Starting phenix.real_space_refine on Sun Jun 29 15:18:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9f5z_50204/06_2025/9f5z_50204.cif Found real_map, /net/cci-nas-00/data/ceres_data/9f5z_50204/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9f5z_50204/06_2025/9f5z_50204.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9f5z_50204/06_2025/9f5z_50204.map" model { file = "/net/cci-nas-00/data/ceres_data/9f5z_50204/06_2025/9f5z_50204.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9f5z_50204/06_2025/9f5z_50204.cif" } resolution = 2.39 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 23.10, per 1000 atoms: 0.67 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: 8.99 Conformation dependent library (CDL) restraints added in 3.9 seconds 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: 4.04 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: 12.12 Time building geometry restraints manager: 10.26 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 377 or resid 401 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 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 n \ ame OA7 or name OA8 or name OA9 or name OB4 or name OB5 or name OB6 or name OB7 \ or name OB8 or name OB9 or name PA1 or name PB2)) or resid 406)) selection = (chain '1B' and (resid 2 through 377 or resid 401 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 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 n \ ame OA7 or name OA8 or name OA9 or name OB4 or name OB5 or name OB6 or name OB7 \ or name OB8 or name OB9 or name PA1 or name PB2)) or (resid 406 and (name C1 or \ name C2 or name C21 or name C22 or name C23 or name C24 or name C25 or name C26 \ or name C27 or name C28 or name C29 or name C2A or name C2B or name C2C or name \ C2D or name C2E or name C2F or name C3 or name C31 or name C32 or name C33 or na \ me C34 or name O11 or name O12 or name O13 or name O14 or name O21 or name O22 o \ r 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: 0.010 Normalize map: mean=0, sd=1: 51.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 1.310 Check model and map are aligned: 0.240 Set scattering table: 0.310 Process input model: 83.110 Find NCS groups from input model: 1.600 Set up NCS constraints: 0.280 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 152.160 ------------------------------------------------------------------------------- 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 : 3.38 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.045 0.002 TRP1P 45 HIS 0.016 0.002 HIS1N 291 PHE 0.051 0.002 PHE1I 65 TYR 0.147 0.003 TYR1A 184 ARG 0.009 0.001 ARG1M 211 Details of bonding type rmsd hydrogen bonds : bond 0.16590 ( 1801) hydrogen bonds : angle 6.07195 ( 5190) metal coordination : bond 0.53134 ( 1) SS BOND : bond 0.00612 ( 8) SS BOND : angle 1.31826 ( 16) covalent geometry : bond 0.00666 (34739) covalent geometry : angle 0.83675 (47162) 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 : 3.354 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: 0.6721 (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: 1.9092 time to fit residues: 1159.8548 Evaluate side-chains 353 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 353 time to evaluate : 3.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 346 optimal weight: 0.9990 chunk 310 optimal weight: 5.9990 chunk 172 optimal weight: 2.9990 chunk 106 optimal weight: 0.0970 chunk 209 optimal weight: 4.9990 chunk 166 optimal weight: 3.9990 chunk 321 optimal weight: 0.9980 chunk 124 optimal weight: 0.7980 chunk 195 optimal weight: 4.9990 chunk 239 optimal weight: 2.9990 chunk 372 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 30 ASN 1M 227 GLN 1N 131 GLN ** 1N 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1Q 198 GLN 1Q 470 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.143290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.112486 restraints weight = 46419.683| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 1.61 r_work: 0.3424 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3330 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.1230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.198 34756 Z= 0.116 Angle : 0.560 14.173 47178 Z= 0.273 Chirality : 0.040 0.170 5097 Planarity : 0.005 0.064 5970 Dihedral : 12.815 88.391 5538 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.02 % Favored : 97.91 % Rotamer: Outliers : 1.26 % Allowed : 6.98 % Favored : 91.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.83 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.13), residues: 4156 helix: 1.20 (0.11), residues: 2203 sheet: 0.11 (0.24), residues: 438 loop : -0.67 (0.16), residues: 1515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP1P 45 HIS 0.009 0.001 HIS1N 291 PHE 0.017 0.001 PHE1I 65 TYR 0.030 0.001 TYR1A 184 ARG 0.006 0.000 ARG1Q 288 Details of bonding type rmsd hydrogen bonds : bond 0.04486 ( 1801) hydrogen bonds : angle 4.36083 ( 5190) metal coordination : bond 0.03019 ( 1) SS BOND : bond 0.00244 ( 8) SS BOND : angle 0.56202 ( 16) covalent geometry : bond 0.00255 (34739) covalent geometry : angle 0.55964 (47162) Misc. bond : bond 0.12463 ( 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 432 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 389 time to evaluate : 5.335 Fit side-chains revert: symmetry clash REVERT: 1A 39 MET cc_start: 0.8991 (mmm) cc_final: 0.8616 (mmp) REVERT: 1A 60 TYR cc_start: 0.7541 (m-80) cc_final: 0.7299 (m-80) REVERT: 1A 268 HIS cc_start: 0.7401 (m90) cc_final: 0.7173 (m90) REVERT: 1A 364 GLN cc_start: 0.8474 (mm110) cc_final: 0.8199 (mm-40) REVERT: 1G 46 ARG cc_start: 0.8649 (ttt90) cc_final: 0.8435 (tpp-160) REVERT: 1I 42 GLN cc_start: 0.7198 (mp10) cc_final: 0.6963 (mp10) REVERT: 1K 25 ARG cc_start: 0.8164 (ttt180) cc_final: 0.7193 (mmt90) REVERT: 1K 71 GLU cc_start: 0.8027 (mt-10) cc_final: 0.7720 (tt0) REVERT: 1L 5 GLN cc_start: 0.7666 (mm110) cc_final: 0.7261 (mp10) REVERT: 1M 128 MET cc_start: 0.8100 (ptt) cc_final: 0.7882 (ptt) REVERT: 1M 399 ARG cc_start: 0.8019 (mtm110) cc_final: 0.7621 (mtp180) REVERT: 1N 163 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8359 (mp) REVERT: 1N 171 ARG cc_start: 0.7150 (mtp85) cc_final: 0.6741 (mpp80) REVERT: 1O 21 ILE cc_start: 0.7507 (mm) cc_final: 0.7304 (mt) REVERT: 1O 34 VAL cc_start: 0.7990 (p) cc_final: 0.7648 (m) REVERT: 1Q 48 ARG cc_start: 0.7229 (mmt90) cc_final: 0.6662 (mtp85) REVERT: 1Q 56 LYS cc_start: 0.7535 (mmtt) cc_final: 0.7332 (mmtt) REVERT: 1Q 270 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.8244 (mt) REVERT: 1Q 278 HIS cc_start: 0.6119 (m90) cc_final: 0.5752 (p90) REVERT: 1Q 333 ASP cc_start: 0.5748 (OUTLIER) cc_final: 0.5062 (m-30) REVERT: 1R 76 HIS cc_start: 0.8483 (m-70) cc_final: 0.8141 (m-70) REVERT: 1S 438 GLU cc_start: 0.7682 (mm-30) cc_final: 0.7401 (mp0) REVERT: 1S 458 MET cc_start: 0.8093 (ttp) cc_final: 0.7787 (ttm) REVERT: 1T 3 SER cc_start: 0.3137 (t) cc_final: 0.2906 (t) REVERT: 1T 6 LYS cc_start: 0.5775 (mtmt) cc_final: 0.5537 (mmtp) outliers start: 43 outliers final: 12 residues processed: 413 average time/residue: 2.8715 time to fit residues: 1391.0281 Evaluate side-chains 365 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 350 time to evaluate : 5.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1A residue 331 LEU Chi-restraints excluded: chain 1B residue 101 MET Chi-restraints excluded: chain 1C residue 97 GLU Chi-restraints excluded: chain 1D residue 250 GLU Chi-restraints excluded: chain 1H residue 3 MET Chi-restraints excluded: chain 1M residue 183 GLU Chi-restraints excluded: chain 1N residue 163 LEU Chi-restraints excluded: chain 1N residue 179 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 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 402 optimal weight: 4.9990 chunk 398 optimal weight: 9.9990 chunk 378 optimal weight: 0.6980 chunk 214 optimal weight: 2.9990 chunk 309 optimal weight: 9.9990 chunk 240 optimal weight: 0.2980 chunk 174 optimal weight: 0.9980 chunk 94 optimal weight: 2.9990 chunk 296 optimal weight: 1.9990 chunk 251 optimal weight: 0.7980 chunk 224 optimal weight: 0.4980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1A 8 GLN 1A 57 HIS 1B 67 HIS 1E 271 GLN 1N 131 GLN 1Q 198 GLN 1Q 470 ASN 1S 276 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.143969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.113211 restraints weight = 46426.136| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 1.61 r_work: 0.3436 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3341 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.1485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.193 34756 Z= 0.101 Angle : 0.523 15.653 47178 Z= 0.251 Chirality : 0.039 0.139 5097 Planarity : 0.004 0.061 5970 Dihedral : 12.231 89.635 5538 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.02 % Favored : 97.93 % Rotamer: Outliers : 1.34 % Allowed : 8.67 % Favored : 89.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.83 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.13), residues: 4156 helix: 1.84 (0.11), residues: 2212 sheet: 0.15 (0.24), residues: 438 loop : -0.51 (0.16), residues: 1506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP1M 485 HIS 0.009 0.001 HIS1M 291 PHE 0.013 0.001 PHE1I 65 TYR 0.016 0.001 TYR1A 184 ARG 0.007 0.000 ARG1Q 288 Details of bonding type rmsd hydrogen bonds : bond 0.03953 ( 1801) hydrogen bonds : angle 4.06861 ( 5190) metal coordination : bond 0.00431 ( 1) SS BOND : bond 0.00238 ( 8) SS BOND : angle 0.49484 ( 16) covalent geometry : bond 0.00223 (34739) covalent geometry : angle 0.52349 (47162) Misc. bond : bond 0.12145 ( 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 426 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 380 time to evaluate : 3.417 Fit side-chains REVERT: 1A 39 MET cc_start: 0.8994 (mmm) cc_final: 0.8623 (mmp) REVERT: 1A 60 TYR cc_start: 0.7597 (m-80) cc_final: 0.7317 (m-80) REVERT: 1A 268 HIS cc_start: 0.7349 (m90) cc_final: 0.7128 (m90) REVERT: 1A 316 ARG cc_start: 0.7651 (mpp-170) cc_final: 0.7284 (mpp-170) REVERT: 1B 314 LYS cc_start: 0.7908 (mttm) cc_final: 0.7651 (ptpp) REVERT: 1E 235 LYS cc_start: 0.7461 (OUTLIER) cc_final: 0.6736 (mmmm) REVERT: 1G 41 LYS cc_start: 0.8289 (tppt) cc_final: 0.8048 (tppt) REVERT: 1I 34 ARG cc_start: 0.8303 (OUTLIER) cc_final: 0.7050 (ptp-110) REVERT: 1K 25 ARG cc_start: 0.8135 (ttt180) cc_final: 0.7170 (mmt90) REVERT: 1K 71 GLU cc_start: 0.8009 (mt-10) cc_final: 0.7692 (tt0) REVERT: 1L 5 GLN cc_start: 0.7668 (mm110) cc_final: 0.7250 (mp10) REVERT: 1M 394 MET cc_start: 0.9166 (OUTLIER) cc_final: 0.8949 (mtp) REVERT: 1M 399 ARG cc_start: 0.7933 (mtm110) cc_final: 0.7517 (mtp180) REVERT: 1N 171 ARG cc_start: 0.7009 (mtp85) cc_final: 0.6661 (mpp80) REVERT: 1O 21 ILE cc_start: 0.7517 (mm) cc_final: 0.7301 (mt) REVERT: 1O 34 VAL cc_start: 0.7828 (p) cc_final: 0.7628 (m) REVERT: 1Q 48 ARG cc_start: 0.7198 (mmt90) cc_final: 0.6641 (mtp85) REVERT: 1Q 56 LYS cc_start: 0.7486 (mmtt) cc_final: 0.7238 (mmtt) REVERT: 1Q 270 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8250 (mt) REVERT: 1Q 278 HIS cc_start: 0.6095 (m90) cc_final: 0.5766 (p90) REVERT: 1Q 333 ASP cc_start: 0.5755 (OUTLIER) cc_final: 0.5120 (m-30) REVERT: 1Q 336 ARG cc_start: 0.6191 (mtp180) cc_final: 0.5909 (ttp-110) REVERT: 1S 438 GLU cc_start: 0.7636 (mm-30) cc_final: 0.7346 (mp0) REVERT: 1S 458 MET cc_start: 0.8108 (ttp) cc_final: 0.7696 (ttm) REVERT: 1T 3 SER cc_start: 0.3243 (t) cc_final: 0.3027 (t) REVERT: 1T 6 LYS cc_start: 0.5672 (mtmt) cc_final: 0.5469 (mmtp) outliers start: 46 outliers final: 14 residues processed: 403 average time/residue: 1.7925 time to fit residues: 840.7669 Evaluate side-chains 363 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 344 time to evaluate : 3.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1A residue 331 LEU Chi-restraints excluded: chain 1B residue 101 MET Chi-restraints excluded: chain 1C residue 97 GLU Chi-restraints excluded: chain 1D residue 250 GLU Chi-restraints excluded: chain 1E residue 235 LYS Chi-restraints excluded: chain 1H residue 9 LEU Chi-restraints excluded: chain 1I residue 34 ARG Chi-restraints excluded: chain 1M residue 183 GLU Chi-restraints excluded: chain 1M residue 394 MET 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 1R residue 92 SER Chi-restraints excluded: chain 1S residue 53 LEU Chi-restraints excluded: chain 1S residue 92 VAL Chi-restraints excluded: chain 1S residue 427 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 172 optimal weight: 10.0000 chunk 230 optimal weight: 4.9990 chunk 35 optimal weight: 5.9990 chunk 85 optimal weight: 1.9990 chunk 153 optimal weight: 4.9990 chunk 89 optimal weight: 8.9990 chunk 395 optimal weight: 5.9990 chunk 141 optimal weight: 0.7980 chunk 111 optimal weight: 7.9990 chunk 175 optimal weight: 4.9990 chunk 78 optimal weight: 6.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1B 43 GLN 1E 108 GLN ** 1N 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1Q 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.137877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.106875 restraints weight = 46557.694| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 1.59 r_work: 0.3339 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3245 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.369 34756 Z= 0.255 Angle : 0.714 18.666 47178 Z= 0.349 Chirality : 0.047 0.228 5097 Planarity : 0.006 0.063 5970 Dihedral : 13.202 88.957 5538 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.55 % Favored : 97.40 % Rotamer: Outliers : 1.98 % Allowed : 10.10 % Favored : 87.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.83 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.13), residues: 4156 helix: 1.42 (0.11), residues: 2195 sheet: -0.05 (0.24), residues: 442 loop : -0.63 (0.16), residues: 1519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP1A 142 HIS 0.017 0.002 HIS1A 197 PHE 0.026 0.002 PHE1I 65 TYR 0.022 0.003 TYR1M 465 ARG 0.010 0.001 ARG1Q 336 Details of bonding type rmsd hydrogen bonds : bond 0.06056 ( 1801) hydrogen bonds : angle 4.47064 ( 5190) metal coordination : bond 0.00482 ( 1) SS BOND : bond 0.00608 ( 8) SS BOND : angle 1.23438 ( 16) covalent geometry : bond 0.00613 (34739) covalent geometry : angle 0.71392 (47162) Misc. bond : bond 0.18155 ( 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 421 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 353 time to evaluate : 3.491 Fit side-chains REVERT: 1A 39 MET cc_start: 0.8950 (mmm) cc_final: 0.8686 (mmp) REVERT: 1A 268 HIS cc_start: 0.7453 (m90) cc_final: 0.7229 (m90) REVERT: 1A 316 ARG cc_start: 0.7899 (mpp-170) cc_final: 0.7648 (mpp-170) REVERT: 1E 218 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.7273 (mp0) REVERT: 1F 116 MET cc_start: 0.8228 (mtp) cc_final: 0.7693 (mtt) REVERT: 1G 41 LYS cc_start: 0.8407 (tppt) cc_final: 0.8118 (tppt) REVERT: 1G 46 ARG cc_start: 0.8692 (OUTLIER) cc_final: 0.7030 (ttp-170) REVERT: 1I 6 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.7099 (mp0) REVERT: 1K 25 ARG cc_start: 0.8350 (ttt180) cc_final: 0.7217 (mmt90) REVERT: 1L 4 ARG cc_start: 0.6261 (ttp-170) cc_final: 0.5737 (ttm170) REVERT: 1L 5 GLN cc_start: 0.7682 (mm110) cc_final: 0.7159 (mp10) REVERT: 1M 119 LYS cc_start: 0.7599 (mmtm) cc_final: 0.7394 (ptmt) REVERT: 1M 394 MET cc_start: 0.9295 (OUTLIER) cc_final: 0.8987 (mtt) REVERT: 1M 399 ARG cc_start: 0.8035 (mtm110) cc_final: 0.7649 (mtp180) REVERT: 1Q 270 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8304 (mp) REVERT: 1Q 278 HIS cc_start: 0.6098 (m90) cc_final: 0.5809 (p-80) REVERT: 1Q 333 ASP cc_start: 0.5728 (OUTLIER) cc_final: 0.5173 (m-30) REVERT: 1S 302 SER cc_start: 0.7281 (t) cc_final: 0.6928 (p) REVERT: 1S 438 GLU cc_start: 0.7735 (mm-30) cc_final: 0.7372 (mp0) REVERT: 1S 458 MET cc_start: 0.8307 (ttp) cc_final: 0.8034 (ttm) REVERT: 1T 3 SER cc_start: 0.3173 (t) cc_final: 0.2857 (t) REVERT: 1T 77 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.7572 (mm-30) REVERT: 1T 90 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.8356 (mt-10) outliers start: 68 outliers final: 28 residues processed: 388 average time/residue: 1.8783 time to fit residues: 849.8492 Evaluate side-chains 368 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 332 time to evaluate : 3.783 ------------------------------------------------------------------------------- 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 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 309 VAL Chi-restraints excluded: chain 1F residue 245 GLU Chi-restraints excluded: chain 1G residue 3 MET Chi-restraints excluded: chain 1G residue 46 ARG Chi-restraints excluded: chain 1H residue 9 LEU Chi-restraints excluded: chain 1H residue 40 ASP Chi-restraints excluded: chain 1I residue 6 GLU Chi-restraints excluded: chain 1M residue 183 GLU Chi-restraints excluded: chain 1M residue 332 ASN Chi-restraints excluded: chain 1M residue 394 MET Chi-restraints excluded: chain 1M residue 426 GLU 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 1P residue 36 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 1Q residue 470 ASN Chi-restraints excluded: chain 1R residue 92 SER 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 77 GLU Chi-restraints excluded: chain 1T residue 90 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 96 optimal weight: 0.5980 chunk 287 optimal weight: 4.9990 chunk 190 optimal weight: 0.6980 chunk 80 optimal weight: 7.9990 chunk 330 optimal weight: 9.9990 chunk 303 optimal weight: 1.9990 chunk 132 optimal weight: 0.8980 chunk 156 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 396 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1B 43 GLN ** 1N 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1Q 198 GLN 1Q 286 GLN 1Q 398 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.141093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.110348 restraints weight = 46352.727| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 1.60 r_work: 0.3391 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3297 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.1701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.241 34756 Z= 0.118 Angle : 0.556 15.180 47178 Z= 0.268 Chirality : 0.041 0.193 5097 Planarity : 0.004 0.059 5970 Dihedral : 12.599 87.668 5538 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.07 % Favored : 97.88 % Rotamer: Outliers : 1.58 % Allowed : 11.27 % Favored : 87.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.83 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.13), residues: 4156 helix: 1.86 (0.11), residues: 2210 sheet: 0.09 (0.24), residues: 438 loop : -0.56 (0.16), residues: 1508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP1M 485 HIS 0.010 0.001 HIS1M 291 PHE 0.011 0.001 PHE1B 299 TYR 0.017 0.001 TYR1A 279 ARG 0.010 0.000 ARG1Q 288 Details of bonding type rmsd hydrogen bonds : bond 0.04312 ( 1801) hydrogen bonds : angle 4.11752 ( 5190) metal coordination : bond 0.00022 ( 1) SS BOND : bond 0.00268 ( 8) SS BOND : angle 0.60270 ( 16) covalent geometry : bond 0.00264 (34739) covalent geometry : angle 0.55593 (47162) Misc. bond : bond 0.14799 ( 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 411 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 357 time to evaluate : 3.715 Fit side-chains REVERT: 1A 268 HIS cc_start: 0.7385 (m90) cc_final: 0.7163 (m90) REVERT: 1A 316 ARG cc_start: 0.7786 (mpp-170) cc_final: 0.7523 (mpp-170) REVERT: 1E 218 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.7267 (mp0) REVERT: 1F 116 MET cc_start: 0.8077 (mtp) cc_final: 0.7509 (mtt) REVERT: 1G 41 LYS cc_start: 0.8365 (tppt) cc_final: 0.8092 (tppt) REVERT: 1K 25 ARG cc_start: 0.8277 (ttt180) cc_final: 0.7231 (mmt90) REVERT: 1L 4 ARG cc_start: 0.6305 (ttp-170) cc_final: 0.5777 (ttm170) REVERT: 1L 5 GLN cc_start: 0.7701 (mm110) cc_final: 0.7190 (mp10) REVERT: 1M 394 MET cc_start: 0.9260 (OUTLIER) cc_final: 0.8994 (mtp) REVERT: 1M 399 ARG cc_start: 0.7993 (mtm110) cc_final: 0.7636 (mtp180) REVERT: 1N 171 ARG cc_start: 0.7042 (mtp85) cc_final: 0.6686 (mpp80) REVERT: 1O 34 VAL cc_start: 0.8032 (p) cc_final: 0.7700 (m) REVERT: 1Q 48 ARG cc_start: 0.6074 (mmt90) cc_final: 0.5023 (mtp85) REVERT: 1Q 270 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8252 (mp) REVERT: 1Q 278 HIS cc_start: 0.6127 (m90) cc_final: 0.5839 (p-80) REVERT: 1Q 320 LYS cc_start: 0.7612 (mtpp) cc_final: 0.7345 (mppt) REVERT: 1Q 333 ASP cc_start: 0.5675 (OUTLIER) cc_final: 0.4984 (m-30) REVERT: 1Q 471 LEU cc_start: 0.4923 (OUTLIER) cc_final: 0.4379 (tt) REVERT: 1S 121 GLU cc_start: 0.8128 (tt0) cc_final: 0.7918 (tt0) REVERT: 1S 438 GLU cc_start: 0.7638 (mm-30) cc_final: 0.7380 (mp0) REVERT: 1S 458 MET cc_start: 0.8189 (ttp) cc_final: 0.7825 (ttm) REVERT: 1T 3 SER cc_start: 0.3604 (t) cc_final: 0.3336 (t) REVERT: 1T 6 LYS cc_start: 0.5345 (mmtp) cc_final: 0.5043 (mmtp) outliers start: 54 outliers final: 22 residues processed: 391 average time/residue: 1.7843 time to fit residues: 814.2207 Evaluate side-chains 367 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 340 time to evaluate : 3.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 394 MET Chi-restraints excluded: chain 1N residue 179 VAL Chi-restraints excluded: chain 1N residue 184 MET 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 336 ARG Chi-restraints excluded: chain 1Q residue 470 ASN Chi-restraints excluded: chain 1Q residue 471 LEU Chi-restraints excluded: chain 1R residue 92 SER 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 331 optimal weight: 0.9990 chunk 345 optimal weight: 5.9990 chunk 50 optimal weight: 4.9990 chunk 244 optimal weight: 0.1980 chunk 33 optimal weight: 10.0000 chunk 376 optimal weight: 3.9990 chunk 212 optimal weight: 1.9990 chunk 377 optimal weight: 3.9990 chunk 142 optimal weight: 0.6980 chunk 397 optimal weight: 0.7980 chunk 393 optimal weight: 4.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1E 108 GLN 1Q 198 GLN ** 1Q 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.141711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.110994 restraints weight = 46354.601| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 1.61 r_work: 0.3401 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3308 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.209 34756 Z= 0.111 Angle : 0.543 14.419 47178 Z= 0.261 Chirality : 0.040 0.193 5097 Planarity : 0.004 0.060 5970 Dihedral : 12.274 89.316 5538 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.29 % Favored : 97.67 % Rotamer: Outliers : 1.52 % Allowed : 12.14 % Favored : 86.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.83 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.13), residues: 4156 helix: 2.07 (0.11), residues: 2222 sheet: 0.07 (0.24), residues: 442 loop : -0.49 (0.16), residues: 1492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP1M 485 HIS 0.009 0.001 HIS1M 291 PHE 0.010 0.001 PHE1B 299 TYR 0.018 0.001 TYR1A 279 ARG 0.011 0.000 ARG1Q 288 Details of bonding type rmsd hydrogen bonds : bond 0.04074 ( 1801) hydrogen bonds : angle 4.00484 ( 5190) metal coordination : bond 0.00117 ( 1) SS BOND : bond 0.00253 ( 8) SS BOND : angle 0.61422 ( 16) covalent geometry : bond 0.00253 (34739) covalent geometry : angle 0.54319 (47162) Misc. bond : bond 0.13182 ( 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 410 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 358 time to evaluate : 3.398 Fit side-chains REVERT: 1A 316 ARG cc_start: 0.7771 (mpp-170) cc_final: 0.7515 (mpp-170) REVERT: 1B 314 LYS cc_start: 0.7886 (mttm) cc_final: 0.7674 (ptpp) REVERT: 1C 230 HIS cc_start: 0.1043 (OUTLIER) cc_final: 0.0840 (m-70) REVERT: 1E 218 GLU cc_start: 0.7816 (OUTLIER) cc_final: 0.7284 (mp0) REVERT: 1F 116 MET cc_start: 0.8026 (mtp) cc_final: 0.7487 (mtt) REVERT: 1F 236 MET cc_start: 0.6684 (OUTLIER) cc_final: 0.6282 (mtp) REVERT: 1G 41 LYS cc_start: 0.8289 (tppt) cc_final: 0.8046 (tppt) REVERT: 1K 25 ARG cc_start: 0.8270 (ttt180) cc_final: 0.7245 (mmt90) REVERT: 1L 4 ARG cc_start: 0.6343 (ttt180) cc_final: 0.5830 (ttm170) REVERT: 1L 5 GLN cc_start: 0.7639 (mm110) cc_final: 0.7140 (mp10) REVERT: 1M 119 LYS cc_start: 0.7652 (mmtm) cc_final: 0.7309 (ptmt) REVERT: 1M 394 MET cc_start: 0.9226 (OUTLIER) cc_final: 0.8964 (mtp) REVERT: 1M 399 ARG cc_start: 0.7964 (mtm110) cc_final: 0.7611 (mtp180) REVERT: 1N 171 ARG cc_start: 0.7032 (mtp85) cc_final: 0.6680 (mpp80) REVERT: 1N 230 GLU cc_start: 0.8001 (mm-30) cc_final: 0.7758 (pt0) REVERT: 1O 34 VAL cc_start: 0.7895 (p) cc_final: 0.7693 (m) REVERT: 1Q 48 ARG cc_start: 0.6126 (mmt90) cc_final: 0.5113 (mtp85) REVERT: 1Q 270 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.8251 (mp) REVERT: 1Q 278 HIS cc_start: 0.6128 (m90) cc_final: 0.5850 (p-80) REVERT: 1Q 320 LYS cc_start: 0.7631 (mtpp) cc_final: 0.7357 (mppt) REVERT: 1Q 333 ASP cc_start: 0.5649 (OUTLIER) cc_final: 0.4968 (m-30) REVERT: 1Q 471 LEU cc_start: 0.4817 (OUTLIER) cc_final: 0.4122 (tt) REVERT: 1S 438 GLU cc_start: 0.7660 (mm-30) cc_final: 0.7339 (mp0) REVERT: 1S 458 MET cc_start: 0.8193 (ttp) cc_final: 0.7835 (ttm) REVERT: 1T 3 SER cc_start: 0.3694 (t) cc_final: 0.3424 (t) REVERT: 1T 90 GLU cc_start: 0.8579 (OUTLIER) cc_final: 0.8310 (mt-10) outliers start: 52 outliers final: 23 residues processed: 390 average time/residue: 1.8636 time to fit residues: 848.8160 Evaluate side-chains 373 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 342 time to evaluate : 3.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 1G residue 3 MET Chi-restraints excluded: chain 1H residue 9 LEU 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 394 MET 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 336 ARG Chi-restraints excluded: chain 1Q residue 471 LEU Chi-restraints excluded: chain 1R residue 92 SER 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 86 optimal weight: 0.0970 chunk 101 optimal weight: 7.9990 chunk 368 optimal weight: 0.7980 chunk 164 optimal weight: 3.9990 chunk 322 optimal weight: 7.9990 chunk 94 optimal weight: 0.7980 chunk 268 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 chunk 123 optimal weight: 0.6980 chunk 50 optimal weight: 4.9990 chunk 252 optimal weight: 4.9990 overall best weight: 1.0780 ------------------------------------------------------------------------------- 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 198 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.141634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.110941 restraints weight = 46476.700| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 1.59 r_work: 0.3400 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3304 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.218 34756 Z= 0.116 Angle : 0.546 13.994 47178 Z= 0.264 Chirality : 0.040 0.207 5097 Planarity : 0.004 0.059 5970 Dihedral : 12.166 89.808 5538 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.14 % Favored : 97.81 % Rotamer: Outliers : 1.46 % Allowed : 12.64 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.83 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.13), residues: 4156 helix: 2.09 (0.11), residues: 2222 sheet: 0.10 (0.24), residues: 442 loop : -0.48 (0.16), residues: 1492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP1M 485 HIS 0.009 0.001 HIS1N 291 PHE 0.011 0.001 PHE1B 299 TYR 0.020 0.001 TYR1A 279 ARG 0.014 0.000 ARG1M 182 Details of bonding type rmsd hydrogen bonds : bond 0.04110 ( 1801) hydrogen bonds : angle 3.98618 ( 5190) metal coordination : bond 0.00107 ( 1) SS BOND : bond 0.00273 ( 8) SS BOND : angle 0.62991 ( 16) covalent geometry : bond 0.00267 (34739) covalent geometry : angle 0.54630 (47162) Misc. bond : bond 0.12455 ( 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 410 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 360 time to evaluate : 3.995 Fit side-chains REVERT: 1A 316 ARG cc_start: 0.7692 (mpp-170) cc_final: 0.7453 (mpp-170) REVERT: 1B 314 LYS cc_start: 0.7883 (mttm) cc_final: 0.7676 (ptpp) REVERT: 1C 230 HIS cc_start: 0.1077 (OUTLIER) cc_final: 0.0836 (m-70) REVERT: 1E 218 GLU cc_start: 0.7826 (OUTLIER) cc_final: 0.7301 (mp0) REVERT: 1F 116 MET cc_start: 0.8027 (mtp) cc_final: 0.7502 (mtt) REVERT: 1F 236 MET cc_start: 0.6809 (OUTLIER) cc_final: 0.6462 (mtp) REVERT: 1G 41 LYS cc_start: 0.8279 (tppt) cc_final: 0.8076 (tppt) REVERT: 1K 12 ILE cc_start: 0.9065 (OUTLIER) cc_final: 0.8604 (mm) REVERT: 1K 25 ARG cc_start: 0.8291 (ttt180) cc_final: 0.7247 (mmt90) REVERT: 1L 4 ARG cc_start: 0.6321 (ttt180) cc_final: 0.5814 (ttm170) REVERT: 1L 5 GLN cc_start: 0.7705 (mm110) cc_final: 0.7097 (mp10) REVERT: 1M 119 LYS cc_start: 0.7639 (mmtm) cc_final: 0.7278 (ptmt) REVERT: 1M 394 MET cc_start: 0.9235 (OUTLIER) cc_final: 0.8973 (mtp) REVERT: 1M 399 ARG cc_start: 0.7926 (mtm110) cc_final: 0.7625 (mtp180) REVERT: 1N 171 ARG cc_start: 0.7028 (OUTLIER) cc_final: 0.6652 (mpp80) REVERT: 1N 230 GLU cc_start: 0.7978 (mm-30) cc_final: 0.7764 (pt0) REVERT: 1Q 48 ARG cc_start: 0.6105 (mmt90) cc_final: 0.5098 (mtp85) REVERT: 1Q 270 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8265 (mp) REVERT: 1Q 278 HIS cc_start: 0.6092 (m90) cc_final: 0.5827 (p-80) REVERT: 1Q 320 LYS cc_start: 0.7610 (mtpp) cc_final: 0.7345 (mppt) REVERT: 1Q 333 ASP cc_start: 0.5671 (OUTLIER) cc_final: 0.4986 (m-30) REVERT: 1Q 471 LEU cc_start: 0.4612 (OUTLIER) cc_final: 0.3971 (tt) REVERT: 1S 294 MET cc_start: 0.6679 (mtt) cc_final: 0.6429 (mtt) REVERT: 1S 458 MET cc_start: 0.8169 (ttp) cc_final: 0.7682 (ttm) REVERT: 1T 3 SER cc_start: 0.3737 (t) cc_final: 0.3471 (t) REVERT: 1T 90 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.8297 (mt-10) outliers start: 50 outliers final: 27 residues processed: 391 average time/residue: 1.8173 time to fit residues: 827.4313 Evaluate side-chains 383 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 346 time to evaluate : 3.739 ------------------------------------------------------------------------------- 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 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 1G residue 3 MET Chi-restraints excluded: chain 1H residue 9 LEU Chi-restraints excluded: chain 1K residue 12 ILE 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 394 MET 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 1P residue 36 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 336 ARG Chi-restraints excluded: chain 1Q residue 471 LEU Chi-restraints excluded: chain 1R residue 92 SER Chi-restraints excluded: chain 1S residue 53 LEU Chi-restraints excluded: chain 1S residue 71 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 126 optimal weight: 4.9990 chunk 34 optimal weight: 0.6980 chunk 135 optimal weight: 4.9990 chunk 337 optimal weight: 2.9990 chunk 368 optimal weight: 0.6980 chunk 248 optimal weight: 0.9980 chunk 271 optimal weight: 7.9990 chunk 8 optimal weight: 10.0000 chunk 266 optimal weight: 3.9990 chunk 202 optimal weight: 7.9990 chunk 3 optimal weight: 8.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1N 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1Q 198 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.139922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.109153 restraints weight = 46327.163| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 1.60 r_work: 0.3374 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3280 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.264 34756 Z= 0.155 Angle : 0.596 15.474 47178 Z= 0.289 Chirality : 0.042 0.185 5097 Planarity : 0.005 0.059 5970 Dihedral : 12.386 89.428 5538 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.45 % Favored : 97.50 % Rotamer: Outliers : 1.63 % Allowed : 12.41 % Favored : 85.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.83 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.13), residues: 4156 helix: 1.98 (0.11), residues: 2198 sheet: 0.07 (0.24), residues: 442 loop : -0.52 (0.16), residues: 1516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP1A 142 HIS 0.010 0.001 HIS1N 291 PHE 0.014 0.001 PHE1B 299 TYR 0.019 0.002 TYR1A 279 ARG 0.012 0.001 ARG1Q 288 Details of bonding type rmsd hydrogen bonds : bond 0.04738 ( 1801) hydrogen bonds : angle 4.11106 ( 5190) metal coordination : bond 0.00191 ( 1) SS BOND : bond 0.00365 ( 8) SS BOND : angle 0.85137 ( 16) covalent geometry : bond 0.00367 (34739) covalent geometry : angle 0.59614 (47162) Misc. bond : bond 0.14192 ( 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: 56 poor density : 356 time to evaluate : 3.851 Fit side-chains REVERT: 1A 316 ARG cc_start: 0.7914 (mpp-170) cc_final: 0.7670 (mpp-170) REVERT: 1C 230 HIS cc_start: 0.1152 (OUTLIER) cc_final: 0.0827 (m-70) REVERT: 1E 218 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.7307 (mp0) REVERT: 1F 236 MET cc_start: 0.6791 (OUTLIER) cc_final: 0.6493 (mtm) REVERT: 1G 41 LYS cc_start: 0.8291 (tppt) cc_final: 0.8083 (tppt) REVERT: 1K 12 ILE cc_start: 0.9084 (OUTLIER) cc_final: 0.8645 (mm) REVERT: 1K 25 ARG cc_start: 0.8305 (ttt180) cc_final: 0.7218 (mmt90) REVERT: 1L 4 ARG cc_start: 0.6397 (ttt180) cc_final: 0.5899 (ttm170) REVERT: 1M 119 LYS cc_start: 0.7676 (mmtm) cc_final: 0.7310 (ptmt) REVERT: 1M 394 MET cc_start: 0.9285 (OUTLIER) cc_final: 0.9009 (mtp) REVERT: 1N 171 ARG cc_start: 0.7052 (OUTLIER) cc_final: 0.6682 (mpp80) REVERT: 1N 230 GLU cc_start: 0.7996 (mm-30) cc_final: 0.7785 (pt0) REVERT: 1Q 270 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8283 (mp) REVERT: 1Q 278 HIS cc_start: 0.6215 (m90) cc_final: 0.5849 (p-80) REVERT: 1Q 320 LYS cc_start: 0.7614 (mtpp) cc_final: 0.7343 (mppt) REVERT: 1Q 333 ASP cc_start: 0.5572 (OUTLIER) cc_final: 0.5051 (m-30) REVERT: 1Q 471 LEU cc_start: 0.4955 (OUTLIER) cc_final: 0.4203 (tt) REVERT: 1S 302 SER cc_start: 0.7231 (t) cc_final: 0.6849 (p) REVERT: 1S 438 GLU cc_start: 0.7380 (mp0) cc_final: 0.7178 (mp0) REVERT: 1S 458 MET cc_start: 0.8159 (ttp) cc_final: 0.7816 (ttm) REVERT: 1T 3 SER cc_start: 0.3665 (t) cc_final: 0.3434 (t) REVERT: 1T 90 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.8321 (mt-10) outliers start: 56 outliers final: 31 residues processed: 388 average time/residue: 1.8056 time to fit residues: 818.4635 Evaluate side-chains 385 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 344 time to evaluate : 3.483 ------------------------------------------------------------------------------- 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 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 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 394 MET 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 232 MET Chi-restraints excluded: chain 1N residue 402 ASP Chi-restraints excluded: chain 1P residue 36 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 336 ARG Chi-restraints excluded: chain 1Q residue 471 LEU Chi-restraints excluded: chain 1R residue 92 SER 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 197 GLU 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 369 optimal weight: 2.9990 chunk 346 optimal weight: 0.9980 chunk 43 optimal weight: 5.9990 chunk 80 optimal weight: 0.9980 chunk 225 optimal weight: 10.0000 chunk 25 optimal weight: 0.0980 chunk 329 optimal weight: 1.9990 chunk 348 optimal weight: 0.8980 chunk 390 optimal weight: 7.9990 chunk 233 optimal weight: 2.9990 chunk 164 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 198 GLN 1S 388 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.141551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.110792 restraints weight = 46486.496| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 1.62 r_work: 0.3398 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3303 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.209 34756 Z= 0.115 Angle : 0.553 13.670 47178 Z= 0.268 Chirality : 0.040 0.171 5097 Planarity : 0.004 0.060 5970 Dihedral : 12.118 89.231 5538 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.14 % Favored : 97.81 % Rotamer: Outliers : 1.28 % Allowed : 13.05 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.83 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.13), residues: 4156 helix: 2.10 (0.11), residues: 2212 sheet: 0.11 (0.24), residues: 442 loop : -0.46 (0.16), residues: 1502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP1M 485 HIS 0.010 0.001 HIS1M 291 PHE 0.010 0.001 PHE1K 35 TYR 0.023 0.001 TYR1A 279 ARG 0.013 0.000 ARG1Q 288 Details of bonding type rmsd hydrogen bonds : bond 0.04083 ( 1801) hydrogen bonds : angle 3.99543 ( 5190) metal coordination : bond 0.00083 ( 1) SS BOND : bond 0.00264 ( 8) SS BOND : angle 0.58992 ( 16) covalent geometry : bond 0.00263 (34739) covalent geometry : angle 0.55259 (47162) Misc. bond : bond 0.12301 ( 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 395 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 351 time to evaluate : 3.700 Fit side-chains REVERT: 1A 316 ARG cc_start: 0.7768 (mpp-170) cc_final: 0.7525 (mpp-170) REVERT: 1B 314 LYS cc_start: 0.7904 (mttm) cc_final: 0.7639 (ptpp) REVERT: 1C 135 MET cc_start: 0.8684 (mmp) cc_final: 0.8482 (mmm) REVERT: 1C 230 HIS cc_start: 0.1116 (OUTLIER) cc_final: 0.0783 (m-70) REVERT: 1E 218 GLU cc_start: 0.7762 (OUTLIER) cc_final: 0.7228 (mp0) REVERT: 1F 236 MET cc_start: 0.6829 (OUTLIER) cc_final: 0.6433 (mtm) REVERT: 1G 41 LYS cc_start: 0.8224 (tppt) cc_final: 0.8016 (tppt) REVERT: 1K 12 ILE cc_start: 0.9075 (OUTLIER) cc_final: 0.8635 (mm) REVERT: 1K 25 ARG cc_start: 0.8348 (ttt180) cc_final: 0.7258 (mmt90) REVERT: 1M 119 LYS cc_start: 0.7677 (mmtm) cc_final: 0.7310 (ptmt) REVERT: 1N 171 ARG cc_start: 0.7013 (mtp85) cc_final: 0.6647 (mpp80) REVERT: 1Q 48 ARG cc_start: 0.6109 (mmt90) cc_final: 0.5149 (mtp85) REVERT: 1Q 197 GLU cc_start: 0.7129 (mp0) cc_final: 0.6868 (mp0) REVERT: 1Q 270 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8273 (mp) REVERT: 1Q 278 HIS cc_start: 0.6185 (m90) cc_final: 0.5834 (p-80) REVERT: 1Q 320 LYS cc_start: 0.7617 (mtpp) cc_final: 0.7351 (mppt) REVERT: 1Q 333 ASP cc_start: 0.5660 (OUTLIER) cc_final: 0.4975 (m-30) REVERT: 1Q 471 LEU cc_start: 0.4961 (OUTLIER) cc_final: 0.4450 (tt) REVERT: 1S 294 MET cc_start: 0.6896 (mtt) cc_final: 0.6603 (mtt) REVERT: 1S 438 GLU cc_start: 0.7453 (mp0) cc_final: 0.7218 (mp0) REVERT: 1S 458 MET cc_start: 0.8138 (ttp) cc_final: 0.7671 (ttm) REVERT: 1T 3 SER cc_start: 0.3695 (t) cc_final: 0.3455 (t) REVERT: 1T 90 GLU cc_start: 0.8565 (OUTLIER) cc_final: 0.8271 (mt-10) outliers start: 44 outliers final: 27 residues processed: 380 average time/residue: 1.7586 time to fit residues: 777.6347 Evaluate side-chains 378 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 343 time to evaluate : 3.459 ------------------------------------------------------------------------------- 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 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 1M residue 269 ASP Chi-restraints excluded: chain 1M residue 291 HIS Chi-restraints excluded: chain 1M residue 332 ASN Chi-restraints excluded: chain 1N residue 179 VAL Chi-restraints excluded: chain 1N residue 184 MET Chi-restraints excluded: chain 1N residue 232 MET Chi-restraints excluded: chain 1N residue 402 ASP Chi-restraints excluded: chain 1P residue 36 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 1R residue 92 SER Chi-restraints excluded: chain 1S residue 53 LEU Chi-restraints excluded: chain 1S residue 197 GLU Chi-restraints excluded: chain 1S residue 234 VAL 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 86 optimal weight: 20.0000 chunk 273 optimal weight: 1.9990 chunk 292 optimal weight: 4.9990 chunk 383 optimal weight: 0.0770 chunk 359 optimal weight: 5.9990 chunk 289 optimal weight: 0.9990 chunk 364 optimal weight: 5.9990 chunk 100 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 344 optimal weight: 1.9990 chunk 388 optimal weight: 0.9990 overall best weight: 1.0146 ------------------------------------------------------------------------------- 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** 1S 388 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.141605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.110954 restraints weight = 46263.446| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 1.59 r_work: 0.3402 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3307 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.208 34756 Z= 0.115 Angle : 0.554 13.774 47178 Z= 0.268 Chirality : 0.040 0.170 5097 Planarity : 0.004 0.067 5970 Dihedral : 11.953 89.816 5538 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.21 % Favored : 97.74 % Rotamer: Outliers : 1.20 % Allowed : 13.40 % Favored : 85.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.83 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.13), residues: 4156 helix: 2.13 (0.11), residues: 2222 sheet: 0.06 (0.24), residues: 460 loop : -0.42 (0.17), residues: 1474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP1M 485 HIS 0.009 0.001 HIS1M 291 PHE 0.011 0.001 PHE1K 35 TYR 0.022 0.001 TYR1A 279 ARG 0.017 0.000 ARG1M 182 Details of bonding type rmsd hydrogen bonds : bond 0.04059 ( 1801) hydrogen bonds : angle 3.97385 ( 5190) metal coordination : bond 0.00084 ( 1) SS BOND : bond 0.00257 ( 8) SS BOND : angle 0.60478 ( 16) covalent geometry : bond 0.00265 (34739) covalent geometry : angle 0.55409 (47162) Misc. bond : bond 0.12175 ( 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 393 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 352 time to evaluate : 3.612 Fit side-chains REVERT: 1A 316 ARG cc_start: 0.7794 (mpp-170) cc_final: 0.7563 (mpp-170) REVERT: 1B 314 LYS cc_start: 0.7856 (mttm) cc_final: 0.7606 (ptpp) REVERT: 1C 230 HIS cc_start: 0.1042 (OUTLIER) cc_final: 0.0751 (m-70) REVERT: 1E 218 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.7230 (mp0) REVERT: 1F 236 MET cc_start: 0.6791 (OUTLIER) cc_final: 0.6419 (mtm) REVERT: 1G 41 LYS cc_start: 0.8260 (tppt) cc_final: 0.8052 (tppt) REVERT: 1K 12 ILE cc_start: 0.9072 (OUTLIER) cc_final: 0.8640 (mm) REVERT: 1K 25 ARG cc_start: 0.8314 (ttt180) cc_final: 0.7251 (mmt90) REVERT: 1L 4 ARG cc_start: 0.5760 (ttt180) cc_final: 0.5300 (ttm170) REVERT: 1M 119 LYS cc_start: 0.7653 (mmtm) cc_final: 0.7101 (ttpp) REVERT: 1N 171 ARG cc_start: 0.7085 (mtp85) cc_final: 0.6708 (mpp80) REVERT: 1Q 48 ARG cc_start: 0.6116 (mmt90) cc_final: 0.5164 (mtp85) REVERT: 1Q 197 GLU cc_start: 0.7100 (mp0) cc_final: 0.6883 (mp0) REVERT: 1Q 270 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8263 (mp) REVERT: 1Q 278 HIS cc_start: 0.6186 (m90) cc_final: 0.5833 (p-80) REVERT: 1Q 320 LYS cc_start: 0.7608 (mtpp) cc_final: 0.7343 (mppt) REVERT: 1Q 333 ASP cc_start: 0.5696 (OUTLIER) cc_final: 0.5069 (m-30) REVERT: 1Q 471 LEU cc_start: 0.5007 (OUTLIER) cc_final: 0.4554 (tt) REVERT: 1S 294 MET cc_start: 0.6919 (mtt) cc_final: 0.6608 (mtt) REVERT: 1S 438 GLU cc_start: 0.7549 (mp0) cc_final: 0.7214 (mp0) REVERT: 1S 458 MET cc_start: 0.8144 (ttp) cc_final: 0.7693 (ttm) REVERT: 1T 3 SER cc_start: 0.3714 (t) cc_final: 0.3479 (t) REVERT: 1T 90 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.8283 (mt-10) outliers start: 41 outliers final: 30 residues processed: 380 average time/residue: 1.8337 time to fit residues: 815.9717 Evaluate side-chains 383 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 345 time to evaluate : 3.491 ------------------------------------------------------------------------------- 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 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 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 1M residue 269 ASP Chi-restraints excluded: chain 1M residue 291 HIS Chi-restraints excluded: chain 1M residue 332 ASN Chi-restraints excluded: chain 1N residue 179 VAL Chi-restraints excluded: chain 1N residue 184 MET Chi-restraints excluded: chain 1N residue 232 MET Chi-restraints excluded: chain 1N residue 402 ASP Chi-restraints excluded: chain 1P residue 36 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 1R residue 92 SER 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 197 GLU Chi-restraints excluded: chain 1S residue 234 VAL 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 90 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 39 optimal weight: 0.9980 chunk 284 optimal weight: 0.1980 chunk 262 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 215 optimal weight: 2.9990 chunk 218 optimal weight: 7.9990 chunk 342 optimal weight: 0.9980 chunk 312 optimal weight: 2.9990 chunk 245 optimal weight: 0.0050 chunk 231 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 overall best weight: 0.8396 ------------------------------------------------------------------------------- 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** 1S 388 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.142357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.111712 restraints weight = 46512.661| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 1.62 r_work: 0.3413 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3318 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.181 34756 Z= 0.107 Angle : 0.543 13.372 47178 Z= 0.262 Chirality : 0.040 0.169 5097 Planarity : 0.004 0.060 5970 Dihedral : 11.770 88.732 5538 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.97 % Favored : 97.98 % Rotamer: Outliers : 1.20 % Allowed : 13.49 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.83 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.13), residues: 4156 helix: 2.20 (0.11), residues: 2222 sheet: 0.10 (0.24), residues: 460 loop : -0.40 (0.17), residues: 1474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP1M 485 HIS 0.010 0.001 HIS1M 291 PHE 0.010 0.001 PHE1K 35 TYR 0.018 0.001 TYR1A 279 ARG 0.012 0.000 ARG1M 182 Details of bonding type rmsd hydrogen bonds : bond 0.03859 ( 1801) hydrogen bonds : angle 3.92761 ( 5190) metal coordination : bond 0.00067 ( 1) SS BOND : bond 0.00238 ( 8) SS BOND : angle 0.53969 ( 16) covalent geometry : bond 0.00246 (34739) covalent geometry : angle 0.54260 (47162) Misc. bond : bond 0.11439 ( 8) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 34947.12 seconds wall clock time: 600 minutes 31.32 seconds (36031.32 seconds total)