Starting phenix.real_space_refine on Tue Aug 26 07:13:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9f5z_50204/08_2025/9f5z_50204.cif Found real_map, /net/cci-nas-00/data/ceres_data/9f5z_50204/08_2025/9f5z_50204.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9f5z_50204/08_2025/9f5z_50204.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9f5z_50204/08_2025/9f5z_50204.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9f5z_50204/08_2025/9f5z_50204.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9f5z_50204/08_2025/9f5z_50204.map" } resolution = 2.39 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= 0.025 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: 7 Type Number sf(0) Gaussians Fe 6 7.16 5 Zn 2 6.06 5 P 27 5.49 5 S 146 5.16 5 C 21867 2.51 5 N 5604 2.21 5 O 6802 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.03s 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: 34454 Number of models: 1 Model: "" Number of chains: 51 Chain: "1A" Number of atoms: 2958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 2958 Classifications: {'peptide': 376} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 356} Chain: "1B" Number of atoms: 2958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 2958 Classifications: {'peptide': 376} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 356} Chain: "1C" Number of atoms: 1602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1602 Classifications: {'peptide': 207} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 191} Chain: "1D" Number of atoms: 1602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1602 Classifications: {'peptide': 207} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 191} Chain: "1E" Number of atoms: 1898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1898 Classifications: {'peptide': 243} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 226} Chain: "1F" Number of atoms: 1898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1898 Classifications: {'peptide': 243} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 226} Chain: "1G" Number of atoms: 486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 486 Classifications: {'peptide': 59} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 57} Chain: "1H" Number of atoms: 486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 486 Classifications: {'peptide': 59} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 57} Chain: "1I" Number of atoms: 550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 550 Classifications: {'peptide': 68} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 63} Chain: "1J" Number of atoms: 550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 550 Classifications: {'peptide': 68} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 63} Chain: "1K" Number of atoms: 594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 594 Classifications: {'peptide': 70} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "1L" Number of atoms: 594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 594 Classifications: {'peptide': 70} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "1M" Number of atoms: 3646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3646 Classifications: {'peptide': 464} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 445} Chain: "1N" Number of atoms: 3646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3646 Classifications: {'peptide': 464} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 445} Chain: "1O" Number of atoms: 371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 371 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 3, 'TRANS': 44} Chain: "1P" Number of atoms: 371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 371 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 3, 'TRANS': 44} Chain: "1Q" Number of atoms: 3204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3204 Classifications: {'peptide': 441} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 418} Chain: "1R" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 980 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 113} Chain: "1S" Number of atoms: 3204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3204 Classifications: {'peptide': 441} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 22, 'TRANS': 417} Chain: "1T" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 980 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 113} Chain: "1A" Number of atoms: 252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 252 Unusual residues: {'3PH': 1, 'CDL': 1, 'HEC': 2, 'UQ5': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 58 Chain: "1B" Number of atoms: 393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 393 Unusual residues: {'3PH': 2, 'CDL': 2, 'HEC': 2, 'UQ5': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 65 Chain: "1E" Number of atoms: 170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 170 Unusual residues: {'3PH': 1, 'CDL': 1, 'HEC': 1, 'PTY': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 71 Chain: "1F" Number of atoms: 137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 137 Unusual residues: {'CDL': 1, 'HEC': 1, 'PTY': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 56 Chain: "1G" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'PC7': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 Chain: "1H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 39 Unusual residues: {'PC7': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Chain: "1K" Number of atoms: 159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 159 Unusual residues: {'3PH': 2, 'CDL': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 37 Chain: "1L" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 59 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 41 Chain: "1M" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 55 Unusual residues: {' ZN': 1, 'CDL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 46 Chain: "1N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "1R" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'3PH': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 Chain: "1A" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 48 Classifications: {'water': 48} Link IDs: {None: 47} Chain: "1B" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 52 Classifications: {'water': 52} Link IDs: {None: 51} Chain: "1C" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "1D" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "1E" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 51 Classifications: {'water': 51} Link IDs: {None: 50} Chain: "1F" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 34 Classifications: {'water': 34} Link IDs: {None: 33} Chain: "1G" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "1H" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "1I" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "1J" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "1K" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "1L" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "1M" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 76 Classifications: {'water': 76} Link IDs: {None: 75} Chain: "1N" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 74 Classifications: {'water': 74} Link IDs: {None: 73} Chain: "1O" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "1P" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "1Q" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "1R" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 32 Classifications: {'water': 32} Link IDs: {None: 31} Chain: "1S" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "1T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 28 Classifications: {'water': 28} Link IDs: {None: 27} Time building chain proxies: 7.17, per 1000 atoms: 0.21 Number of scatterers: 34454 At special positions: 0 Unit cell: (144.392, 146.397, 176.479, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 Fe 6 26.01 S 146 16.00 P 27 15.00 O 6802 8.00 N 5604 7.00 C 21867 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS1C 210 " - pdb=" SG CYS1C 226 " distance=2.03 Simple disulfide: pdb=" SG CYS1D 210 " - pdb=" SG CYS1D 226 " distance=2.03 Simple disulfide: pdb=" SG CYS1I 17 " - pdb=" SG CYS1I 59 " distance=2.04 Simple disulfide: pdb=" SG CYS1I 21 " - pdb=" SG CYS1I 55 " distance=2.03 Simple disulfide: pdb=" SG CYS1I 31 " - pdb=" SG CYS1I 45 " distance=2.04 Simple disulfide: pdb=" SG CYS1J 17 " - pdb=" SG CYS1J 59 " distance=2.04 Simple disulfide: pdb=" SG CYS1J 21 " - pdb=" SG CYS1J 55 " distance=2.03 Simple disulfide: pdb=" SG CYS1J 31 " - pdb=" SG CYS1J 45 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=8, symmetry=0 Number of additional bonds: simple=8, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.50 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 715.3 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN1M 502 " pdb="ZN ZN1M 502 " - pdb=" NE2 HIS1M 103 " 8312 Ramachandran restraints generated. 4156 Oldfield, 0 Emsley, 4156 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7764 Finding SS restraints... Secondary structure from input PDB file: 191 helices and 24 sheets defined 57.3% alpha, 8.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.03 Creating SS restraints... Processing helix chain '1A' and resid 2 through 6 removed outlier: 3.546A pdb=" N LYS1A 6 " --> pdb=" O MET1A 3 " (cutoff:3.500A) Processing helix chain '1A' and resid 7 through 18 Processing helix chain '1A' and resid 27 through 30 Processing helix chain '1A' and resid 31 through 51 Processing helix chain '1A' and resid 60 through 71 Processing helix chain '1A' and resid 74 through 104 removed outlier: 3.755A pdb=" N ALA1A 86 " --> pdb=" O HIS1A 82 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N SER1A 87 " --> pdb=" O ALA1A 83 " (cutoff:3.500A) Processing helix chain '1A' and resid 110 through 134 removed outlier: 3.812A pdb=" N LEU1A 134 " --> pdb=" O ILE1A 130 " (cutoff:3.500A) Processing helix chain '1A' and resid 137 through 149 Processing helix chain '1A' and resid 158 through 167 Processing helix chain '1A' and resid 172 through 202 removed outlier: 3.633A pdb=" N SER1A 181 " --> pdb=" O ASN1A 177 " (cutoff:3.500A) Proline residue: 1A 187 - end of helix Processing helix chain '1A' and resid 221 through 246 removed outlier: 4.419A pdb=" N GLY1A 226 " --> pdb=" O GLY1A 222 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ALA1A 227 " --> pdb=" O SER1A 223 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LYS1A 228 " --> pdb=" O TYR1A 224 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASP1A 229 " --> pdb=" O PHE1A 225 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLY1A 232 " --> pdb=" O LYS1A 228 " (cutoff:3.500A) Processing helix chain '1A' and resid 253 through 258 Processing helix chain '1A' and resid 272 through 274 No H-bonds generated for 'chain '1A' and resid 272 through 274' Processing helix chain '1A' and resid 275 through 285 removed outlier: 3.737A pdb=" N ILE1A 285 " --> pdb=" O ILE1A 281 " (cutoff:3.500A) Processing helix chain '1A' and resid 287 through 304 removed outlier: 3.530A pdb=" N PHE1A 299 " --> pdb=" O ILE1A 295 " (cutoff:3.500A) Processing helix chain '1A' and resid 304 through 309 Processing helix chain '1A' and resid 316 through 337 removed outlier: 4.032A pdb=" N TRP1A 324 " --> pdb=" O GLU1A 320 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N THR1A 325 " --> pdb=" O TRP1A 321 " (cutoff:3.500A) Processing helix chain '1A' and resid 342 through 362 Processing helix chain '1A' and resid 362 through 377 removed outlier: 3.634A pdb=" N GLY1A 368 " --> pdb=" O GLN1A 364 " (cutoff:3.500A) Processing helix chain '1B' and resid 2 through 6 Processing helix chain '1B' and resid 7 through 18 Processing helix chain '1B' and resid 27 through 30 Processing helix chain '1B' and resid 31 through 51 Processing helix chain '1B' and resid 60 through 71 Processing helix chain '1B' and resid 74 through 104 removed outlier: 4.002A pdb=" N SER1B 87 " --> pdb=" O ALA1B 83 " (cutoff:3.500A) Processing helix chain '1B' and resid 110 through 134 removed outlier: 3.500A pdb=" N TRP1B 114 " --> pdb=" O ARG1B 110 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N VAL1B 133 " --> pdb=" O PHE1B 129 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LEU1B 134 " --> pdb=" O ILE1B 130 " (cutoff:3.500A) Processing helix chain '1B' and resid 137 through 149 removed outlier: 3.689A pdb=" N ALA1B 144 " --> pdb=" O SER1B 140 " (cutoff:3.500A) Processing helix chain '1B' and resid 150 through 154 Processing helix chain '1B' and resid 157 through 167 removed outlier: 3.520A pdb=" N ILE1B 161 " --> pdb=" O VAL1B 157 " (cutoff:3.500A) Processing helix chain '1B' and resid 172 through 202 Proline residue: 1B 187 - end of helix Processing helix chain '1B' and resid 221 through 246 removed outlier: 3.844A pdb=" N GLY1B 226 " --> pdb=" O GLY1B 222 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N ALA1B 227 " --> pdb=" O SER1B 223 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LYS1B 228 " --> pdb=" O TYR1B 224 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLY1B 232 " --> pdb=" O LYS1B 228 " (cutoff:3.500A) Processing helix chain '1B' and resid 253 through 258 Processing helix chain '1B' and resid 272 through 274 No H-bonds generated for 'chain '1B' and resid 272 through 274' Processing helix chain '1B' and resid 275 through 285 removed outlier: 3.899A pdb=" N ILE1B 285 " --> pdb=" O ILE1B 281 " (cutoff:3.500A) Processing helix chain '1B' and resid 287 through 304 Processing helix chain '1B' and resid 304 through 309 Processing helix chain '1B' and resid 316 through 338 removed outlier: 4.153A pdb=" N TRP1B 324 " --> pdb=" O GLU1B 320 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N THR1B 325 " --> pdb=" O TRP1B 321 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLY1B 338 " --> pdb=" O THR1B 334 " (cutoff:3.500A) Processing helix chain '1B' and resid 342 through 362 Processing helix chain '1B' and resid 362 through 377 removed outlier: 3.659A pdb=" N GLY1B 368 " --> pdb=" O GLN1B 364 " (cutoff:3.500A) Processing helix chain '1C' and resid 57 through 62 Processing helix chain '1C' and resid 69 through 77 removed outlier: 3.602A pdb=" N LEU1C 74 " --> pdb=" O PRO1C 70 " (cutoff:3.500A) Processing helix chain '1C' and resid 101 through 126 removed outlier: 3.606A pdb=" N GLY1C 108 " --> pdb=" O PHE1C 104 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLY1C 109 " --> pdb=" O VAL1C 105 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU1C 112 " --> pdb=" O GLY1C 108 " (cutoff:3.500A) Processing helix chain '1C' and resid 131 through 137 Processing helix chain '1C' and resid 168 through 177 Processing helix chain '1C' and resid 188 through 192 removed outlier: 3.566A pdb=" N ARG1C 192 " --> pdb=" O ASP1C 189 " (cutoff:3.500A) Processing helix chain '1D' and resid 57 through 62 Processing helix chain '1D' and resid 69 through 77 removed outlier: 3.573A pdb=" N LEU1D 74 " --> pdb=" O PRO1D 70 " (cutoff:3.500A) Processing helix chain '1D' and resid 101 through 127 removed outlier: 3.608A pdb=" N VAL1D 105 " --> pdb=" O PHE1D 101 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU1D 112 " --> pdb=" O GLY1D 108 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N SER1D 115 " --> pdb=" O PHE1D 111 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N SER1D 127 " --> pdb=" O LYS1D 123 " (cutoff:3.500A) Processing helix chain '1D' and resid 131 through 137 Processing helix chain '1D' and resid 168 through 177 Processing helix chain '1D' and resid 179 through 183 removed outlier: 3.719A pdb=" N GLU1D 182 " --> pdb=" O ALA1D 179 " (cutoff:3.500A) Processing helix chain '1E' and resid 73 through 77 Processing helix chain '1E' and resid 95 through 109 Processing helix chain '1E' and resid 110 through 113 Processing helix chain '1E' and resid 120 through 125 Processing helix chain '1E' and resid 130 through 139 Processing helix chain '1E' and resid 170 through 177 Processing helix chain '1E' and resid 195 through 205 Processing helix chain '1E' and resid 251 through 268 Processing helix chain '1E' and resid 270 through 300 removed outlier: 3.612A pdb=" N GLY1E 290 " --> pdb=" O SER1E 286 " (cutoff:3.500A) Processing helix chain '1E' and resid 300 through 305 Processing helix chain '1F' and resid 73 through 77 Processing helix chain '1F' and resid 95 through 109 removed outlier: 3.591A pdb=" N LYS1F 104 " --> pdb=" O ARG1F 100 " (cutoff:3.500A) Processing helix chain '1F' and resid 120 through 125 removed outlier: 3.711A pdb=" N VAL1F 125 " --> pdb=" O ARG1F 122 " (cutoff:3.500A) Processing helix chain '1F' and resid 130 through 139 Processing helix chain '1F' and resid 170 through 177 Processing helix chain '1F' and resid 195 through 205 Processing helix chain '1F' and resid 251 through 268 Processing helix chain '1F' and resid 270 through 300 removed outlier: 3.633A pdb=" N GLY1F 290 " --> pdb=" O SER1F 286 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG1F 299 " --> pdb=" O SER1F 295 " (cutoff:3.500A) Processing helix chain '1F' and resid 300 through 305 Processing helix chain '1G' and resid 6 through 14 removed outlier: 3.662A pdb=" N THR1G 12 " --> pdb=" O ALA1G 8 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE1G 13 " --> pdb=" O LEU1G 9 " (cutoff:3.500A) Processing helix chain '1G' and resid 16 through 47 Proline residue: 1G 22 - end of helix Processing helix chain '1G' and resid 51 through 59 removed outlier: 3.541A pdb=" N ILE1G 55 " --> pdb=" O LEU1G 51 " (cutoff:3.500A) Processing helix chain '1H' and resid 6 through 14 Processing helix chain '1H' and resid 16 through 47 Proline residue: 1H 22 - end of helix Processing helix chain '1H' and resid 51 through 58 Processing helix chain '1I' and resid 9 through 18 Processing helix chain '1I' and resid 21 through 35 Processing helix chain '1I' and resid 45 through 67 Proline residue: 1I 62 - end of helix removed outlier: 3.764A pdb=" N PHE1I 65 " --> pdb=" O ALA1I 61 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N HIS1I 67 " --> pdb=" O LYS1I 63 " (cutoff:3.500A) Processing helix chain '1J' and resid 9 through 17 Processing helix chain '1J' and resid 18 through 20 No H-bonds generated for 'chain '1J' and resid 18 through 20' Processing helix chain '1J' and resid 21 through 35 Processing helix chain '1J' and resid 36 through 38 No H-bonds generated for 'chain '1J' and resid 36 through 38' Processing helix chain '1J' and resid 45 through 67 Proline residue: 1J 62 - end of helix removed outlier: 3.831A pdb=" N PHE1J 65 " --> pdb=" O ALA1J 61 " (cutoff:3.500A) Processing helix chain '1K' and resid 25 through 42 removed outlier: 4.225A pdb=" N THR1K 29 " --> pdb=" O ARG1K 25 " (cutoff:3.500A) Proline residue: 1K 32 - end of helix Processing helix chain '1K' and resid 42 through 71 removed outlier: 3.500A pdb=" N GLU1K 71 " --> pdb=" O GLU1K 67 " (cutoff:3.500A) Processing helix chain '1L' and resid 18 through 21 removed outlier: 3.929A pdb=" N GLN1L 21 " --> pdb=" O PRO1L 18 " (cutoff:3.500A) No H-bonds generated for 'chain '1L' and resid 18 through 21' Processing helix chain '1L' and resid 26 through 42 Proline residue: 1L 32 - end of helix Processing helix chain '1L' and resid 42 through 71 removed outlier: 3.555A pdb=" N GLU1L 71 " --> pdb=" O GLU1L 67 " (cutoff:3.500A) Processing helix chain '1M' and resid 49 through 54 removed outlier: 3.615A pdb=" N SER1M 54 " --> pdb=" O PRO1M 51 " (cutoff:3.500A) Processing helix chain '1M' and resid 90 through 94 removed outlier: 3.639A pdb=" N GLU1M 94 " --> pdb=" O SER1M 91 " (cutoff:3.500A) Processing helix chain '1M' and resid 100 through 109 removed outlier: 3.769A pdb=" N GLU1M 106 " --> pdb=" O ALA1M 102 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N HIS1M 107 " --> pdb=" O HIS1M 103 " (cutoff:3.500A) Processing helix chain '1M' and resid 117 through 128 Processing helix chain '1M' and resid 151 through 165 Processing helix chain '1M' and resid 169 through 186 removed outlier: 3.722A pdb=" N ASP1M 178 " --> pdb=" O ASP1M 174 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N VAL1M 179 " --> pdb=" O LYS1M 175 " (cutoff:3.500A) Processing helix chain '1M' and resid 190 through 204 Processing helix chain '1M' and resid 207 through 211 removed outlier: 3.547A pdb=" N ARG1M 211 " --> pdb=" O PRO1M 208 " (cutoff:3.500A) Processing helix chain '1M' and resid 216 through 222 removed outlier: 3.653A pdb=" N ILE1M 220 " --> pdb=" O PRO1M 216 " (cutoff:3.500A) Processing helix chain '1M' and resid 224 through 236 removed outlier: 3.765A pdb=" N LEU1M 228 " --> pdb=" O ASN1M 224 " (cutoff:3.500A) Processing helix chain '1M' and resid 237 through 239 No H-bonds generated for 'chain '1M' and resid 237 through 239' Processing helix chain '1M' and resid 250 through 262 Processing helix chain '1M' and resid 263 through 265 No H-bonds generated for 'chain '1M' and resid 263 through 265' Processing helix chain '1M' and resid 269 through 272 Processing helix chain '1M' and resid 273 through 281 Processing helix chain '1M' and resid 315 through 327 Processing helix chain '1M' and resid 335 through 339 Processing helix chain '1M' and resid 341 through 351 Processing helix chain '1M' and resid 379 through 397 removed outlier: 3.869A pdb=" N MET1M 394 " --> pdb=" O ASN1M 390 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N CYS1M 395 " --> pdb=" O LEU1M 391 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N PHE1M 396 " --> pdb=" O THR1M 392 " (cutoff:3.500A) Processing helix chain '1M' and resid 399 through 418 removed outlier: 3.595A pdb=" N VAL1M 403 " --> pdb=" O ARG1M 399 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLN1M 418 " --> pdb=" O LEU1M 414 " (cutoff:3.500A) Processing helix chain '1M' and resid 420 through 435 Processing helix chain '1M' and resid 440 through 450 Processing helix chain '1M' and resid 452 through 464 Processing helix chain '1M' and resid 482 through 489 removed outlier: 3.575A pdb=" N PHE1M 486 " --> pdb=" O ASP1M 482 " (cutoff:3.500A) Processing helix chain '1N' and resid 49 through 53 Processing helix chain '1N' and resid 90 through 94 removed outlier: 3.556A pdb=" N GLU1N 94 " --> pdb=" O SER1N 91 " (cutoff:3.500A) Processing helix chain '1N' and resid 100 through 109 removed outlier: 3.711A pdb=" N GLU1N 106 " --> pdb=" O ALA1N 102 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N HIS1N 107 " --> pdb=" O HIS1N 103 " (cutoff:3.500A) Processing helix chain '1N' and resid 117 through 128 removed outlier: 3.696A pdb=" N MET1N 128 " --> pdb=" O GLU1N 124 " (cutoff:3.500A) Processing helix chain '1N' and resid 151 through 165 Processing helix chain '1N' and resid 169 through 186 removed outlier: 3.583A pdb=" N ASP1N 178 " --> pdb=" O ASP1N 174 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL1N 179 " --> pdb=" O LYS1N 175 " (cutoff:3.500A) Processing helix chain '1N' and resid 190 through 204 Processing helix chain '1N' and resid 207 through 211 removed outlier: 3.526A pdb=" N ARG1N 211 " --> pdb=" O PRO1N 208 " (cutoff:3.500A) Processing helix chain '1N' and resid 216 through 222 Processing helix chain '1N' and resid 224 through 236 removed outlier: 3.803A pdb=" N LEU1N 228 " --> pdb=" O ASN1N 224 " (cutoff:3.500A) Processing helix chain '1N' and resid 250 through 262 Processing helix chain '1N' and resid 269 through 272 Processing helix chain '1N' and resid 273 through 281 Processing helix chain '1N' and resid 315 through 327 Processing helix chain '1N' and resid 335 through 339 Processing helix chain '1N' and resid 341 through 351 Processing helix chain '1N' and resid 376 through 378 No H-bonds generated for 'chain '1N' and resid 376 through 378' Processing helix chain '1N' and resid 379 through 394 removed outlier: 3.872A pdb=" N MET1N 394 " --> pdb=" O ASN1N 390 " (cutoff:3.500A) Processing helix chain '1N' and resid 399 through 419 removed outlier: 3.574A pdb=" N GLN1N 418 " --> pdb=" O LEU1N 414 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASP1N 419 " --> pdb=" O MET1N 415 " (cutoff:3.500A) Processing helix chain '1N' and resid 420 through 436 Processing helix chain '1N' and resid 440 through 450 Processing helix chain '1N' and resid 452 through 464 Processing helix chain '1N' and resid 482 through 489 removed outlier: 3.650A pdb=" N ARG1N 489 " --> pdb=" O TRP1N 485 " (cutoff:3.500A) Processing helix chain '1O' and resid 4 through 10 removed outlier: 3.651A pdb=" N VAL1O 8 " --> pdb=" O GLY1O 4 " (cutoff:3.500A) Processing helix chain '1O' and resid 20 through 29 Processing helix chain '1O' and resid 29 through 43 removed outlier: 4.090A pdb=" N VAL1O 33 " --> pdb=" O ALA1O 29 " (cutoff:3.500A) Processing helix chain '1P' and resid 5 through 10 Processing helix chain '1P' and resid 20 through 29 Processing helix chain '1P' and resid 29 through 43 removed outlier: 3.955A pdb=" N VAL1P 33 " --> pdb=" O ALA1P 29 " (cutoff:3.500A) Processing helix chain '1Q' and resid 105 through 109 Processing helix chain '1Q' and resid 115 through 124 removed outlier: 3.678A pdb=" N VAL1Q 122 " --> pdb=" O LYS1Q 118 " (cutoff:3.500A) Processing helix chain '1Q' and resid 132 through 143 removed outlier: 4.006A pdb=" N ILE1Q 143 " --> pdb=" O GLU1Q 139 " (cutoff:3.500A) Processing helix chain '1Q' and resid 166 through 180 Processing helix chain '1Q' and resid 184 through 203 removed outlier: 4.545A pdb=" N ASP1Q 193 " --> pdb=" O ARG1Q 189 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N ALA1Q 194 " --> pdb=" O ASP1Q 190 " (cutoff:3.500A) Processing helix chain '1Q' and resid 205 through 218 removed outlier: 3.693A pdb=" N ALA1Q 209 " --> pdb=" O ASN1Q 205 " (cutoff:3.500A) Processing helix chain '1Q' and resid 230 through 235 removed outlier: 3.515A pdb=" N ASP1Q 235 " --> pdb=" O SER1Q 232 " (cutoff:3.500A) Processing helix chain '1Q' and resid 238 through 250 Processing helix chain '1Q' and resid 251 through 253 No H-bonds generated for 'chain '1Q' and resid 251 through 253' Processing helix chain '1Q' and resid 263 through 272 Processing helix chain '1Q' and resid 318 through 332 Processing helix chain '1Q' and resid 372 through 374 No H-bonds generated for 'chain '1Q' and resid 372 through 374' Processing helix chain '1Q' and resid 375 through 392 Processing helix chain '1Q' and resid 396 through 414 removed outlier: 3.811A pdb=" N VAL1Q 414 " --> pdb=" O LEU1Q 410 " (cutoff:3.500A) Processing helix chain '1Q' and resid 416 through 431 Processing helix chain '1Q' and resid 435 through 445 Processing helix chain '1Q' and resid 447 through 461 removed outlier: 3.531A pdb=" N LYS1Q 460 " --> pdb=" O ASN1Q 456 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N THR1Q 461 " --> pdb=" O ALA1Q 457 " (cutoff:3.500A) Processing helix chain '1Q' and resid 476 through 481 Processing helix chain '1R' and resid 3 through 29 Proline residue: 1R 11 - end of helix Processing helix chain '1R' and resid 35 through 39 removed outlier: 3.633A pdb=" N GLN1R 39 " --> pdb=" O ASP1R 36 " (cutoff:3.500A) Processing helix chain '1R' and resid 44 through 53 Processing helix chain '1R' and resid 55 through 76 Processing helix chain '1R' and resid 80 through 85 Processing helix chain '1R' and resid 94 through 110 Processing helix chain '1S' and resid 105 through 109 Processing helix chain '1S' and resid 115 through 124 Processing helix chain '1S' and resid 132 through 143 removed outlier: 3.905A pdb=" N ILE1S 143 " --> pdb=" O GLU1S 139 " (cutoff:3.500A) Processing helix chain '1S' and resid 166 through 180 Processing helix chain '1S' and resid 184 through 190 Processing helix chain '1S' and resid 191 through 203 Processing helix chain '1S' and resid 205 through 218 removed outlier: 3.544A pdb=" N ALA1S 209 " --> pdb=" O ASN1S 205 " (cutoff:3.500A) Processing helix chain '1S' and resid 221 through 225 Processing helix chain '1S' and resid 230 through 235 Processing helix chain '1S' and resid 238 through 250 Processing helix chain '1S' and resid 263 through 272 Processing helix chain '1S' and resid 318 through 333 Processing helix chain '1S' and resid 372 through 374 No H-bonds generated for 'chain '1S' and resid 372 through 374' Processing helix chain '1S' and resid 375 through 393 removed outlier: 3.953A pdb=" N VAL1S 387 " --> pdb=" O LEU1S 383 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLN1S 388 " --> pdb=" O THR1S 384 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLY1S 393 " --> pdb=" O SER1S 389 " (cutoff:3.500A) Processing helix chain '1S' and resid 395 through 414 removed outlier: 3.726A pdb=" N VAL1S 414 " --> pdb=" O LEU1S 410 " (cutoff:3.500A) Processing helix chain '1S' and resid 416 through 432 Processing helix chain '1S' and resid 435 through 445 removed outlier: 3.623A pdb=" N VAL1S 439 " --> pdb=" O SER1S 435 " (cutoff:3.500A) Processing helix chain '1S' and resid 447 through 459 Processing helix chain '1S' and resid 476 through 482 removed outlier: 3.745A pdb=" N ILE1S 480 " --> pdb=" O ARG1S 476 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ALA1S 481 " --> pdb=" O VAL1S 477 " (cutoff:3.500A) Processing helix chain '1T' and resid 8 through 30 removed outlier: 4.126A pdb=" N VAL1T 12 " --> pdb=" O VAL1T 8 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N LYS1T 30 " --> pdb=" O ALA1T 26 " (cutoff:3.500A) Processing helix chain '1T' and resid 35 through 39 removed outlier: 3.538A pdb=" N GLN1T 39 " --> pdb=" O ASP1T 36 " (cutoff:3.500A) Processing helix chain '1T' and resid 44 through 53 removed outlier: 3.562A pdb=" N ARG1T 52 " --> pdb=" O ALA1T 48 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG1T 53 " --> pdb=" O GLU1T 49 " (cutoff:3.500A) Processing helix chain '1T' and resid 55 through 75 Processing helix chain '1T' and resid 80 through 85 Processing helix chain '1T' and resid 94 through 111 removed outlier: 3.511A pdb=" N GLN1T 110 " --> pdb=" O ARG1T 106 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU1T 111 " --> pdb=" O GLU1T 107 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain '1A' and resid 21 through 23 Processing sheet with id=AA2, first strand: chain '1B' and resid 21 through 23 Processing sheet with id=AA3, first strand: chain '1C' and resid 140 through 143 removed outlier: 3.747A pdb=" N LEU1C 140 " --> pdb=" O ILE1C 261 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS1C 258 " --> pdb=" O THR1C 254 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL1C 260 " --> pdb=" O ARG1C 252 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain '1C' and resid 152 through 157 removed outlier: 3.602A pdb=" N ARG1C 165 " --> pdb=" O LEU1C 199 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU1C 199 " --> pdb=" O ARG1C 165 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain '1C' and resid 213 through 214 removed outlier: 3.789A pdb=" N GLU1C 239 " --> pdb=" O HIS1C 230 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain '1D' and resid 99 through 100 removed outlier: 3.636A pdb=" N ARG1D 99 " --> pdb=" O LEU1H 5 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain '1D' and resid 140 through 143 removed outlier: 3.530A pdb=" N LEU1D 140 " --> pdb=" O ILE1D 261 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL1D 260 " --> pdb=" O ARG1D 252 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ARG1D 252 " --> pdb=" O VAL1D 260 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain '1D' and resid 152 through 157 removed outlier: 3.539A pdb=" N LEU1D 199 " --> pdb=" O ARG1D 165 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain '1D' and resid 213 through 214 removed outlier: 3.711A pdb=" N GLU1D 239 " --> pdb=" O HIS1D 230 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain '1E' and resid 142 through 145 Processing sheet with id=AB2, first strand: chain '1E' and resid 221 through 222 Processing sheet with id=AB3, first strand: chain '1E' and resid 307 through 309 removed outlier: 6.530A pdb=" N SER1M 288 " --> pdb=" O VAL1M 471 " (cutoff:3.500A) removed outlier: 8.674A pdb=" N SER1M 473 " --> pdb=" O SER1M 288 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N VAL1M 290 " --> pdb=" O SER1M 473 " (cutoff:3.500A) removed outlier: 8.632A pdb=" N GLY1M 475 " --> pdb=" O VAL1M 290 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ASP1M 292 " --> pdb=" O GLY1M 475 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA1M 355 " --> pdb=" O VAL1M 374 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain '1F' and resid 142 through 145 Processing sheet with id=AB5, first strand: chain '1F' and resid 221 through 222 Processing sheet with id=AB6, first strand: chain '1F' and resid 307 through 309 removed outlier: 6.657A pdb=" N SER1N 288 " --> pdb=" O VAL1N 471 " (cutoff:3.500A) removed outlier: 8.755A pdb=" N SER1N 473 " --> pdb=" O SER1N 288 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N VAL1N 290 " --> pdb=" O SER1N 473 " (cutoff:3.500A) removed outlier: 8.801A pdb=" N GLY1N 475 " --> pdb=" O VAL1N 290 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ASP1N 292 " --> pdb=" O GLY1N 475 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain '1M' and resid 59 through 63 removed outlier: 6.690A pdb=" N ARG1M 69 " --> pdb=" O LEU1M 243 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N ALA1M 245 " --> pdb=" O ARG1M 69 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ALA1M 71 " --> pdb=" O ALA1M 245 " (cutoff:3.500A) removed outlier: 8.440A pdb=" N GLY1M 247 " --> pdb=" O ALA1M 71 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N GLU1M 73 " --> pdb=" O GLY1M 247 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLN1M 131 " --> pdb=" O LYS1M 146 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain '1N' and resid 59 through 63 removed outlier: 6.497A pdb=" N ARG1N 69 " --> pdb=" O LEU1N 243 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N ALA1N 245 " --> pdb=" O ARG1N 69 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ALA1N 71 " --> pdb=" O ALA1N 245 " (cutoff:3.500A) removed outlier: 8.629A pdb=" N GLY1N 247 " --> pdb=" O ALA1N 71 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N GLU1N 73 " --> pdb=" O GLY1N 247 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain '1Q' and resid 75 through 79 removed outlier: 6.725A pdb=" N LYS1Q 85 " --> pdb=" O LEU1Q 257 " (cutoff:3.500A) removed outlier: 8.245A pdb=" N ALA1Q 259 " --> pdb=" O LYS1Q 85 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ALA1Q 87 " --> pdb=" O ALA1Q 259 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain '1Q' and resid 219 through 220 Processing sheet with id=AC2, first strand: chain '1Q' and resid 292 through 293 removed outlier: 6.806A pdb=" N GLY1Q 292 " --> pdb=" O PHE1Q 465 " (cutoff:3.500A) removed outlier: 8.874A pdb=" N THR1Q 467 " --> pdb=" O GLY1Q 292 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLY1Q 361 " --> pdb=" O GLY1Q 314 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLY1Q 314 " --> pdb=" O GLY1Q 361 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain '1Q' and resid 292 through 293 removed outlier: 6.806A pdb=" N GLY1Q 292 " --> pdb=" O PHE1Q 465 " (cutoff:3.500A) removed outlier: 8.874A pdb=" N THR1Q 467 " --> pdb=" O GLY1Q 292 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain '1S' and resid 76 through 79 removed outlier: 6.434A pdb=" N LYS1S 85 " --> pdb=" O LEU1S 257 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N ALA1S 259 " --> pdb=" O LYS1S 85 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ALA1S 87 " --> pdb=" O ALA1S 259 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain '1S' and resid 219 through 220 Processing sheet with id=AC6, first strand: chain '1S' and resid 292 through 296 1813 hydrogen bonds defined for protein. 5190 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: 5.70 Time building geometry restraints manager: 3.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.37: 11970 1.37 - 1.55: 22448 1.55 - 1.73: 51 1.73 - 1.92: 246 1.92 - 2.10: 24 Bond restraints: 34739 Sorted by residual: bond pdb=" C2D HEC1B 403 " pdb=" C3D HEC1B 403 " ideal model delta sigma weight residual 1.544 1.330 0.214 2.00e-02 2.50e+03 1.15e+02 bond pdb=" C2D HEC1A 404 " pdb=" C3D HEC1A 404 " ideal model delta sigma weight residual 1.544 1.331 0.213 2.00e-02 2.50e+03 1.14e+02 bond pdb=" CAC HEC1B 403 " pdb=" CBC HEC1B 403 " ideal model delta sigma weight residual 1.544 1.332 0.212 2.00e-02 2.50e+03 1.12e+02 bond pdb=" C2D HEC1A 403 " pdb=" C3D HEC1A 403 " ideal model delta sigma weight residual 1.544 1.333 0.211 2.00e-02 2.50e+03 1.12e+02 bond pdb=" CAB HEC1B 404 " pdb=" CBB HEC1B 404 " ideal model delta sigma weight residual 1.544 1.333 0.211 2.00e-02 2.50e+03 1.11e+02 ... (remaining 34734 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.30: 46961 4.30 - 8.60: 172 8.60 - 12.89: 13 12.89 - 17.19: 6 17.19 - 21.49: 10 Bond angle restraints: 47162 Sorted by residual: angle pdb=" C3B HEC1B 403 " pdb=" CAB HEC1B 403 " pdb=" CBB HEC1B 403 " ideal model delta sigma weight residual 109.00 130.44 -21.44 3.00e+00 1.11e-01 5.11e+01 angle pdb=" C3B HEC1A 403 " pdb=" CAB HEC1A 403 " pdb=" CBB HEC1A 403 " ideal model delta sigma weight residual 109.00 128.05 -19.05 3.00e+00 1.11e-01 4.03e+01 angle pdb=" C3B HEC1A 404 " pdb=" CAB HEC1A 404 " pdb=" CBB HEC1A 404 " ideal model delta sigma weight residual 109.00 127.97 -18.97 3.00e+00 1.11e-01 4.00e+01 angle pdb=" C3B HEC1B 404 " pdb=" CAB HEC1B 404 " pdb=" CBB HEC1B 404 " ideal model delta sigma weight residual 109.00 127.59 -18.59 3.00e+00 1.11e-01 3.84e+01 angle pdb=" N TYR1A 184 " pdb=" CA TYR1A 184 " pdb=" C TYR1A 184 " ideal model delta sigma weight residual 111.36 104.87 6.49 1.09e+00 8.42e-01 3.55e+01 ... (remaining 47157 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 18421 17.89 - 35.77: 1768 35.77 - 53.66: 374 53.66 - 71.55: 98 71.55 - 89.44: 47 Dihedral angle restraints: 20708 sinusoidal: 8586 harmonic: 12122 Sorted by residual: dihedral pdb=" C2C HEC1B 404 " pdb=" C3C HEC1B 404 " pdb=" CAC HEC1B 404 " pdb=" CBC HEC1B 404 " ideal model delta sinusoidal sigma weight residual 60.00 -17.18 77.18 2 1.00e+01 1.00e-02 4.56e+01 dihedral pdb=" C2C HEC1A 404 " pdb=" C3C HEC1A 404 " pdb=" CAC HEC1A 404 " pdb=" CBC HEC1A 404 " ideal model delta sinusoidal sigma weight residual 60.00 -12.59 72.59 2 1.00e+01 1.00e-02 4.37e+01 dihedral pdb=" C2B HEC1B 404 " pdb=" C3B HEC1B 404 " pdb=" CAB HEC1B 404 " pdb=" CBB HEC1B 404 " ideal model delta sinusoidal sigma weight residual 60.00 -11.65 71.65 2 1.00e+01 1.00e-02 4.32e+01 ... (remaining 20705 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 4518 0.078 - 0.155: 553 0.155 - 0.233: 23 0.233 - 0.310: 2 0.310 - 0.388: 1 Chirality restraints: 5097 Sorted by residual: chirality pdb=" CB VAL1M 434 " pdb=" CA VAL1M 434 " pdb=" CG1 VAL1M 434 " pdb=" CG2 VAL1M 434 " both_signs ideal model delta sigma weight residual False -2.63 -2.24 -0.39 2.00e-01 2.50e+01 3.76e+00 chirality pdb=" CB ILE1S 89 " pdb=" CA ILE1S 89 " pdb=" CG1 ILE1S 89 " pdb=" CG2 ILE1S 89 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" CB ILE1M 162 " pdb=" CA ILE1M 162 " pdb=" CG1 ILE1M 162 " pdb=" CG2 ILE1M 162 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.39e+00 ... (remaining 5094 not shown) Planarity restraints: 5970 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR1A 184 " 0.032 2.00e-02 2.50e+03 6.28e-02 7.89e+01 pdb=" CG TYR1A 184 " -0.147 2.00e-02 2.50e+03 pdb=" CD1 TYR1A 184 " 0.079 2.00e-02 2.50e+03 pdb=" CD2 TYR1A 184 " 0.042 2.00e-02 2.50e+03 pdb=" CE1 TYR1A 184 " -0.014 2.00e-02 2.50e+03 pdb=" CE2 TYR1A 184 " 0.023 2.00e-02 2.50e+03 pdb=" CZ TYR1A 184 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR1A 184 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR1B 184 " -0.017 2.00e-02 2.50e+03 6.02e-02 7.25e+01 pdb=" CG TYR1B 184 " 0.135 2.00e-02 2.50e+03 pdb=" CD1 TYR1B 184 " -0.059 2.00e-02 2.50e+03 pdb=" CD2 TYR1B 184 " -0.081 2.00e-02 2.50e+03 pdb=" CE1 TYR1B 184 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR1B 184 " 0.013 2.00e-02 2.50e+03 pdb=" CZ TYR1B 184 " 0.006 2.00e-02 2.50e+03 pdb=" OH TYR1B 184 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1C HEC1E 404 " 0.022 2.00e-02 2.50e+03 4.72e-02 5.01e+01 pdb=" C2C HEC1E 404 " -0.129 2.00e-02 2.50e+03 pdb=" C3C HEC1E 404 " 0.016 2.00e-02 2.50e+03 pdb=" C4C HEC1E 404 " 0.004 2.00e-02 2.50e+03 pdb=" CAC HEC1E 404 " 0.019 2.00e-02 2.50e+03 pdb=" CHC HEC1E 404 " 0.016 2.00e-02 2.50e+03 pdb=" CHD HEC1E 404 " 0.002 2.00e-02 2.50e+03 pdb=" CMC HEC1E 404 " 0.045 2.00e-02 2.50e+03 pdb=" NC HEC1E 404 " 0.005 2.00e-02 2.50e+03 ... (remaining 5967 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 713 2.68 - 3.24: 30479 3.24 - 3.79: 56457 3.79 - 4.35: 76171 4.35 - 4.90: 124147 Nonbonded interactions: 287967 Sorted by model distance: nonbonded pdb=" CG HIS1M 103 " pdb="ZN ZN1M 502 " model vdw 2.126 1.960 nonbonded pdb=" OH TYR1A 184 " pdb=" OG1 THR1B 185 " model vdw 2.207 3.040 nonbonded pdb=" OG SER1S 435 " pdb=" OE1 GLU1S 438 " model vdw 2.245 3.040 nonbonded pdb=" O PRO1C 93 " pdb=" OG1 THR1C 96 " model vdw 2.255 3.040 nonbonded pdb=" OD1 ASP1D 189 " pdb=" OG SER1D 234 " model vdw 2.269 3.040 ... (remaining 287962 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 '1A' and (resid 2 through 404 or (resid 405 and (name CB2 or name OB2 or \ name CB3 or name OB3 or name C1 or name C11 or name C12 or name C13 or name C14 \ or name C31 or name C32 or name C33 or name C34 or name C35 or name C36 or name \ C51 or name C52 or name C53 or name C54 or name C55 or name C71 or name C72 or n \ ame C73 or name C74 or name CA2 or name CA3 or name CA4 or name CA5 or name CA6 \ or name CA7 or name CB4 or name CB5 or name CB6 or name CB7 or name O1 or name O \ A2 or name OA3 or name OA4 or name OA5 or name OA6 or name OA7 or name OA8 or na \ me OA9 or name OB4 or name OB5 or name OB6 or name OB7 or name OB8 or name OB9 o \ r name PA1 or name PB2)) or resid 406)) selection = (chain '1B' and (resid 2 through 404 or (resid 405 and (name CB2 or name OB2 or \ name CB3 or name OB3 or name C1 or name C11 or name C12 or name C13 or name C14 \ or name C31 or name C32 or name C33 or name C34 or name C35 or name C36 or name \ C51 or name C52 or name C53 or name C54 or name C55 or name C71 or name C72 or n \ ame C73 or name C74 or name CA2 or name CA3 or name CA4 or name CA5 or name CA6 \ or name CA7 or name CB4 or name CB5 or name CB6 or name CB7 or name O1 or name O \ A2 or name OA3 or name OA4 or name OA5 or name OA6 or name OA7 or name OA8 or na \ me OA9 or name OB4 or name OB5 or name OB6 or name OB7 or name OB8 or name OB9 o \ r name PA1 or name PB2)) or (resid 406 and (name C1 or name C2 or name C21 or na \ me C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C28 o \ r name C29 or name C2A or name C2B or name C2C or name C2D or name C2E or name C \ 2F or name C3 or name C31 or name C32 or name C33 or name C34 or name O11 or nam \ e O12 or name O13 or name O14 or name O21 or name O22 or name O31 or name O32 or \ name P )))) } ncs_group { reference = chain '1C' selection = chain '1D' } ncs_group { reference = (chain '1E' and (resid 72 through 314 or (resid 401 and (name CB2 or name OB2 or \ name CB3 or name OB3 or name C1 or name C11 or name C12 or name C13 or name C14 \ or name C31 or name C32 or name C33 or name C34 or name C35 or name C51 or name \ C52 or name C53 or name C54 or name C71 or name C72 or name C73 or name C74 or \ name CA2 or name CA3 or name CA4 or name CA5 or name CA6 or name CA7 or name CB4 \ or name CB5 or name CB6 or name CB7 or name O1 or name OA2 or name OA3 or name \ OA4 or name OA5 or name OA6 or name OA7 or name OA8 or name OA9 or name OB4 or n \ ame OB5 or name OB6 or name OB7 or name OB8 or name OB9 or name PA1 or name PB2) \ ) or resid 403)) selection = (chain '1F' and (resid 72 through 314 or (resid 401 and (name CB2 or name OB2 or \ name CB3 or name OB3 or name C1 or name C11 or name C12 or name C13 or name C14 \ or name C31 or name C32 or name C33 or name C34 or name C35 or name C51 or name \ C52 or name C53 or name C54 or name C71 or name C72 or name C73 or name C74 or \ name CA2 or name CA3 or name CA4 or name CA5 or name CA6 or name CA7 or name CB4 \ or name CB5 or name CB6 or name CB7 or name O1 or name OA2 or name OA3 or name \ OA4 or name OA5 or name OA6 or name OA7 or name OA8 or name OA9 or name OB4 or n \ ame OB5 or name OB6 or name OB7 or name OB8 or name OB9 or name PA1 or name PB2) \ ) or (resid 403 and (name C1 or name C11 or name C12 or name C13 or name C14 or \ name C15 or name C16 or name C17 or name C18 or name C2 or name C3 or name C30 o \ r name C31 or name C32 or name C33 or name C34 or name C35 or name C36 or name C \ 37 or name C38 or name C39 or name C5 or name C6 or name C8 or name N1 or name O \ 10 or name O11 or name O12 or name O13 or name O14 or name O30 or name O4 or nam \ e O7 or name P1 )))) } ncs_group { reference = chain '1G' selection = (chain '1H' and (resid 2 through 60 or (resid 101 and (name N or name C1 or name \ C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name C17 or \ name C18 or name C19 or name C2 or name C20 or name C21 or name C22 or name C3 o \ r name C31 or name C32 or name C33 or name C34 or name C35 or name C36 or name C \ 4 or name C5 or name C6 or name C7 or name C8 or name O11 or name O1P or name O2 \ or name O2P or name O3 or name O31 or name O3P or name O4P or name P )))) } ncs_group { reference = chain '1I' selection = chain '1J' } ncs_group { reference = (chain '1K' and (resid 4 through 73 or (resid 101 and (name CB2 or name OB2 or n \ ame CB3 or name OB3 or name C1 or name C11 or name C12 or name C13 or name C14 o \ r name C15 or name C16 or name C31 or name C32 or name C33 or name C34 or name C \ 35 or name C51 or name C52 or name C53 or name C54 or name C55 or name C56 or na \ me C57 or name C71 or name C72 or name C73 or name C74 or name C75 or name C76 o \ r name C77 or name C78 or name C79 or name CA2 or name CA3 or name CA4 or name C \ A5 or name CA6 or name CA7 or name CB4 or name CB5 or name CB6 or name CB7 or na \ me O1 or name OA2 or name OA3 or name OA4 or name OA5 or name OA6 or name OA7 or \ name OA8 or name OA9 or name OB4 or name OB5 or name OB6 or name OB7 or name OB \ 8 or name OB9 or name PA1 or name PB2)))) selection = chain '1L' } ncs_group { reference = (chain '1M' and resid 32 through 495) selection = (chain '1N' and resid 32 through 495) } ncs_group { reference = chain '1O' selection = chain '1P' } ncs_group { reference = chain '1Q' selection = chain '1S' } ncs_group { reference = (chain '1R' and resid 2 through 123) selection = chain '1T' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 14.040 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: 0.030 Extract box with map and model: 0.370 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 31.150 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.531 34756 Z= 0.313 Angle : 0.837 21.490 47178 Z= 0.407 Chirality : 0.050 0.388 5097 Planarity : 0.007 0.075 5970 Dihedral : 15.400 89.437 12920 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.53 % Favored : 97.38 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.83 % Cis-general : 0.03 % 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: -0.84 (0.12), residues: 4156 helix: -0.24 (0.10), residues: 2182 sheet: 0.19 (0.25), residues: 420 loop : -1.05 (0.15), residues: 1554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG1M 211 TYR 0.147 0.003 TYR1A 184 PHE 0.051 0.002 PHE1I 65 TRP 0.045 0.002 TRP1P 45 HIS 0.016 0.002 HIS1N 291 Details of bonding type rmsd covalent geometry : bond 0.00666 (34739) covalent geometry : angle 0.83675 (47162) SS BOND : bond 0.00612 ( 8) SS BOND : angle 1.31826 ( 16) hydrogen bonds : bond 0.16590 ( 1801) hydrogen bonds : angle 6.07195 ( 5190) metal coordination : bond 0.53134 ( 1) Misc. bond : bond 0.17685 ( 8) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8312 Ramachandran restraints generated. 4156 Oldfield, 0 Emsley, 4156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8312 Ramachandran restraints generated. 4156 Oldfield, 0 Emsley, 4156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 521 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 521 time to evaluate : 1.257 Fit side-chains REVERT: 1A 39 MET cc_start: 0.8985 (mmm) cc_final: 0.8618 (mmp) REVERT: 1A 69 MET cc_start: 0.9137 (mmm) cc_final: 0.8862 (mmm) REVERT: 1A 267 GLN cc_start: 0.8594 (mm-40) cc_final: 0.8366 (mm110) REVERT: 1A 268 HIS cc_start: 0.7547 (m90) cc_final: 0.7307 (m90) REVERT: 1A 290 MET cc_start: 0.6954 (mtm) cc_final: 0.6722 (mtm) REVERT: 1A 364 GLN cc_start: 0.8470 (mm110) cc_final: 0.8172 (mm-40) REVERT: 1B 139 MET cc_start: 0.9059 (mmt) cc_final: 0.8847 (mmt) REVERT: 1D 140 LEU cc_start: 0.6969 (tt) cc_final: 0.6694 (pt) REVERT: 1K 25 ARG cc_start: 0.7906 (ttt180) cc_final: 0.7083 (mmt90) REVERT: 1L 4 ARG cc_start: 0.5888 (ttt180) cc_final: 0.5563 (ttp-170) REVERT: 1L 5 GLN cc_start: 0.7678 (mm110) cc_final: 0.7192 (mp10) REVERT: 1M 122 GLU cc_start: 0.7195 (tp30) cc_final: 0.6979 (tp30) REVERT: 1M 128 MET cc_start: 0.8145 (ptt) cc_final: 0.7923 (ptt) REVERT: 1O 21 ILE cc_start: 0.7578 (mm) cc_final: 0.7354 (mt) REVERT: 1Q 48 ARG cc_start: 0.6839 (mmt90) cc_final: 0.6383 (mtp85) REVERT: 1Q 278 HIS cc_start: 0.6169 (m90) cc_final: 0.5858 (p90) REVERT: 1S 320 LYS cc_start: 0.8368 (tptm) cc_final: 0.8115 (tptm) REVERT: 1S 458 MET cc_start: 0.8276 (ttp) cc_final: 0.8018 (ttm) REVERT: 1T 3 SER cc_start: 0.3276 (t) cc_final: 0.2900 (t) REVERT: 1T 6 LYS cc_start: 0.5862 (mtmt) cc_final: 0.5547 (mtpt) outliers start: 0 outliers final: 0 residues processed: 521 average time/residue: 0.7920 time to fit residues: 476.7628 Evaluate side-chains 352 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 352 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 197 optimal weight: 6.9990 chunk 388 optimal weight: 5.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 0.5980 chunk 132 optimal weight: 0.6980 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 5.9990 chunk 401 optimal weight: 3.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 3.9990 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1B 67 HIS 1B 261 ASN 1I 42 GLN 1L 21 GLN 1L 30 ASN 1M 227 GLN 1N 131 GLN 1Q 198 GLN 1Q 470 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.140291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.109190 restraints weight = 46690.153| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 1.62 r_work: 0.3374 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3279 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.1227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.273 34756 Z= 0.173 Angle : 0.633 16.222 47178 Z= 0.309 Chirality : 0.043 0.196 5097 Planarity : 0.005 0.064 5970 Dihedral : 13.252 86.971 5538 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.17 % Favored : 97.76 % Rotamer: Outliers : 1.52 % Allowed : 7.09 % Favored : 91.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.83 % Cis-general : 0.03 % 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: 0.41 (0.13), residues: 4156 helix: 1.05 (0.11), residues: 2202 sheet: 0.03 (0.24), residues: 436 loop : -0.73 (0.16), residues: 1518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG1E 100 TYR 0.036 0.002 TYR1A 184 PHE 0.025 0.002 PHE1I 65 TRP 0.020 0.002 TRP1P 45 HIS 0.015 0.001 HIS1A 197 Details of bonding type rmsd covalent geometry : bond 0.00406 (34739) covalent geometry : angle 0.63268 (47162) SS BOND : bond 0.00642 ( 8) SS BOND : angle 0.79040 ( 16) hydrogen bonds : bond 0.05321 ( 1801) hydrogen bonds : angle 4.49477 ( 5190) metal coordination : bond 0.02040 ( 1) Misc. bond : bond 0.14280 ( 8) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8312 Ramachandran restraints generated. 4156 Oldfield, 0 Emsley, 4156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8312 Ramachandran restraints generated. 4156 Oldfield, 0 Emsley, 4156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 370 time to evaluate : 1.419 Fit side-chains revert: symmetry clash REVERT: 1A 39 MET cc_start: 0.8994 (mmm) cc_final: 0.8607 (mmp) REVERT: 1A 60 TYR cc_start: 0.7642 (m-80) cc_final: 0.7427 (m-80) REVERT: 1A 268 HIS cc_start: 0.7477 (m90) cc_final: 0.7236 (m90) REVERT: 1A 316 ARG cc_start: 0.7650 (mtm-85) cc_final: 0.7319 (mpp-170) REVERT: 1A 364 GLN cc_start: 0.8534 (mm110) cc_final: 0.8260 (mm-40) REVERT: 1E 218 GLU cc_start: 0.7826 (OUTLIER) cc_final: 0.7334 (mp0) REVERT: 1E 235 LYS cc_start: 0.7667 (OUTLIER) cc_final: 0.6878 (mmmm) REVERT: 1E 274 MET cc_start: 0.8249 (mmm) cc_final: 0.7908 (mmp) REVERT: 1K 25 ARG cc_start: 0.8212 (ttt180) cc_final: 0.7141 (mmt90) REVERT: 1K 71 GLU cc_start: 0.8044 (mt-10) cc_final: 0.7712 (tt0) REVERT: 1L 4 ARG cc_start: 0.5989 (ttt180) cc_final: 0.5669 (ttm170) REVERT: 1L 5 GLN cc_start: 0.7752 (mm110) cc_final: 0.7279 (mp10) REVERT: 1M 399 ARG cc_start: 0.7991 (mtm110) cc_final: 0.7747 (mtm110) REVERT: 1N 163 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8356 (mp) REVERT: 1O 21 ILE cc_start: 0.7545 (mm) cc_final: 0.7339 (mt) REVERT: 1Q 270 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8261 (mt) REVERT: 1Q 278 HIS cc_start: 0.6058 (m90) cc_final: 0.5754 (p90) REVERT: 1Q 333 ASP cc_start: 0.5950 (OUTLIER) cc_final: 0.5269 (m-30) REVERT: 1S 320 LYS cc_start: 0.8268 (tptm) cc_final: 0.8053 (tptm) REVERT: 1S 438 GLU cc_start: 0.7725 (mm-30) cc_final: 0.7394 (mp0) REVERT: 1S 458 MET cc_start: 0.8249 (ttp) cc_final: 0.7990 (ttm) REVERT: 1T 3 SER cc_start: 0.3316 (t) cc_final: 0.2986 (t) REVERT: 1T 6 LYS cc_start: 0.5877 (mtmt) cc_final: 0.5620 (mmtp) REVERT: 1T 90 GLU cc_start: 0.8495 (OUTLIER) cc_final: 0.8288 (mt-10) outliers start: 52 outliers final: 19 residues processed: 395 average time/residue: 0.8083 time to fit residues: 368.5034 Evaluate side-chains 373 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 348 time to evaluate : 1.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1A residue 331 LEU Chi-restraints excluded: chain 1B residue 101 MET Chi-restraints excluded: chain 1D residue 250 GLU Chi-restraints excluded: chain 1E residue 218 GLU Chi-restraints excluded: chain 1E residue 235 LYS Chi-restraints excluded: chain 1F residue 245 GLU Chi-restraints excluded: chain 1H residue 9 LEU Chi-restraints excluded: chain 1H residue 45 THR Chi-restraints excluded: chain 1M residue 183 GLU Chi-restraints excluded: chain 1M residue 434 VAL Chi-restraints excluded: chain 1N residue 163 LEU Chi-restraints excluded: chain 1N residue 179 VAL Chi-restraints excluded: chain 1N residue 402 ASP Chi-restraints excluded: chain 1Q residue 75 VAL Chi-restraints excluded: chain 1Q residue 270 LEU Chi-restraints excluded: chain 1Q residue 333 ASP Chi-restraints excluded: chain 1Q residue 394 VAL Chi-restraints excluded: chain 1S residue 53 LEU Chi-restraints excluded: chain 1S residue 71 THR Chi-restraints excluded: chain 1S residue 92 VAL Chi-restraints excluded: chain 1S residue 389 SER Chi-restraints excluded: chain 1S residue 427 SER Chi-restraints excluded: chain 1T residue 43 LYS Chi-restraints excluded: chain 1T residue 90 GLU Chi-restraints excluded: chain 1T residue 95 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 352 optimal weight: 0.6980 chunk 401 optimal weight: 3.9990 chunk 375 optimal weight: 9.9990 chunk 371 optimal weight: 3.9990 chunk 8 optimal weight: 0.0670 chunk 76 optimal weight: 8.9990 chunk 14 optimal weight: 7.9990 chunk 175 optimal weight: 0.0870 chunk 113 optimal weight: 1.9990 chunk 194 optimal weight: 3.9990 chunk 232 optimal weight: 4.9990 overall best weight: 1.3700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1A 57 HIS 1B 67 HIS 1E 271 GLN 1Q 198 GLN 1S 276 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.141208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.110251 restraints weight = 46519.407| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 1.62 r_work: 0.3389 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3295 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.1469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.259 34756 Z= 0.131 Angle : 0.572 18.926 47178 Z= 0.275 Chirality : 0.041 0.170 5097 Planarity : 0.004 0.062 5970 Dihedral : 12.776 87.280 5538 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.26 % Favored : 97.69 % Rotamer: Outliers : 1.49 % Allowed : 9.52 % Favored : 89.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.83 % Cis-general : 0.03 % 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: 1.00 (0.13), residues: 4156 helix: 1.65 (0.11), residues: 2203 sheet: 0.07 (0.24), residues: 436 loop : -0.59 (0.16), residues: 1517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG1Q 288 TYR 0.016 0.001 TYR1A 184 PHE 0.017 0.001 PHE1I 65 TRP 0.018 0.001 TRP1M 485 HIS 0.010 0.001 HIS1A 197 Details of bonding type rmsd covalent geometry : bond 0.00300 (34739) covalent geometry : angle 0.57199 (47162) SS BOND : bond 0.00352 ( 8) SS BOND : angle 0.66888 ( 16) hydrogen bonds : bond 0.04575 ( 1801) hydrogen bonds : angle 4.22028 ( 5190) metal coordination : bond 0.00306 ( 1) Misc. bond : bond 0.15566 ( 8) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8312 Ramachandran restraints generated. 4156 Oldfield, 0 Emsley, 4156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8312 Ramachandran restraints generated. 4156 Oldfield, 0 Emsley, 4156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 370 time to evaluate : 1.260 Fit side-chains REVERT: 1A 39 MET cc_start: 0.8949 (mmm) cc_final: 0.8725 (mmp) REVERT: 1A 268 HIS cc_start: 0.7405 (m90) cc_final: 0.7181 (m90) REVERT: 1A 316 ARG cc_start: 0.7654 (mtm-85) cc_final: 0.7341 (mpp-170) REVERT: 1A 364 GLN cc_start: 0.8449 (mm110) cc_final: 0.8188 (mm-40) REVERT: 1E 218 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.7281 (mp0) REVERT: 1E 235 LYS cc_start: 0.7609 (OUTLIER) cc_final: 0.6602 (mmmm) REVERT: 1G 41 LYS cc_start: 0.8391 (tppt) cc_final: 0.8124 (tppt) REVERT: 1G 46 ARG cc_start: 0.8701 (ttt90) cc_final: 0.8480 (tpp-160) REVERT: 1K 25 ARG cc_start: 0.8226 (ttt180) cc_final: 0.7195 (mmt90) REVERT: 1K 71 GLU cc_start: 0.8033 (mt-10) cc_final: 0.7652 (tt0) REVERT: 1L 4 ARG cc_start: 0.6024 (ttt180) cc_final: 0.5651 (ttp-170) REVERT: 1L 5 GLN cc_start: 0.7763 (mm110) cc_final: 0.7314 (mp10) REVERT: 1M 184 MET cc_start: 0.8339 (mtt) cc_final: 0.8122 (mtt) REVERT: 1M 394 MET cc_start: 0.9220 (mtm) cc_final: 0.8960 (mtt) REVERT: 1M 399 ARG cc_start: 0.7975 (mtm110) cc_final: 0.7559 (mtp180) REVERT: 1N 163 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8382 (mp) REVERT: 1Q 270 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8232 (mp) REVERT: 1Q 278 HIS cc_start: 0.6148 (m90) cc_final: 0.5825 (p-80) REVERT: 1Q 286 GLN cc_start: 0.7090 (mp-120) cc_final: 0.6823 (mp10) REVERT: 1Q 333 ASP cc_start: 0.5800 (OUTLIER) cc_final: 0.5130 (m-30) REVERT: 1R 76 HIS cc_start: 0.8492 (m-70) cc_final: 0.8216 (m-70) REVERT: 1S 320 LYS cc_start: 0.8263 (tptm) cc_final: 0.7993 (tptm) REVERT: 1S 438 GLU cc_start: 0.7696 (mm-30) cc_final: 0.7350 (mp0) REVERT: 1S 458 MET cc_start: 0.8252 (ttp) cc_final: 0.8026 (ttm) REVERT: 1T 3 SER cc_start: 0.3426 (t) cc_final: 0.3103 (t) REVERT: 1T 90 GLU cc_start: 0.8526 (OUTLIER) cc_final: 0.8312 (mt-10) outliers start: 51 outliers final: 20 residues processed: 393 average time/residue: 0.8106 time to fit residues: 367.1501 Evaluate side-chains 374 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 348 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1A residue 331 LEU Chi-restraints excluded: chain 1A residue 370 LEU Chi-restraints excluded: chain 1B residue 101 MET Chi-restraints excluded: chain 1D residue 250 GLU Chi-restraints excluded: chain 1E residue 218 GLU Chi-restraints excluded: chain 1E residue 235 LYS Chi-restraints excluded: chain 1E residue 309 VAL Chi-restraints excluded: chain 1F residue 245 GLU Chi-restraints excluded: chain 1G residue 3 MET Chi-restraints excluded: chain 1H residue 9 LEU Chi-restraints excluded: chain 1L residue 41 GLU Chi-restraints excluded: chain 1M residue 183 GLU Chi-restraints excluded: chain 1M residue 332 ASN Chi-restraints excluded: chain 1N residue 163 LEU Chi-restraints excluded: chain 1N residue 179 VAL Chi-restraints excluded: chain 1N residue 184 MET Chi-restraints excluded: chain 1N residue 402 ASP Chi-restraints excluded: chain 1Q residue 75 VAL Chi-restraints excluded: chain 1Q residue 270 LEU Chi-restraints excluded: chain 1Q residue 333 ASP Chi-restraints excluded: chain 1S residue 53 LEU Chi-restraints excluded: chain 1S residue 92 VAL Chi-restraints excluded: chain 1S residue 389 SER Chi-restraints excluded: chain 1S residue 427 SER Chi-restraints excluded: chain 1T residue 43 LYS Chi-restraints excluded: chain 1T residue 90 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 285 optimal weight: 5.9990 chunk 213 optimal weight: 6.9990 chunk 122 optimal weight: 6.9990 chunk 246 optimal weight: 2.9990 chunk 232 optimal weight: 2.9990 chunk 243 optimal weight: 1.9990 chunk 102 optimal weight: 8.9990 chunk 370 optimal weight: 2.9990 chunk 156 optimal weight: 5.9990 chunk 98 optimal weight: 5.9990 chunk 168 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1E 108 GLN ** 1N 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1Q 398 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.138157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.107262 restraints weight = 46316.735| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 1.60 r_work: 0.3345 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3251 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.321 34756 Z= 0.220 Angle : 0.674 18.116 47178 Z= 0.328 Chirality : 0.046 0.216 5097 Planarity : 0.005 0.061 5970 Dihedral : 13.287 88.680 5538 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.65 % Favored : 97.31 % Rotamer: Outliers : 2.10 % Allowed : 10.33 % Favored : 87.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.83 % Cis-general : 0.03 % 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: 0.78 (0.13), residues: 4156 helix: 1.48 (0.11), residues: 2197 sheet: -0.03 (0.24), residues: 436 loop : -0.68 (0.16), residues: 1523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG1M 182 TYR 0.019 0.002 TYR1M 465 PHE 0.019 0.002 PHE1I 65 TRP 0.018 0.002 TRP1A 142 HIS 0.013 0.002 HIS1N 291 Details of bonding type rmsd covalent geometry : bond 0.00528 (34739) covalent geometry : angle 0.67414 (47162) SS BOND : bond 0.00534 ( 8) SS BOND : angle 1.10680 ( 16) hydrogen bonds : bond 0.05689 ( 1801) hydrogen bonds : angle 4.41594 ( 5190) metal coordination : bond 0.00400 ( 1) Misc. bond : bond 0.17195 ( 8) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8312 Ramachandran restraints generated. 4156 Oldfield, 0 Emsley, 4156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8312 Ramachandran restraints generated. 4156 Oldfield, 0 Emsley, 4156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 350 time to evaluate : 1.375 Fit side-chains REVERT: 1A 268 HIS cc_start: 0.7470 (m90) cc_final: 0.7232 (m90) REVERT: 1A 316 ARG cc_start: 0.7755 (mtm-85) cc_final: 0.7285 (tpp-160) REVERT: 1E 218 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7286 (mp0) REVERT: 1F 116 MET cc_start: 0.8164 (mtp) cc_final: 0.7649 (mtt) REVERT: 1G 41 LYS cc_start: 0.8411 (tppt) cc_final: 0.8117 (tppt) REVERT: 1K 25 ARG cc_start: 0.8353 (ttt180) cc_final: 0.7198 (mmt90) REVERT: 1L 5 GLN cc_start: 0.7704 (mm110) cc_final: 0.7176 (mp10) REVERT: 1L 40 LYS cc_start: 0.8614 (OUTLIER) cc_final: 0.8332 (tttt) REVERT: 1M 119 LYS cc_start: 0.7646 (mmtm) cc_final: 0.7331 (ptmt) REVERT: 1M 394 MET cc_start: 0.9299 (mtm) cc_final: 0.9068 (mtp) REVERT: 1M 399 ARG cc_start: 0.8046 (mtm110) cc_final: 0.7663 (mtp180) REVERT: 1N 163 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8347 (mp) REVERT: 1N 171 ARG cc_start: 0.7232 (OUTLIER) cc_final: 0.6858 (mpp80) REVERT: 1N 320 MET cc_start: 0.8057 (mtp) cc_final: 0.7833 (mtp) REVERT: 1Q 270 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8279 (mp) REVERT: 1Q 278 HIS cc_start: 0.6080 (m90) cc_final: 0.5752 (p-80) REVERT: 1Q 333 ASP cc_start: 0.5697 (OUTLIER) cc_final: 0.5153 (m-30) REVERT: 1Q 339 MET cc_start: 0.8693 (mtt) cc_final: 0.8329 (mtt) REVERT: 1S 302 SER cc_start: 0.7265 (t) cc_final: 0.6900 (p) REVERT: 1S 438 GLU cc_start: 0.7745 (mm-30) cc_final: 0.7367 (mp0) REVERT: 1S 458 MET cc_start: 0.8263 (ttp) cc_final: 0.7881 (ttm) REVERT: 1T 3 SER cc_start: 0.3766 (t) cc_final: 0.3486 (t) REVERT: 1T 6 LYS cc_start: 0.5278 (mmtp) cc_final: 0.4873 (mmtp) REVERT: 1T 77 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.7564 (mm-30) outliers start: 72 outliers final: 35 residues processed: 385 average time/residue: 0.9038 time to fit residues: 402.2367 Evaluate side-chains 385 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 343 time to evaluate : 1.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1A residue 101 MET Chi-restraints excluded: chain 1A residue 290 MET Chi-restraints excluded: chain 1A residue 331 LEU Chi-restraints excluded: chain 1A residue 342 THR Chi-restraints excluded: chain 1A residue 370 LEU Chi-restraints excluded: chain 1C residue 162 VAL Chi-restraints excluded: chain 1D residue 155 VAL Chi-restraints excluded: chain 1D residue 250 GLU Chi-restraints excluded: chain 1E residue 218 GLU Chi-restraints excluded: chain 1E residue 235 LYS Chi-restraints excluded: chain 1E residue 309 VAL Chi-restraints excluded: chain 1F residue 88 GLU Chi-restraints excluded: chain 1F residue 245 GLU Chi-restraints excluded: chain 1G residue 3 MET Chi-restraints excluded: chain 1H residue 3 MET Chi-restraints excluded: chain 1H residue 9 LEU Chi-restraints excluded: chain 1H residue 40 ASP Chi-restraints excluded: chain 1I residue 2 VAL Chi-restraints excluded: chain 1L residue 40 LYS Chi-restraints excluded: chain 1L residue 41 GLU Chi-restraints excluded: chain 1M residue 183 GLU Chi-restraints excluded: chain 1M residue 291 HIS Chi-restraints excluded: chain 1M residue 332 ASN Chi-restraints excluded: chain 1M residue 434 VAL Chi-restraints excluded: chain 1N residue 163 LEU Chi-restraints excluded: chain 1N residue 171 ARG Chi-restraints excluded: chain 1N residue 179 VAL Chi-restraints excluded: chain 1N residue 184 MET Chi-restraints excluded: chain 1N residue 402 ASP Chi-restraints excluded: chain 1P residue 34 VAL Chi-restraints excluded: chain 1Q residue 75 VAL Chi-restraints excluded: chain 1Q residue 270 LEU Chi-restraints excluded: chain 1Q residue 333 ASP Chi-restraints excluded: chain 1Q residue 394 VAL Chi-restraints excluded: chain 1S residue 53 LEU Chi-restraints excluded: chain 1S residue 71 THR Chi-restraints excluded: chain 1S residue 92 VAL Chi-restraints excluded: chain 1S residue 163 THR Chi-restraints excluded: chain 1S residue 389 SER Chi-restraints excluded: chain 1S residue 427 SER Chi-restraints excluded: chain 1T residue 43 LYS Chi-restraints excluded: chain 1T residue 77 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 32 optimal weight: 4.9990 chunk 131 optimal weight: 1.9990 chunk 326 optimal weight: 5.9990 chunk 186 optimal weight: 5.9990 chunk 271 optimal weight: 6.9990 chunk 369 optimal weight: 2.9990 chunk 111 optimal weight: 20.0000 chunk 56 optimal weight: 0.9980 chunk 331 optimal weight: 0.9980 chunk 167 optimal weight: 0.6980 chunk 294 optimal weight: 3.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1E 108 GLN 1F 108 GLN ** 1N 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1Q 198 GLN 1Q 286 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.139949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.109133 restraints weight = 46284.764| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 1.60 r_work: 0.3374 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3279 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.247 34756 Z= 0.138 Angle : 0.580 15.251 47178 Z= 0.281 Chirality : 0.042 0.195 5097 Planarity : 0.004 0.059 5970 Dihedral : 12.913 89.774 5538 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.17 % Favored : 97.79 % Rotamer: Outliers : 1.78 % Allowed : 11.38 % Favored : 86.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.83 % Cis-general : 0.03 % 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: 1.09 (0.13), residues: 4156 helix: 1.78 (0.11), residues: 2202 sheet: -0.03 (0.24), residues: 440 loop : -0.59 (0.16), residues: 1514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG1Q 288 TYR 0.020 0.001 TYR1A 279 PHE 0.012 0.001 PHE1B 299 TRP 0.018 0.001 TRP1M 485 HIS 0.009 0.001 HIS1N 291 Details of bonding type rmsd covalent geometry : bond 0.00322 (34739) covalent geometry : angle 0.58029 (47162) SS BOND : bond 0.00344 ( 8) SS BOND : angle 0.74076 ( 16) hydrogen bonds : bond 0.04620 ( 1801) hydrogen bonds : angle 4.18392 ( 5190) metal coordination : bond 0.00116 ( 1) Misc. bond : bond 0.15129 ( 8) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8312 Ramachandran restraints generated. 4156 Oldfield, 0 Emsley, 4156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8312 Ramachandran restraints generated. 4156 Oldfield, 0 Emsley, 4156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 359 time to evaluate : 0.863 Fit side-chains REVERT: 1A 268 HIS cc_start: 0.7406 (m90) cc_final: 0.7176 (m90) REVERT: 1A 316 ARG cc_start: 0.7685 (mtm-85) cc_final: 0.7347 (mpp-170) REVERT: 1E 218 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.7258 (mp0) REVERT: 1E 235 LYS cc_start: 0.7593 (OUTLIER) cc_final: 0.6548 (mmmm) REVERT: 1F 236 MET cc_start: 0.6806 (OUTLIER) cc_final: 0.6522 (mtp) REVERT: 1G 41 LYS cc_start: 0.8381 (tppt) cc_final: 0.8111 (tppt) REVERT: 1K 12 ILE cc_start: 0.9129 (OUTLIER) cc_final: 0.8688 (mm) REVERT: 1K 25 ARG cc_start: 0.8305 (ttt180) cc_final: 0.7228 (mmt90) REVERT: 1K 63 GLU cc_start: 0.8115 (mm-30) cc_final: 0.7833 (tm-30) REVERT: 1L 5 GLN cc_start: 0.7679 (mm110) cc_final: 0.7094 (mp10) REVERT: 1L 40 LYS cc_start: 0.8661 (OUTLIER) cc_final: 0.8327 (tttt) REVERT: 1M 119 LYS cc_start: 0.7661 (mmtm) cc_final: 0.7321 (ptmt) REVERT: 1M 157 ASN cc_start: 0.8921 (t0) cc_final: 0.8721 (t0) REVERT: 1M 394 MET cc_start: 0.9294 (mtm) cc_final: 0.9029 (mtp) REVERT: 1M 399 ARG cc_start: 0.7998 (mtm110) cc_final: 0.7652 (mtp180) REVERT: 1N 163 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8311 (mp) REVERT: 1N 171 ARG cc_start: 0.7068 (mtp85) cc_final: 0.6693 (mpp80) REVERT: 1O 34 VAL cc_start: 0.8041 (p) cc_final: 0.7704 (m) REVERT: 1Q 270 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8226 (mp) REVERT: 1Q 278 HIS cc_start: 0.5998 (m90) cc_final: 0.5739 (p-80) REVERT: 1Q 333 ASP cc_start: 0.5717 (OUTLIER) cc_final: 0.5016 (m-30) REVERT: 1Q 471 LEU cc_start: 0.5016 (OUTLIER) cc_final: 0.4464 (tt) REVERT: 1S 302 SER cc_start: 0.7262 (t) cc_final: 0.6886 (p) REVERT: 1S 438 GLU cc_start: 0.7714 (mm-30) cc_final: 0.7365 (mp0) REVERT: 1S 458 MET cc_start: 0.8179 (ttp) cc_final: 0.7836 (ttm) REVERT: 1T 3 SER cc_start: 0.3423 (t) cc_final: 0.3170 (t) REVERT: 1T 6 LYS cc_start: 0.5174 (mmtp) cc_final: 0.4947 (mmtp) outliers start: 61 outliers final: 26 residues processed: 393 average time/residue: 0.7628 time to fit residues: 348.0778 Evaluate side-chains 379 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 344 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1A residue 290 MET Chi-restraints excluded: chain 1A residue 331 LEU Chi-restraints excluded: chain 1A residue 342 THR Chi-restraints excluded: chain 1A residue 370 LEU Chi-restraints excluded: chain 1C residue 204 ILE Chi-restraints excluded: chain 1D residue 250 GLU Chi-restraints excluded: chain 1E residue 218 GLU Chi-restraints excluded: chain 1E residue 235 LYS Chi-restraints excluded: chain 1E residue 309 VAL Chi-restraints excluded: chain 1F residue 88 GLU Chi-restraints excluded: chain 1F residue 236 MET Chi-restraints excluded: chain 1F residue 245 GLU Chi-restraints excluded: chain 1G residue 3 MET Chi-restraints excluded: chain 1H residue 9 LEU Chi-restraints excluded: chain 1K residue 12 ILE Chi-restraints excluded: chain 1L residue 40 LYS Chi-restraints excluded: chain 1L residue 41 GLU Chi-restraints excluded: chain 1M residue 183 GLU Chi-restraints excluded: chain 1M residue 269 ASP Chi-restraints excluded: chain 1M residue 291 HIS Chi-restraints excluded: chain 1M residue 332 ASN Chi-restraints excluded: chain 1M residue 434 VAL Chi-restraints excluded: chain 1N residue 118 VAL Chi-restraints excluded: chain 1N residue 163 LEU Chi-restraints excluded: chain 1N residue 179 VAL Chi-restraints excluded: chain 1N residue 184 MET Chi-restraints excluded: chain 1N residue 402 ASP Chi-restraints excluded: chain 1Q residue 75 VAL Chi-restraints excluded: chain 1Q residue 270 LEU Chi-restraints excluded: chain 1Q residue 333 ASP Chi-restraints excluded: chain 1Q residue 471 LEU Chi-restraints excluded: chain 1S residue 364 LEU Chi-restraints excluded: chain 1S residue 389 SER Chi-restraints excluded: chain 1S residue 427 SER Chi-restraints excluded: chain 1T residue 43 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 92 optimal weight: 20.0000 chunk 294 optimal weight: 0.6980 chunk 164 optimal weight: 1.9990 chunk 69 optimal weight: 5.9990 chunk 324 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 171 optimal weight: 1.9990 chunk 177 optimal weight: 0.9980 chunk 155 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 235 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1E 108 GLN 1F 108 GLN ** 1N 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1Q 198 GLN 1Q 286 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.140058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.109353 restraints weight = 46212.829| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 1.59 r_work: 0.3377 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3283 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.269 34756 Z= 0.139 Angle : 0.583 17.660 47178 Z= 0.280 Chirality : 0.042 0.196 5097 Planarity : 0.004 0.059 5970 Dihedral : 12.743 89.911 5538 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.38 % Favored : 97.57 % Rotamer: Outliers : 1.75 % Allowed : 12.14 % Favored : 86.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.83 % Cis-general : 0.03 % 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: 1.19 (0.13), residues: 4156 helix: 1.90 (0.11), residues: 2200 sheet: -0.02 (0.24), residues: 440 loop : -0.58 (0.16), residues: 1516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG1Q 288 TYR 0.019 0.001 TYR1A 279 PHE 0.012 0.001 PHE1B 299 TRP 0.018 0.001 TRP1M 485 HIS 0.009 0.001 HIS1N 291 Details of bonding type rmsd covalent geometry : bond 0.00326 (34739) covalent geometry : angle 0.58256 (47162) SS BOND : bond 0.00328 ( 8) SS BOND : angle 0.76502 ( 16) hydrogen bonds : bond 0.04594 ( 1801) hydrogen bonds : angle 4.14246 ( 5190) metal coordination : bond 0.00145 ( 1) Misc. bond : bond 0.15285 ( 8) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8312 Ramachandran restraints generated. 4156 Oldfield, 0 Emsley, 4156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8312 Ramachandran restraints generated. 4156 Oldfield, 0 Emsley, 4156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 353 time to evaluate : 1.354 Fit side-chains REVERT: 1A 268 HIS cc_start: 0.7400 (m90) cc_final: 0.7172 (m90) REVERT: 1A 316 ARG cc_start: 0.7640 (mtm-85) cc_final: 0.7303 (mpp-170) REVERT: 1C 230 HIS cc_start: 0.1059 (OUTLIER) cc_final: 0.0839 (m-70) REVERT: 1E 218 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.7260 (mp0) REVERT: 1E 235 LYS cc_start: 0.7591 (OUTLIER) cc_final: 0.6554 (mmmm) REVERT: 1F 236 MET cc_start: 0.6894 (OUTLIER) cc_final: 0.6651 (mtp) REVERT: 1G 41 LYS cc_start: 0.8378 (tppt) cc_final: 0.8121 (tppt) REVERT: 1K 12 ILE cc_start: 0.9108 (OUTLIER) cc_final: 0.8639 (mm) REVERT: 1K 25 ARG cc_start: 0.8321 (ttt180) cc_final: 0.7221 (mmt90) REVERT: 1K 63 GLU cc_start: 0.8128 (mm-30) cc_final: 0.7837 (tm-30) REVERT: 1L 4 ARG cc_start: 0.5775 (ttt-90) cc_final: 0.5231 (ttp-170) REVERT: 1L 5 GLN cc_start: 0.7684 (mm110) cc_final: 0.7088 (mp10) REVERT: 1L 40 LYS cc_start: 0.8658 (OUTLIER) cc_final: 0.8327 (tttt) REVERT: 1M 119 LYS cc_start: 0.7662 (mmtm) cc_final: 0.7330 (ptmt) REVERT: 1M 157 ASN cc_start: 0.8934 (t0) cc_final: 0.8713 (t0) REVERT: 1M 394 MET cc_start: 0.9285 (OUTLIER) cc_final: 0.9019 (mtp) REVERT: 1N 163 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8301 (mp) REVERT: 1N 171 ARG cc_start: 0.7050 (OUTLIER) cc_final: 0.6682 (mpp80) REVERT: 1O 34 VAL cc_start: 0.8037 (p) cc_final: 0.7703 (m) REVERT: 1Q 270 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.8225 (mp) REVERT: 1Q 278 HIS cc_start: 0.6022 (m90) cc_final: 0.5761 (p-80) REVERT: 1Q 333 ASP cc_start: 0.5707 (OUTLIER) cc_final: 0.5033 (m-30) REVERT: 1Q 471 LEU cc_start: 0.4859 (OUTLIER) cc_final: 0.4259 (tt) REVERT: 1S 302 SER cc_start: 0.7261 (t) cc_final: 0.6887 (p) REVERT: 1S 438 GLU cc_start: 0.7639 (mm-30) cc_final: 0.7358 (mp0) REVERT: 1S 458 MET cc_start: 0.8186 (ttp) cc_final: 0.7840 (ttm) REVERT: 1T 3 SER cc_start: 0.3779 (t) cc_final: 0.3486 (t) REVERT: 1T 6 LYS cc_start: 0.5189 (mmtp) cc_final: 0.4903 (mmtp) REVERT: 1T 90 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.8342 (mt-10) outliers start: 60 outliers final: 31 residues processed: 387 average time/residue: 0.7764 time to fit residues: 349.0680 Evaluate side-chains 391 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 347 time to evaluate : 1.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1A residue 290 MET Chi-restraints excluded: chain 1A residue 331 LEU Chi-restraints excluded: chain 1A residue 370 LEU Chi-restraints excluded: chain 1C residue 204 ILE Chi-restraints excluded: chain 1C residue 230 HIS Chi-restraints excluded: chain 1D residue 155 VAL Chi-restraints excluded: chain 1D residue 250 GLU Chi-restraints excluded: chain 1E residue 218 GLU Chi-restraints excluded: chain 1E residue 235 LYS Chi-restraints excluded: chain 1E residue 309 VAL Chi-restraints excluded: chain 1F residue 88 GLU Chi-restraints excluded: chain 1F residue 236 MET Chi-restraints excluded: chain 1F residue 245 GLU Chi-restraints excluded: chain 1G residue 3 MET Chi-restraints excluded: chain 1H residue 9 LEU Chi-restraints excluded: chain 1H residue 40 ASP Chi-restraints excluded: chain 1K residue 12 ILE Chi-restraints excluded: chain 1L residue 40 LYS Chi-restraints excluded: chain 1L residue 41 GLU Chi-restraints excluded: chain 1M residue 183 GLU Chi-restraints excluded: chain 1M residue 269 ASP Chi-restraints excluded: chain 1M residue 275 ARG Chi-restraints excluded: chain 1M residue 291 HIS Chi-restraints excluded: chain 1M residue 332 ASN Chi-restraints excluded: chain 1M residue 394 MET Chi-restraints excluded: chain 1M residue 434 VAL Chi-restraints excluded: chain 1N residue 163 LEU Chi-restraints excluded: chain 1N residue 171 ARG Chi-restraints excluded: chain 1N residue 179 VAL Chi-restraints excluded: chain 1N residue 184 MET Chi-restraints excluded: chain 1N residue 272 THR Chi-restraints excluded: chain 1N residue 402 ASP Chi-restraints excluded: chain 1Q residue 75 VAL Chi-restraints excluded: chain 1Q residue 270 LEU Chi-restraints excluded: chain 1Q residue 333 ASP Chi-restraints excluded: chain 1Q residue 471 LEU Chi-restraints excluded: chain 1S residue 53 LEU Chi-restraints excluded: chain 1S residue 92 VAL Chi-restraints excluded: chain 1S residue 163 THR Chi-restraints excluded: chain 1S residue 364 LEU Chi-restraints excluded: chain 1S residue 389 SER Chi-restraints excluded: chain 1S residue 427 SER Chi-restraints excluded: chain 1T residue 43 LYS Chi-restraints excluded: chain 1T residue 90 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 227 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 chunk 307 optimal weight: 2.9990 chunk 230 optimal weight: 0.9990 chunk 191 optimal weight: 0.9980 chunk 394 optimal weight: 3.9990 chunk 134 optimal weight: 1.9990 chunk 138 optimal weight: 7.9990 chunk 385 optimal weight: 0.0060 chunk 261 optimal weight: 0.9990 chunk 341 optimal weight: 2.9990 overall best weight: 0.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1A 8 GLN 1E 108 GLN 1L 21 GLN ** 1N 131 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 = 0.3909 r_free = 0.3909 target = 0.141894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.111263 restraints weight = 46422.058| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 1.59 r_work: 0.3406 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3312 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.1858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.172 34756 Z= 0.106 Angle : 0.534 13.379 47178 Z= 0.259 Chirality : 0.040 0.170 5097 Planarity : 0.004 0.058 5970 Dihedral : 12.290 89.890 5538 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.00 % Favored : 97.95 % Rotamer: Outliers : 1.75 % Allowed : 12.64 % Favored : 85.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.83 % Cis-general : 0.03 % 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: 1.41 (0.13), residues: 4156 helix: 2.07 (0.11), residues: 2224 sheet: 0.05 (0.24), residues: 440 loop : -0.51 (0.16), residues: 1492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG1Q 288 TYR 0.018 0.001 TYR1A 279 PHE 0.009 0.001 PHE1K 35 TRP 0.018 0.001 TRP1M 485 HIS 0.010 0.001 HIS1M 291 Details of bonding type rmsd covalent geometry : bond 0.00238 (34739) covalent geometry : angle 0.53418 (47162) SS BOND : bond 0.00227 ( 8) SS BOND : angle 0.53513 ( 16) hydrogen bonds : bond 0.03939 ( 1801) hydrogen bonds : angle 3.99078 ( 5190) metal coordination : bond 0.00038 ( 1) Misc. bond : bond 0.11839 ( 8) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8312 Ramachandran restraints generated. 4156 Oldfield, 0 Emsley, 4156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8312 Ramachandran restraints generated. 4156 Oldfield, 0 Emsley, 4156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 375 time to evaluate : 1.315 Fit side-chains REVERT: 1A 268 HIS cc_start: 0.7336 (m90) cc_final: 0.7120 (m90) REVERT: 1A 316 ARG cc_start: 0.7617 (mtm-85) cc_final: 0.7116 (mpp-170) REVERT: 1C 230 HIS cc_start: 0.1035 (OUTLIER) cc_final: 0.0780 (m-70) REVERT: 1E 218 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.7306 (mp0) REVERT: 1E 235 LYS cc_start: 0.7542 (OUTLIER) cc_final: 0.6450 (mmmm) REVERT: 1F 236 MET cc_start: 0.6742 (OUTLIER) cc_final: 0.6383 (mtm) REVERT: 1G 41 LYS cc_start: 0.8253 (tppt) cc_final: 0.8040 (tppt) REVERT: 1I 12 GLN cc_start: 0.8074 (tp-100) cc_final: 0.7867 (tp40) REVERT: 1K 12 ILE cc_start: 0.9096 (OUTLIER) cc_final: 0.8639 (mm) REVERT: 1K 25 ARG cc_start: 0.8247 (ttt180) cc_final: 0.7202 (mmt90) REVERT: 1K 63 GLU cc_start: 0.8080 (mm-30) cc_final: 0.7769 (tm-30) REVERT: 1L 5 GLN cc_start: 0.7648 (mm110) cc_final: 0.7066 (mp10) REVERT: 1L 40 LYS cc_start: 0.8645 (OUTLIER) cc_final: 0.8301 (tttt) REVERT: 1M 119 LYS cc_start: 0.7719 (mmtm) cc_final: 0.7333 (ptmt) REVERT: 1M 157 ASN cc_start: 0.8893 (t0) cc_final: 0.8680 (t0) REVERT: 1N 163 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.8297 (mp) REVERT: 1N 171 ARG cc_start: 0.7018 (OUTLIER) cc_final: 0.6626 (mpp80) REVERT: 1O 34 VAL cc_start: 0.7842 (p) cc_final: 0.7635 (m) REVERT: 1Q 270 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8246 (mp) REVERT: 1Q 278 HIS cc_start: 0.6071 (m90) cc_final: 0.5791 (p-80) REVERT: 1Q 333 ASP cc_start: 0.5561 (OUTLIER) cc_final: 0.5013 (m-30) REVERT: 1Q 471 LEU cc_start: 0.4764 (OUTLIER) cc_final: 0.4159 (tt) REVERT: 1S 302 SER cc_start: 0.7196 (t) cc_final: 0.6840 (p) REVERT: 1S 438 GLU cc_start: 0.7618 (mm-30) cc_final: 0.7327 (mp0) REVERT: 1S 458 MET cc_start: 0.8198 (ttp) cc_final: 0.7836 (ttm) REVERT: 1T 3 SER cc_start: 0.3834 (t) cc_final: 0.3544 (t) REVERT: 1T 6 LYS cc_start: 0.5286 (mmtp) cc_final: 0.4989 (mmtp) REVERT: 1T 90 GLU cc_start: 0.8569 (OUTLIER) cc_final: 0.8279 (mt-10) outliers start: 60 outliers final: 24 residues processed: 407 average time/residue: 0.8133 time to fit residues: 384.0985 Evaluate side-chains 380 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 344 time to evaluate : 1.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1A residue 331 LEU Chi-restraints excluded: chain 1B residue 342 THR Chi-restraints excluded: chain 1C residue 204 ILE Chi-restraints excluded: chain 1C residue 230 HIS Chi-restraints excluded: chain 1D residue 250 GLU Chi-restraints excluded: chain 1E residue 218 GLU Chi-restraints excluded: chain 1E residue 235 LYS Chi-restraints excluded: chain 1E residue 309 VAL Chi-restraints excluded: chain 1F residue 236 MET Chi-restraints excluded: chain 1F residue 245 GLU Chi-restraints excluded: chain 1G residue 3 MET Chi-restraints excluded: chain 1H residue 9 LEU Chi-restraints excluded: chain 1K residue 12 ILE Chi-restraints excluded: chain 1L residue 40 LYS Chi-restraints excluded: chain 1M residue 183 GLU Chi-restraints excluded: chain 1M residue 269 ASP Chi-restraints excluded: chain 1M residue 275 ARG Chi-restraints excluded: chain 1M residue 291 HIS Chi-restraints excluded: chain 1M residue 434 VAL Chi-restraints excluded: chain 1N residue 118 VAL Chi-restraints excluded: chain 1N residue 163 LEU Chi-restraints excluded: chain 1N residue 171 ARG Chi-restraints excluded: chain 1N residue 179 VAL Chi-restraints excluded: chain 1N residue 184 MET Chi-restraints excluded: chain 1N residue 272 THR Chi-restraints excluded: chain 1Q residue 75 VAL Chi-restraints excluded: chain 1Q residue 270 LEU Chi-restraints excluded: chain 1Q residue 333 ASP Chi-restraints excluded: chain 1Q residue 348 VAL Chi-restraints excluded: chain 1Q residue 471 LEU Chi-restraints excluded: chain 1S residue 53 LEU Chi-restraints excluded: chain 1S residue 364 LEU Chi-restraints excluded: chain 1S residue 389 SER Chi-restraints excluded: chain 1S residue 427 SER Chi-restraints excluded: chain 1T residue 43 LYS Chi-restraints excluded: chain 1T residue 90 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 236 optimal weight: 6.9990 chunk 35 optimal weight: 4.9990 chunk 269 optimal weight: 7.9990 chunk 243 optimal weight: 2.9990 chunk 314 optimal weight: 5.9990 chunk 296 optimal weight: 2.9990 chunk 389 optimal weight: 8.9990 chunk 271 optimal weight: 0.0970 chunk 355 optimal weight: 9.9990 chunk 263 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1E 108 GLN 1F 108 GLN ** 1N 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1Q 198 GLN 1S 388 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.139873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.109169 restraints weight = 46239.070| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 1.58 r_work: 0.3374 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3278 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.1833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.236 34756 Z= 0.151 Angle : 0.594 15.529 47178 Z= 0.289 Chirality : 0.042 0.200 5097 Planarity : 0.005 0.061 5970 Dihedral : 12.466 89.197 5538 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.41 % Favored : 97.55 % Rotamer: Outliers : 1.81 % Allowed : 12.61 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.83 % Cis-general : 0.03 % 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: 1.29 (0.13), residues: 4156 helix: 1.98 (0.11), residues: 2204 sheet: 0.02 (0.24), residues: 440 loop : -0.54 (0.16), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG1Q 288 TYR 0.021 0.002 TYR1A 279 PHE 0.014 0.001 PHE1B 299 TRP 0.016 0.001 TRP1M 485 HIS 0.010 0.001 HIS1N 291 Details of bonding type rmsd covalent geometry : bond 0.00358 (34739) covalent geometry : angle 0.59380 (47162) SS BOND : bond 0.00347 ( 8) SS BOND : angle 0.83367 ( 16) hydrogen bonds : bond 0.04689 ( 1801) hydrogen bonds : angle 4.11610 ( 5190) metal coordination : bond 0.00165 ( 1) Misc. bond : bond 0.13389 ( 8) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8312 Ramachandran restraints generated. 4156 Oldfield, 0 Emsley, 4156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8312 Ramachandran restraints generated. 4156 Oldfield, 0 Emsley, 4156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 350 time to evaluate : 0.917 Fit side-chains REVERT: 1A 268 HIS cc_start: 0.7349 (m90) cc_final: 0.7122 (m90) REVERT: 1A 316 ARG cc_start: 0.7704 (mtm-85) cc_final: 0.7224 (mpp-170) REVERT: 1C 230 HIS cc_start: 0.1051 (OUTLIER) cc_final: 0.0757 (m-70) REVERT: 1E 218 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.7256 (mp0) REVERT: 1E 235 LYS cc_start: 0.7606 (OUTLIER) cc_final: 0.6593 (mmmm) REVERT: 1F 236 MET cc_start: 0.6862 (OUTLIER) cc_final: 0.6584 (mtm) REVERT: 1G 41 LYS cc_start: 0.8395 (tppt) cc_final: 0.8120 (tppt) REVERT: 1K 12 ILE cc_start: 0.9109 (OUTLIER) cc_final: 0.8642 (mm) REVERT: 1K 25 ARG cc_start: 0.8343 (ttt180) cc_final: 0.7233 (mmt90) REVERT: 1L 5 GLN cc_start: 0.7685 (mm110) cc_final: 0.7057 (mp10) REVERT: 1L 40 LYS cc_start: 0.8667 (OUTLIER) cc_final: 0.8324 (tttt) REVERT: 1M 119 LYS cc_start: 0.7729 (mmtm) cc_final: 0.7372 (ptmt) REVERT: 1M 157 ASN cc_start: 0.8919 (t0) cc_final: 0.8708 (t0) REVERT: 1N 163 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8313 (mp) REVERT: 1N 171 ARG cc_start: 0.7049 (OUTLIER) cc_final: 0.6721 (mtm-85) REVERT: 1N 320 MET cc_start: 0.7998 (mtp) cc_final: 0.7795 (mtp) REVERT: 1Q 270 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8256 (mp) REVERT: 1Q 278 HIS cc_start: 0.6096 (m90) cc_final: 0.5803 (p-80) REVERT: 1Q 333 ASP cc_start: 0.5556 (OUTLIER) cc_final: 0.5002 (m-30) REVERT: 1Q 471 LEU cc_start: 0.4772 (OUTLIER) cc_final: 0.4140 (tt) REVERT: 1S 302 SER cc_start: 0.7231 (t) cc_final: 0.6843 (p) REVERT: 1S 438 GLU cc_start: 0.7643 (mm-30) cc_final: 0.7388 (mp0) REVERT: 1S 458 MET cc_start: 0.8222 (ttp) cc_final: 0.7820 (ttm) REVERT: 1T 3 SER cc_start: 0.3687 (t) cc_final: 0.3416 (t) REVERT: 1T 6 LYS cc_start: 0.5233 (mmtp) cc_final: 0.4934 (mmtp) REVERT: 1T 90 GLU cc_start: 0.8608 (OUTLIER) cc_final: 0.8328 (mt-10) outliers start: 62 outliers final: 32 residues processed: 388 average time/residue: 0.7854 time to fit residues: 354.5636 Evaluate side-chains 386 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 342 time to evaluate : 1.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1A residue 331 LEU Chi-restraints excluded: chain 1A residue 370 LEU Chi-restraints excluded: chain 1B residue 342 THR Chi-restraints excluded: chain 1C residue 60 GLU Chi-restraints excluded: chain 1C residue 204 ILE Chi-restraints excluded: chain 1C residue 230 HIS Chi-restraints excluded: chain 1D residue 250 GLU Chi-restraints excluded: chain 1E residue 218 GLU Chi-restraints excluded: chain 1E residue 235 LYS Chi-restraints excluded: chain 1E residue 309 VAL Chi-restraints excluded: chain 1F residue 216 ILE Chi-restraints excluded: chain 1F residue 236 MET Chi-restraints excluded: chain 1F residue 245 GLU Chi-restraints excluded: chain 1G residue 3 MET Chi-restraints excluded: chain 1H residue 9 LEU Chi-restraints excluded: chain 1I residue 2 VAL Chi-restraints excluded: chain 1K residue 12 ILE Chi-restraints excluded: chain 1L residue 40 LYS Chi-restraints excluded: chain 1M residue 183 GLU Chi-restraints excluded: chain 1M residue 269 ASP Chi-restraints excluded: chain 1M residue 275 ARG Chi-restraints excluded: chain 1M residue 291 HIS Chi-restraints excluded: chain 1M residue 332 ASN Chi-restraints excluded: chain 1M residue 434 VAL Chi-restraints excluded: chain 1N residue 118 VAL Chi-restraints excluded: chain 1N residue 163 LEU Chi-restraints excluded: chain 1N residue 171 ARG Chi-restraints excluded: chain 1N residue 179 VAL Chi-restraints excluded: chain 1N residue 184 MET Chi-restraints excluded: chain 1N residue 402 ASP Chi-restraints excluded: chain 1P residue 34 VAL Chi-restraints excluded: chain 1Q residue 75 VAL Chi-restraints excluded: chain 1Q residue 270 LEU Chi-restraints excluded: chain 1Q residue 333 ASP Chi-restraints excluded: chain 1Q residue 471 LEU Chi-restraints excluded: chain 1S residue 53 LEU Chi-restraints excluded: chain 1S residue 163 THR Chi-restraints excluded: chain 1S residue 197 GLU Chi-restraints excluded: chain 1S residue 296 ILE Chi-restraints excluded: chain 1S residue 364 LEU Chi-restraints excluded: chain 1S residue 389 SER Chi-restraints excluded: chain 1S residue 427 SER Chi-restraints excluded: chain 1T residue 43 LYS Chi-restraints excluded: chain 1T residue 90 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 271 optimal weight: 7.9990 chunk 321 optimal weight: 6.9990 chunk 255 optimal weight: 4.9990 chunk 289 optimal weight: 0.9990 chunk 307 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 chunk 204 optimal weight: 6.9990 chunk 186 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 chunk 311 optimal weight: 6.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1E 108 GLN 1F 108 GLN 1M 103 HIS ** 1N 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1Q 198 GLN 1S 388 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.141875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.112171 restraints weight = 46241.462| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 1.76 r_work: 0.3364 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3265 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.1917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.272 34756 Z= 0.119 Angle : 0.545 13.462 47178 Z= 0.265 Chirality : 0.040 0.176 5097 Planarity : 0.004 0.060 5970 Dihedral : 12.096 89.326 5538 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.00 % Favored : 97.95 % Rotamer: Outliers : 1.52 % Allowed : 12.96 % Favored : 85.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.83 % Cis-general : 0.03 % 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: 1.47 (0.13), residues: 4156 helix: 2.12 (0.11), residues: 2224 sheet: 0.07 (0.24), residues: 440 loop : -0.48 (0.17), residues: 1492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG1Q 288 TYR 0.018 0.001 TYR1A 279 PHE 0.009 0.001 PHE1K 35 TRP 0.018 0.001 TRP1M 485 HIS 0.010 0.001 HIS1M 291 Details of bonding type rmsd covalent geometry : bond 0.00248 (34739) covalent geometry : angle 0.54473 (47162) SS BOND : bond 0.00237 ( 8) SS BOND : angle 0.54950 ( 16) hydrogen bonds : bond 0.03960 ( 1801) hydrogen bonds : angle 3.97801 ( 5190) metal coordination : bond 0.27195 ( 1) Misc. bond : bond 0.11558 ( 8) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8312 Ramachandran restraints generated. 4156 Oldfield, 0 Emsley, 4156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8312 Ramachandran restraints generated. 4156 Oldfield, 0 Emsley, 4156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 357 time to evaluate : 1.317 Fit side-chains REVERT: 1A 268 HIS cc_start: 0.7352 (m90) cc_final: 0.7136 (m90) REVERT: 1A 316 ARG cc_start: 0.7688 (mtm-85) cc_final: 0.7182 (mpp-170) REVERT: 1C 135 MET cc_start: 0.8698 (mmp) cc_final: 0.8494 (mmm) REVERT: 1C 230 HIS cc_start: 0.1020 (OUTLIER) cc_final: 0.0711 (m-70) REVERT: 1E 218 GLU cc_start: 0.7869 (OUTLIER) cc_final: 0.7351 (mp0) REVERT: 1E 235 LYS cc_start: 0.7571 (OUTLIER) cc_final: 0.6533 (mmmm) REVERT: 1F 236 MET cc_start: 0.7092 (OUTLIER) cc_final: 0.6286 (mtm) REVERT: 1G 41 LYS cc_start: 0.8402 (tppt) cc_final: 0.8170 (tppt) REVERT: 1K 12 ILE cc_start: 0.9101 (OUTLIER) cc_final: 0.8646 (mm) REVERT: 1K 25 ARG cc_start: 0.8329 (ttt180) cc_final: 0.7234 (mmt90) REVERT: 1K 63 GLU cc_start: 0.8105 (mm-30) cc_final: 0.7775 (tm-30) REVERT: 1L 5 GLN cc_start: 0.7672 (mm110) cc_final: 0.7070 (mp10) REVERT: 1L 40 LYS cc_start: 0.8692 (OUTLIER) cc_final: 0.8357 (tttt) REVERT: 1N 163 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8328 (mp) REVERT: 1N 171 ARG cc_start: 0.7083 (OUTLIER) cc_final: 0.6679 (mpp80) REVERT: 1Q 270 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8285 (mp) REVERT: 1Q 278 HIS cc_start: 0.6072 (m90) cc_final: 0.5786 (p-80) REVERT: 1Q 333 ASP cc_start: 0.5618 (OUTLIER) cc_final: 0.5056 (m-30) REVERT: 1Q 471 LEU cc_start: 0.4835 (OUTLIER) cc_final: 0.4290 (tt) REVERT: 1S 302 SER cc_start: 0.7252 (t) cc_final: 0.6859 (p) REVERT: 1S 438 GLU cc_start: 0.7687 (mm-30) cc_final: 0.7430 (mp0) REVERT: 1S 458 MET cc_start: 0.8197 (ttp) cc_final: 0.7802 (ttm) REVERT: 1T 3 SER cc_start: 0.3802 (t) cc_final: 0.3498 (t) REVERT: 1T 6 LYS cc_start: 0.5318 (mmtp) cc_final: 0.4644 (mmtp) REVERT: 1T 90 GLU cc_start: 0.8655 (OUTLIER) cc_final: 0.8379 (mt-10) outliers start: 52 outliers final: 25 residues processed: 386 average time/residue: 0.9151 time to fit residues: 407.7942 Evaluate side-chains 377 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 340 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1B residue 342 THR Chi-restraints excluded: chain 1C residue 204 ILE Chi-restraints excluded: chain 1C residue 230 HIS Chi-restraints excluded: chain 1D residue 250 GLU Chi-restraints excluded: chain 1E residue 218 GLU Chi-restraints excluded: chain 1E residue 235 LYS Chi-restraints excluded: chain 1E residue 309 VAL Chi-restraints excluded: chain 1F residue 116 MET Chi-restraints excluded: chain 1F residue 236 MET Chi-restraints excluded: chain 1F residue 245 GLU Chi-restraints excluded: chain 1G residue 3 MET Chi-restraints excluded: chain 1H residue 9 LEU Chi-restraints excluded: chain 1K residue 12 ILE Chi-restraints excluded: chain 1L residue 40 LYS Chi-restraints excluded: chain 1M residue 269 ASP Chi-restraints excluded: chain 1M residue 275 ARG Chi-restraints excluded: chain 1M residue 291 HIS Chi-restraints excluded: chain 1M residue 434 VAL Chi-restraints excluded: chain 1N residue 118 VAL Chi-restraints excluded: chain 1N residue 163 LEU Chi-restraints excluded: chain 1N residue 171 ARG Chi-restraints excluded: chain 1N residue 179 VAL Chi-restraints excluded: chain 1N residue 184 MET Chi-restraints excluded: chain 1N residue 402 ASP Chi-restraints excluded: chain 1Q residue 75 VAL Chi-restraints excluded: chain 1Q residue 270 LEU Chi-restraints excluded: chain 1Q residue 333 ASP Chi-restraints excluded: chain 1Q residue 471 LEU Chi-restraints excluded: chain 1S residue 53 LEU Chi-restraints excluded: chain 1S residue 163 THR Chi-restraints excluded: chain 1S residue 197 GLU Chi-restraints excluded: chain 1S residue 296 ILE Chi-restraints excluded: chain 1S residue 364 LEU Chi-restraints excluded: chain 1S residue 389 SER Chi-restraints excluded: chain 1S residue 427 SER Chi-restraints excluded: chain 1T residue 43 LYS Chi-restraints excluded: chain 1T residue 90 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 56 optimal weight: 0.9980 chunk 123 optimal weight: 3.9990 chunk 322 optimal weight: 10.0000 chunk 378 optimal weight: 5.9990 chunk 381 optimal weight: 4.9990 chunk 16 optimal weight: 0.0870 chunk 166 optimal weight: 6.9990 chunk 92 optimal weight: 0.3980 chunk 363 optimal weight: 4.9990 chunk 373 optimal weight: 4.9990 chunk 296 optimal weight: 1.9990 overall best weight: 1.4962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1E 108 GLN 1F 108 GLN ** 1N 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1S 388 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.140618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.109856 restraints weight = 46167.339| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 1.61 r_work: 0.3384 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3289 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.217 34756 Z= 0.136 Angle : 0.578 14.266 47178 Z= 0.281 Chirality : 0.041 0.186 5097 Planarity : 0.004 0.066 5970 Dihedral : 12.178 89.305 5538 Min Nonbonded Distance : 1.734 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.29 % Favored : 97.67 % Rotamer: Outliers : 1.28 % Allowed : 13.49 % Favored : 85.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.83 % Cis-general : 0.03 % 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: 1.41 (0.13), residues: 4156 helix: 2.08 (0.11), residues: 2206 sheet: 0.04 (0.24), residues: 440 loop : -0.48 (0.16), residues: 1510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG1Q 288 TYR 0.024 0.001 TYR1A 279 PHE 0.012 0.001 PHE1B 299 TRP 0.016 0.001 TRP1M 485 HIS 0.009 0.001 HIS1N 291 Details of bonding type rmsd covalent geometry : bond 0.00320 (34739) covalent geometry : angle 0.57792 (47162) SS BOND : bond 0.00308 ( 8) SS BOND : angle 0.72244 ( 16) hydrogen bonds : bond 0.04394 ( 1801) hydrogen bonds : angle 4.05110 ( 5190) metal coordination : bond 0.01441 ( 1) Misc. bond : bond 0.12575 ( 8) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8312 Ramachandran restraints generated. 4156 Oldfield, 0 Emsley, 4156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8312 Ramachandran restraints generated. 4156 Oldfield, 0 Emsley, 4156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 346 time to evaluate : 1.704 Fit side-chains REVERT: 1A 268 HIS cc_start: 0.7320 (m90) cc_final: 0.7099 (m90) REVERT: 1A 316 ARG cc_start: 0.7703 (mtm-85) cc_final: 0.7228 (mpp-170) REVERT: 1C 230 HIS cc_start: 0.1055 (OUTLIER) cc_final: 0.0740 (m-70) REVERT: 1E 218 GLU cc_start: 0.7755 (OUTLIER) cc_final: 0.7231 (mp0) REVERT: 1E 235 LYS cc_start: 0.7574 (OUTLIER) cc_final: 0.6549 (mmmm) REVERT: 1F 236 MET cc_start: 0.6854 (OUTLIER) cc_final: 0.6283 (mtm) REVERT: 1G 41 LYS cc_start: 0.8355 (tppt) cc_final: 0.8133 (tppt) REVERT: 1K 12 ILE cc_start: 0.9101 (OUTLIER) cc_final: 0.8642 (mm) REVERT: 1K 25 ARG cc_start: 0.8299 (ttt180) cc_final: 0.7242 (mmt90) REVERT: 1K 63 GLU cc_start: 0.8064 (mm-30) cc_final: 0.7738 (tm-30) REVERT: 1L 40 LYS cc_start: 0.8667 (OUTLIER) cc_final: 0.8323 (tttt) REVERT: 1M 182 ARG cc_start: 0.8022 (mmm160) cc_final: 0.7731 (mmm160) REVERT: 1N 163 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8268 (mp) REVERT: 1N 171 ARG cc_start: 0.7030 (OUTLIER) cc_final: 0.6655 (mpp80) REVERT: 1Q 270 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8274 (mp) REVERT: 1Q 278 HIS cc_start: 0.6180 (m90) cc_final: 0.5801 (p-80) REVERT: 1Q 333 ASP cc_start: 0.5621 (OUTLIER) cc_final: 0.5043 (m-30) REVERT: 1Q 471 LEU cc_start: 0.4997 (OUTLIER) cc_final: 0.4324 (tt) REVERT: 1S 302 SER cc_start: 0.7239 (t) cc_final: 0.6858 (p) REVERT: 1S 438 GLU cc_start: 0.7639 (mm-30) cc_final: 0.7409 (mp0) REVERT: 1S 458 MET cc_start: 0.8210 (ttp) cc_final: 0.7815 (ttm) REVERT: 1T 3 SER cc_start: 0.3828 (t) cc_final: 0.3524 (t) REVERT: 1T 6 LYS cc_start: 0.5296 (mmtp) cc_final: 0.4684 (mmtp) REVERT: 1T 90 GLU cc_start: 0.8610 (OUTLIER) cc_final: 0.8319 (mt-10) outliers start: 44 outliers final: 28 residues processed: 374 average time/residue: 0.9402 time to fit residues: 407.2530 Evaluate side-chains 377 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 337 time to evaluate : 1.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1A residue 290 MET Chi-restraints excluded: chain 1B residue 342 THR Chi-restraints excluded: chain 1C residue 204 ILE Chi-restraints excluded: chain 1C residue 230 HIS Chi-restraints excluded: chain 1D residue 250 GLU Chi-restraints excluded: chain 1E residue 218 GLU Chi-restraints excluded: chain 1E residue 235 LYS Chi-restraints excluded: chain 1E residue 309 VAL Chi-restraints excluded: chain 1F residue 236 MET Chi-restraints excluded: chain 1F residue 245 GLU Chi-restraints excluded: chain 1G residue 3 MET Chi-restraints excluded: chain 1H residue 9 LEU Chi-restraints excluded: chain 1I residue 2 VAL Chi-restraints excluded: chain 1K residue 12 ILE Chi-restraints excluded: chain 1L residue 40 LYS Chi-restraints excluded: chain 1M residue 269 ASP Chi-restraints excluded: chain 1M residue 275 ARG Chi-restraints excluded: chain 1M residue 291 HIS Chi-restraints excluded: chain 1M residue 434 VAL Chi-restraints excluded: chain 1N residue 118 VAL Chi-restraints excluded: chain 1N residue 163 LEU Chi-restraints excluded: chain 1N residue 171 ARG Chi-restraints excluded: chain 1N residue 179 VAL Chi-restraints excluded: chain 1N residue 184 MET Chi-restraints excluded: chain 1N residue 402 ASP Chi-restraints excluded: chain 1P residue 34 VAL Chi-restraints excluded: chain 1Q residue 75 VAL Chi-restraints excluded: chain 1Q residue 270 LEU Chi-restraints excluded: chain 1Q residue 333 ASP Chi-restraints excluded: chain 1Q residue 471 LEU Chi-restraints excluded: chain 1S residue 53 LEU Chi-restraints excluded: chain 1S residue 92 VAL Chi-restraints excluded: chain 1S residue 163 THR Chi-restraints excluded: chain 1S residue 197 GLU Chi-restraints excluded: chain 1S residue 296 ILE Chi-restraints excluded: chain 1S residue 364 LEU Chi-restraints excluded: chain 1S residue 389 SER Chi-restraints excluded: chain 1S residue 427 SER Chi-restraints excluded: chain 1T residue 43 LYS Chi-restraints excluded: chain 1T residue 90 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 331 optimal weight: 1.9990 chunk 339 optimal weight: 7.9990 chunk 276 optimal weight: 7.9990 chunk 195 optimal weight: 5.9990 chunk 295 optimal weight: 6.9990 chunk 369 optimal weight: 1.9990 chunk 228 optimal weight: 0.1980 chunk 124 optimal weight: 0.9980 chunk 148 optimal weight: 2.9990 chunk 188 optimal weight: 7.9990 chunk 397 optimal weight: 6.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1E 108 GLN 1F 108 GLN ** 1N 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1S 388 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.140114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.109424 restraints weight = 45977.500| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 1.59 r_work: 0.3379 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3284 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.225 34756 Z= 0.143 Angle : 0.589 14.990 47178 Z= 0.286 Chirality : 0.042 0.195 5097 Planarity : 0.004 0.060 5970 Dihedral : 12.253 89.611 5538 Min Nonbonded Distance : 1.670 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.43 % Favored : 97.52 % Rotamer: Outliers : 1.26 % Allowed : 13.69 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.83 % Cis-general : 0.03 % 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: 1.34 (0.13), residues: 4156 helix: 1.99 (0.11), residues: 2218 sheet: 0.03 (0.24), residues: 440 loop : -0.50 (0.16), residues: 1498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG1E 159 TYR 0.022 0.002 TYR1A 279 PHE 0.013 0.001 PHE1B 299 TRP 0.016 0.001 TRP1M 485 HIS 0.009 0.001 HIS1N 291 Details of bonding type rmsd covalent geometry : bond 0.00338 (34739) covalent geometry : angle 0.58891 (47162) SS BOND : bond 0.00326 ( 8) SS BOND : angle 0.76020 ( 16) hydrogen bonds : bond 0.04560 ( 1801) hydrogen bonds : angle 4.09058 ( 5190) metal coordination : bond 0.00088 ( 1) Misc. bond : bond 0.13145 ( 8) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15914.68 seconds wall clock time: 270 minutes 46.50 seconds (16246.50 seconds total)