi-restraints excluded: chain H residue 22 TYR Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain I residue 9 SER Chi-restraints excluded: chain I residue 15 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 77 optimal weight: 8.9990 chunk 116 optimal weight: 20.0000 chunk 167 optimal weight: 10.0000 chunk 241 optimal weight: 3.9990 chunk 84 optimal weight: 30.0000 chunk 380 optimal weight: 5.9990 chunk 146 optimal weight: 40.0000 chunk 403 optimal weight: 9.9990 chunk 202 optimal weight: 0.0170 chunk 164 optimal weight: 20.0000 chunk 20 optimal weight: 30.0000 overall best weight: 5.8026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 6 57 ASN ** M 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 114 HIS ** Y 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 220 GLN ** A 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 15 ASN ** I 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.130079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.077013 restraints weight = 114590.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.078731 restraints weight = 54779.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.079715 restraints weight = 34184.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.080475 restraints weight = 25784.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.080815 restraints weight = 21604.694| |-----------------------------------------------------------------------------| r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.2856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.110 39393 Z= 0.286 Angle : 0.778 21.237 53370 Z= 0.382 Chirality : 0.046 0.448 6322 Planarity : 0.005 0.074 6814 Dihedral : 6.065 154.196 5468 Min Nonbonded Distance : 1.768 Molprobity Statistics. All-atom Clashscore : 16.45 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.95 % Favored : 93.81 % Rotamer: Outliers : 2.58 % Allowed : 20.05 % Favored : 77.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.20 (0.12), residues: 5042 helix: 1.15 (0.10), residues: 2701 sheet: -1.32 (0.23), residues: 509 loop : -0.89 (0.16), residues: 1832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG E 412 TYR 0.048 0.002 TYR F 345 PHE 0.029 0.002 PHE S 55 TRP 0.042 0.002 TRP 6 79 HIS 0.010 0.001 HIS E 178 Details of bonding type rmsd covalent geometry : bond 0.00626 (39393) covalent geometry : angle 0.77769 (53370) hydrogen bonds : bond 0.03959 ( 2203) hydrogen bonds : angle 4.86859 ( 6411) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10084 Ramachandran restraints generated. 5042 Oldfield, 0 Emsley, 5042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10084 Ramachandran restraints generated. 5042 Oldfield, 0 Emsley, 5042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 575 residues out of total 4147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 469 time to evaluate : 1.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 250 ARG cc_start: 0.9043 (ttp-110) cc_final: 0.8598 (ttp-110) REVERT: Z 151 LYS cc_start: 0.8637 (ptpp) cc_final: 0.8183 (mmtt) REVERT: 7 164 LYS cc_start: 0.8687 (mmtp) cc_final: 0.8273 (tppt) REVERT: 6 57 ASN cc_start: 0.4782 (OUTLIER) cc_final: 0.4487 (p0) REVERT: U 4 LEU cc_start: 0.6613 (OUTLIER) cc_final: 0.6127 (tt) REVERT: K 1 MET cc_start: 0.4676 (ptt) cc_final: 0.4473 (tpp) REVERT: K 39 ARG cc_start: 0.7970 (ptm160) cc_final: 0.7329 (ttp80) REVERT: Q 16 THR cc_start: -0.0368 (OUTLIER) cc_final: -0.0639 (p) REVERT: Q 66 LEU cc_start: 0.3728 (OUTLIER) cc_final: 0.3319 (mp) REVERT: Q 67 MET cc_start: -0.3325 (tpt) cc_final: -0.3851 (mmt) REVERT: Y 11 ARG cc_start: 0.8745 (mmp80) cc_final: 0.8410 (mmp80) REVERT: Y 68 ASN cc_start: 0.9554 (m-40) cc_final: 0.9325 (m110) REVERT: Y 90 LYS cc_start: 0.9525 (OUTLIER) cc_final: 0.9069 (mttt) REVERT: Y 107 ASP cc_start: 0.9092 (m-30) cc_final: 0.8795 (m-30) REVERT: A 34 LEU cc_start: 0.9589 (tp) cc_final: 0.9250 (mt) REVERT: A 52 GLU cc_start: 0.8584 (mm-30) cc_final: 0.8240 (mm-30) REVERT: B 82 ARG cc_start: 0.8330 (mtt-85) cc_final: 0.8007 (ttm110) REVERT: B 217 GLN cc_start: 0.9177 (mm110) cc_final: 0.8872 (mm-40) REVERT: B 271 ASP cc_start: 0.8723 (t70) cc_final: 0.8230 (t0) REVERT: B 294 GLU cc_start: 0.8925 (pm20) cc_final: 0.8720 (pm20) REVERT: B 299 ASP cc_start: 0.8924 (OUTLIER) cc_final: 0.8432 (p0) REVERT: B 349 ASP cc_start: 0.8915 (OUTLIER) cc_final: 0.7574 (m-30) REVERT: B 351 GLN cc_start: 0.9142 (pm20) cc_final: 0.8549 (pm20) REVERT: B 355 GLU cc_start: 0.8439 (pm20) cc_final: 0.7722 (pm20) REVERT: B 357 GLU cc_start: 0.8987 (tp30) cc_final: 0.8639 (tp30) REVERT: C 178 THR cc_start: 0.9364 (OUTLIER) cc_final: 0.9040 (m) REVERT: C 270 TYR cc_start: 0.9036 (m-10) cc_final: 0.8432 (m-80) REVERT: C 331 THR cc_start: 0.9685 (OUTLIER) cc_final: 0.9424 (t) REVERT: C 375 ARG cc_start: 0.8912 (mmm-85) cc_final: 0.8451 (mmm-85) REVERT: C 396 LEU cc_start: 0.9745 (OUTLIER) cc_final: 0.9504 (mm) REVERT: C 417 LYS cc_start: 0.9264 (ptpp) cc_final: 0.8899 (mtmm) REVERT: D 38 GLU cc_start: 0.8730 (OUTLIER) cc_final: 0.8280 (mm-30) REVERT: D 191 THR cc_start: 0.8826 (OUTLIER) cc_final: 0.8529 (p) REVERT: D 201 MET cc_start: 0.9172 (mtm) cc_final: 0.8935 (mtm) REVERT: D 257 ASN cc_start: 0.8832 (t0) cc_final: 0.8287 (t0) REVERT: D 281 TYR cc_start: 0.8533 (m-80) cc_final: 0.8245 (m-80) REVERT: D 311 TYR cc_start: 0.9188 (t80) cc_final: 0.8772 (t80) REVERT: D 352 ASP cc_start: 0.9221 (m-30) cc_final: 0.8856 (p0) REVERT: D 375 GLN cc_start: 0.9183 (OUTLIER) cc_final: 0.8864 (mm-40) REVERT: E 324 THR cc_start: 0.9727 (m) cc_final: 0.9445 (p) REVERT: E 459 MET cc_start: 0.8735 (mmm) cc_final: 0.8120 (mmm) REVERT: F 400 ASP cc_start: 0.8914 (m-30) cc_final: 0.8625 (m-30) outliers start: 106 outliers final: 78 residues processed: 545 average time/residue: 0.2422 time to fit residues: 221.1483 Evaluate side-chains 542 residues out of total 4147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 451 time to evaluate : 1.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 126 ILE Chi-restraints excluded: chain G residue 164 ILE Chi-restraints excluded: chain G residue 165 PHE Chi-restraints excluded: chain Z residue 126 VAL Chi-restraints excluded: chain 7 residue 29 LEU Chi-restraints excluded: chain 7 residue 43 LEU Chi-restraints excluded: chain 7 residue 55 PHE Chi-restraints excluded: chain 7 residue 65 THR Chi-restraints excluded: chain 7 residue 95 PHE Chi-restraints excluded: chain 7 residue 100 MET Chi-restraints excluded: chain 7 residue 173 MET Chi-restraints excluded: chain 6 residue 42 LEU Chi-restraints excluded: chain 6 residue 57 ASN Chi-restraints excluded: chain 6 residue 60 THR Chi-restraints excluded: chain U residue 3 THR Chi-restraints excluded: chain U residue 4 LEU Chi-restraints excluded: chain U residue 82 TYR Chi-restraints excluded: chain S residue 57 LEU Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain N residue 24 ILE Chi-restraints excluded: chain N residue 55 PHE Chi-restraints excluded: chain O residue 55 PHE Chi-restraints excluded: chain Q residue 16 THR Chi-restraints excluded: chain Q residue 40 ASN Chi-restraints excluded: chain Q residue 66 LEU Chi-restraints excluded: chain R residue 53 LEU Chi-restraints excluded: chain X residue 101 LEU Chi-restraints excluded: chain Y residue 23 LEU Chi-restraints excluded: chain Y residue 38 GLN Chi-restraints excluded: chain Y residue 66 ASP Chi-restraints excluded: chain Y residue 90 LYS Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 375 ARG Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 246 TYR Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 299 ASP Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 349 ASP Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 467 GLU Chi-restraints excluded: chain B residue 493 LYS Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 246 TYR Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 401 GLU Chi-restraints excluded: chain C residue 415 SER Chi-restraints excluded: chain D residue 38 GLU Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 182 SER Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 263 GLN Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 375 GLN Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 207 ILE Chi-restraints excluded: chain E residue 213 SER Chi-restraints excluded: chain E residue 297 THR Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 396 LEU Chi-restraints excluded: chain F residue 129 THR Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 279 VAL Chi-restraints excluded: chain F residue 308 GLN Chi-restraints excluded: chain F residue 348 VAL Chi-restraints excluded: chain F residue 357 LEU Chi-restraints excluded: chain H residue 22 TYR Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain I residue 9 SER Chi-restraints excluded: chain I residue 15 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 441 optimal weight: 5.9990 chunk 44 optimal weight: 6.9990 chunk 166 optimal weight: 3.9990 chunk 204 optimal weight: 0.9990 chunk 255 optimal weight: 2.9990 chunk 45 optimal weight: 30.0000 chunk 410 optimal weight: 2.9990 chunk 58 optimal weight: 9.9990 chunk 86 optimal weight: 50.0000 chunk 421 optimal weight: 4.9990 chunk 49 optimal weight: 30.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 114 HIS ** Y 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 220 GLN ** H 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 15 ASN I 19 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.131877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 94)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.078814 restraints weight = 113831.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.080827 restraints weight = 53994.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.081865 restraints weight = 33144.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.082568 restraints weight = 24791.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.082926 restraints weight = 20568.410| |-----------------------------------------------------------------------------| r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.2917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 39393 Z= 0.187 Angle : 0.734 16.017 53370 Z= 0.360 Chirality : 0.046 0.449 6322 Planarity : 0.004 0.055 6814 Dihedral : 6.015 153.882 5468 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 15.10 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.34 % Favored : 94.43 % Rotamer: Outliers : 2.31 % Allowed : 20.58 % Favored : 77.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.21 (0.12), residues: 5042 helix: 1.15 (0.10), residues: 2696 sheet: -1.32 (0.23), residues: 508 loop : -0.86 (0.16), residues: 1838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 130 TYR 0.043 0.002 TYR F 345 PHE 0.028 0.001 PHE S 55 TRP 0.061 0.002 TRP 6 79 HIS 0.007 0.001 HIS E 178 Details of bonding type rmsd covalent geometry : bond 0.00416 (39393) covalent geometry : angle 0.73400 (53370) hydrogen bonds : bond 0.03840 ( 2203) hydrogen bonds : angle 4.80435 ( 6411) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10710.54 seconds wall clock time: 184 minutes 32.65 seconds (11072.65 seconds total)