Starting phenix.real_space_refine on Thu Mar 5 08:39:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7f93_31496/03_2026/7f93_31496.cif Found real_map, /net/cci-nas-00/data/ceres_data/7f93_31496/03_2026/7f93_31496.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7f93_31496/03_2026/7f93_31496.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7f93_31496/03_2026/7f93_31496.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7f93_31496/03_2026/7f93_31496.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7f93_31496/03_2026/7f93_31496.map" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.047 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 96 5.16 5 C 14460 2.51 5 N 3048 2.21 5 O 3204 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 96 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20808 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 1594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1594 Classifications: {'peptide': 196} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 189} Chain breaks: 1 Chain: "B" Number of atoms: 1594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1594 Classifications: {'peptide': 196} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 189} Chain breaks: 1 Chain: "C" Number of atoms: 1594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1594 Classifications: {'peptide': 196} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 189} Chain breaks: 1 Chain: "D" Number of atoms: 1594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1594 Classifications: {'peptide': 196} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 189} Chain breaks: 1 Chain: "E" Number of atoms: 1594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1594 Classifications: {'peptide': 196} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 189} Chain breaks: 1 Chain: "F" Number of atoms: 1594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1594 Classifications: {'peptide': 196} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 189} Chain breaks: 1 Chain: "G" Number of atoms: 1594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1594 Classifications: {'peptide': 196} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 189} Chain breaks: 1 Chain: "H" Number of atoms: 1594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1594 Classifications: {'peptide': 196} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 189} Chain breaks: 1 Chain: "I" Number of atoms: 1594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1594 Classifications: {'peptide': 196} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 189} Chain breaks: 1 Chain: "J" Number of atoms: 1594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1594 Classifications: {'peptide': 196} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 189} Chain breaks: 1 Chain: "K" Number of atoms: 1594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1594 Classifications: {'peptide': 196} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 189} Chain breaks: 1 Chain: "L" Number of atoms: 1594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1594 Classifications: {'peptide': 196} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 189} Chain breaks: 1 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'C14': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'C14': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'C14': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain: "D" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'C14': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Chain: "E" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'C14': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain: "F" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'C14': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain: "G" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'C14': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain: "H" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'C14': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain: "I" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'C14': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain: "J" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'C14': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Chain: "K" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'C14': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain: "L" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'C14': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Time building chain proxies: 4.52, per 1000 atoms: 0.22 Number of scatterers: 20808 At special positions: 0 Unit cell: (97.8945, 103.13, 172.232, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 96 16.00 O 3204 8.00 N 3048 7.00 C 14460 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 198 " distance=2.03 Simple disulfide: pdb=" SG CYS A 61 " - pdb=" SG CYS A 192 " distance=2.03 Simple disulfide: pdb=" SG CYS A 65 " - pdb=" SG CYS A 187 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 198 " distance=2.03 Simple disulfide: pdb=" SG CYS B 61 " - pdb=" SG CYS B 192 " distance=2.03 Simple disulfide: pdb=" SG CYS B 65 " - pdb=" SG CYS B 187 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 198 " distance=2.03 Simple disulfide: pdb=" SG CYS C 61 " - pdb=" SG CYS C 192 " distance=2.03 Simple disulfide: pdb=" SG CYS C 65 " - pdb=" SG CYS C 187 " distance=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 198 " distance=2.03 Simple disulfide: pdb=" SG CYS D 61 " - pdb=" SG CYS D 192 " distance=2.03 Simple disulfide: pdb=" SG CYS D 65 " - pdb=" SG CYS D 187 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 198 " distance=2.03 Simple disulfide: pdb=" SG CYS E 61 " - pdb=" SG CYS E 192 " distance=2.03 Simple disulfide: pdb=" SG CYS E 65 " - pdb=" SG CYS E 187 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 198 " distance=2.03 Simple disulfide: pdb=" SG CYS F 61 " - pdb=" SG CYS F 192 " distance=2.03 Simple disulfide: pdb=" SG CYS F 65 " - pdb=" SG CYS F 187 " distance=2.03 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 198 " distance=2.03 Simple disulfide: pdb=" SG CYS G 61 " - pdb=" SG CYS G 192 " distance=2.03 Simple disulfide: pdb=" SG CYS G 65 " - pdb=" SG CYS G 187 " distance=2.03 Simple disulfide: pdb=" SG CYS H 54 " - pdb=" SG CYS H 198 " distance=2.03 Simple disulfide: pdb=" SG CYS H 61 " - pdb=" SG CYS H 192 " distance=2.03 Simple disulfide: pdb=" SG CYS H 65 " - pdb=" SG CYS H 187 " distance=2.03 Simple disulfide: pdb=" SG CYS I 54 " - pdb=" SG CYS I 198 " distance=2.03 Simple disulfide: pdb=" SG CYS I 61 " - pdb=" SG CYS I 192 " distance=2.03 Simple disulfide: pdb=" SG CYS I 65 " - pdb=" SG CYS I 187 " distance=2.03 Simple disulfide: pdb=" SG CYS J 54 " - pdb=" SG CYS J 198 " distance=2.03 Simple disulfide: pdb=" SG CYS J 61 " - pdb=" SG CYS J 192 " distance=2.03 Simple disulfide: pdb=" SG CYS J 65 " - pdb=" SG CYS J 187 " distance=2.03 Simple disulfide: pdb=" SG CYS K 54 " - pdb=" SG CYS K 198 " distance=2.03 Simple disulfide: pdb=" SG CYS K 61 " - pdb=" SG CYS K 192 " distance=2.03 Simple disulfide: pdb=" SG CYS K 65 " - pdb=" SG CYS K 187 " distance=2.03 Simple disulfide: pdb=" SG CYS L 54 " - pdb=" SG CYS L 198 " distance=2.03 Simple disulfide: pdb=" SG CYS L 61 " - pdb=" SG CYS L 192 " distance=2.03 Simple disulfide: pdb=" SG CYS L 65 " - pdb=" SG CYS L 187 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.32 Conformation dependent library (CDL) restraints added in 780.0 milliseconds 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4440 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 12 sheets defined 68.4% alpha, 3.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing helix chain 'A' and resid 4 through 14 removed outlier: 3.728A pdb=" N LYS A 9 " --> pdb=" O SER A 5 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 40 removed outlier: 4.107A pdb=" N SER A 27 " --> pdb=" O LYS A 23 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N VAL A 28 " --> pdb=" O VAL A 24 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N THR A 39 " --> pdb=" O LEU A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 70 removed outlier: 3.763A pdb=" N ASP A 67 " --> pdb=" O ASN A 63 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LYS A 68 " --> pdb=" O VAL A 64 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER A 69 " --> pdb=" O CYS A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 105 removed outlier: 3.746A pdb=" N PHE A 84 " --> pdb=" O LEU A 80 " (cutoff:3.500A) Proline residue: A 88 - end of helix removed outlier: 3.584A pdb=" N TYR A 98 " --> pdb=" O ALA A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 177 removed outlier: 3.562A pdb=" N ILE A 159 " --> pdb=" O TYR A 155 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LYS A 162 " --> pdb=" O SER A 158 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE A 172 " --> pdb=" O ALA A 168 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN A 173 " --> pdb=" O PHE A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 233 removed outlier: 3.690A pdb=" N PHE A 209 " --> pdb=" O GLU A 205 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER A 217 " --> pdb=" O MET A 213 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLU A 227 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE A 232 " --> pdb=" O LEU A 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 14 removed outlier: 3.728A pdb=" N LYS B 9 " --> pdb=" O SER B 5 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 40 removed outlier: 4.107A pdb=" N SER B 27 " --> pdb=" O LYS B 23 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N VAL B 28 " --> pdb=" O VAL B 24 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N THR B 39 " --> pdb=" O LEU B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 70 removed outlier: 3.763A pdb=" N ASP B 67 " --> pdb=" O ASN B 63 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LYS B 68 " --> pdb=" O VAL B 64 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER B 69 " --> pdb=" O CYS B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 105 removed outlier: 3.746A pdb=" N PHE B 84 " --> pdb=" O LEU B 80 " (cutoff:3.500A) Proline residue: B 88 - end of helix removed outlier: 3.583A pdb=" N TYR B 98 " --> pdb=" O ALA B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 177 removed outlier: 3.561A pdb=" N ILE B 159 " --> pdb=" O TYR B 155 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS B 162 " --> pdb=" O SER B 158 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE B 172 " --> pdb=" O ALA B 168 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLN B 173 " --> pdb=" O PHE B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 233 removed outlier: 3.689A pdb=" N PHE B 209 " --> pdb=" O GLU B 205 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER B 217 " --> pdb=" O MET B 213 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLU B 227 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE B 232 " --> pdb=" O LEU B 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 14 removed outlier: 3.728A pdb=" N LYS C 9 " --> pdb=" O SER C 5 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 40 removed outlier: 4.107A pdb=" N SER C 27 " --> pdb=" O LYS C 23 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N VAL C 28 " --> pdb=" O VAL C 24 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N THR C 39 " --> pdb=" O LEU C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 70 removed outlier: 3.763A pdb=" N ASP C 67 " --> pdb=" O ASN C 63 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LYS C 68 " --> pdb=" O VAL C 64 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER C 69 " --> pdb=" O CYS C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 105 removed outlier: 3.746A pdb=" N PHE C 84 " --> pdb=" O LEU C 80 " (cutoff:3.500A) Proline residue: C 88 - end of helix removed outlier: 3.583A pdb=" N TYR C 98 " --> pdb=" O ALA C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 151 through 177 removed outlier: 3.561A pdb=" N ILE C 159 " --> pdb=" O TYR C 155 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS C 162 " --> pdb=" O SER C 158 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE C 172 " --> pdb=" O ALA C 168 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLN C 173 " --> pdb=" O PHE C 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 233 removed outlier: 3.688A pdb=" N PHE C 209 " --> pdb=" O GLU C 205 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER C 217 " --> pdb=" O MET C 213 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLU C 227 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE C 232 " --> pdb=" O LEU C 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 4 through 14 removed outlier: 3.728A pdb=" N LYS D 9 " --> pdb=" O SER D 5 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 40 removed outlier: 4.107A pdb=" N SER D 27 " --> pdb=" O LYS D 23 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N VAL D 28 " --> pdb=" O VAL D 24 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N THR D 39 " --> pdb=" O LEU D 35 " (cutoff:3.500A) Processing helix chain 'D' and resid 60 through 70 removed outlier: 3.763A pdb=" N ASP D 67 " --> pdb=" O ASN D 63 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LYS D 68 " --> pdb=" O VAL D 64 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER D 69 " --> pdb=" O CYS D 65 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 105 removed outlier: 3.747A pdb=" N PHE D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) Proline residue: D 88 - end of helix removed outlier: 3.583A pdb=" N TYR D 98 " --> pdb=" O ALA D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 151 through 177 removed outlier: 3.560A pdb=" N ILE D 159 " --> pdb=" O TYR D 155 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS D 162 " --> pdb=" O SER D 158 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE D 172 " --> pdb=" O ALA D 168 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLN D 173 " --> pdb=" O PHE D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 233 removed outlier: 3.688A pdb=" N PHE D 209 " --> pdb=" O GLU D 205 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER D 217 " --> pdb=" O MET D 213 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLU D 227 " --> pdb=" O LEU D 223 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE D 232 " --> pdb=" O LEU D 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 14 removed outlier: 3.728A pdb=" N LYS E 9 " --> pdb=" O SER E 5 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 40 removed outlier: 4.108A pdb=" N SER E 27 " --> pdb=" O LYS E 23 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N VAL E 28 " --> pdb=" O VAL E 24 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N THR E 39 " --> pdb=" O LEU E 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 70 removed outlier: 3.764A pdb=" N ASP E 67 " --> pdb=" O ASN E 63 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LYS E 68 " --> pdb=" O VAL E 64 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER E 69 " --> pdb=" O CYS E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 105 removed outlier: 3.746A pdb=" N PHE E 84 " --> pdb=" O LEU E 80 " (cutoff:3.500A) Proline residue: E 88 - end of helix removed outlier: 3.584A pdb=" N TYR E 98 " --> pdb=" O ALA E 94 " (cutoff:3.500A) Processing helix chain 'E' and resid 151 through 177 removed outlier: 3.561A pdb=" N ILE E 159 " --> pdb=" O TYR E 155 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LYS E 162 " --> pdb=" O SER E 158 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE E 172 " --> pdb=" O ALA E 168 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLN E 173 " --> pdb=" O PHE E 169 " (cutoff:3.500A) Processing helix chain 'E' and resid 202 through 233 removed outlier: 3.688A pdb=" N PHE E 209 " --> pdb=" O GLU E 205 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N SER E 217 " --> pdb=" O MET E 213 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLU E 227 " --> pdb=" O LEU E 223 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE E 232 " --> pdb=" O LEU E 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 4 through 14 removed outlier: 3.728A pdb=" N LYS F 9 " --> pdb=" O SER F 5 " (cutoff:3.500A) Processing helix chain 'F' and resid 21 through 40 removed outlier: 4.107A pdb=" N SER F 27 " --> pdb=" O LYS F 23 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N VAL F 28 " --> pdb=" O VAL F 24 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N THR F 39 " --> pdb=" O LEU F 35 " (cutoff:3.500A) Processing helix chain 'F' and resid 60 through 70 removed outlier: 3.763A pdb=" N ASP F 67 " --> pdb=" O ASN F 63 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LYS F 68 " --> pdb=" O VAL F 64 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER F 69 " --> pdb=" O CYS F 65 " (cutoff:3.500A) Processing helix chain 'F' and resid 73 through 105 removed outlier: 3.746A pdb=" N PHE F 84 " --> pdb=" O LEU F 80 " (cutoff:3.500A) Proline residue: F 88 - end of helix removed outlier: 3.583A pdb=" N TYR F 98 " --> pdb=" O ALA F 94 " (cutoff:3.500A) Processing helix chain 'F' and resid 151 through 177 removed outlier: 3.560A pdb=" N ILE F 159 " --> pdb=" O TYR F 155 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS F 162 " --> pdb=" O SER F 158 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE F 172 " --> pdb=" O ALA F 168 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLN F 173 " --> pdb=" O PHE F 169 " (cutoff:3.500A) Processing helix chain 'F' and resid 202 through 233 removed outlier: 3.689A pdb=" N PHE F 209 " --> pdb=" O GLU F 205 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER F 217 " --> pdb=" O MET F 213 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLU F 227 " --> pdb=" O LEU F 223 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE F 232 " --> pdb=" O LEU F 228 " (cutoff:3.500A) Processing helix chain 'G' and resid 4 through 14 removed outlier: 3.729A pdb=" N LYS G 9 " --> pdb=" O SER G 5 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 40 removed outlier: 4.107A pdb=" N SER G 27 " --> pdb=" O LYS G 23 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N VAL G 28 " --> pdb=" O VAL G 24 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N THR G 39 " --> pdb=" O LEU G 35 " (cutoff:3.500A) Processing helix chain 'G' and resid 60 through 70 removed outlier: 3.763A pdb=" N ASP G 67 " --> pdb=" O ASN G 63 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LYS G 68 " --> pdb=" O VAL G 64 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER G 69 " --> pdb=" O CYS G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 73 through 105 removed outlier: 3.746A pdb=" N PHE G 84 " --> pdb=" O LEU G 80 " (cutoff:3.500A) Proline residue: G 88 - end of helix removed outlier: 3.584A pdb=" N TYR G 98 " --> pdb=" O ALA G 94 " (cutoff:3.500A) Processing helix chain 'G' and resid 151 through 177 removed outlier: 3.562A pdb=" N ILE G 159 " --> pdb=" O TYR G 155 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LYS G 162 " --> pdb=" O SER G 158 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE G 172 " --> pdb=" O ALA G 168 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLN G 173 " --> pdb=" O PHE G 169 " (cutoff:3.500A) Processing helix chain 'G' and resid 202 through 233 removed outlier: 3.689A pdb=" N PHE G 209 " --> pdb=" O GLU G 205 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER G 217 " --> pdb=" O MET G 213 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLU G 227 " --> pdb=" O LEU G 223 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE G 232 " --> pdb=" O LEU G 228 " (cutoff:3.500A) Processing helix chain 'H' and resid 4 through 14 removed outlier: 3.728A pdb=" N LYS H 9 " --> pdb=" O SER H 5 " (cutoff:3.500A) Processing helix chain 'H' and resid 21 through 40 removed outlier: 4.107A pdb=" N SER H 27 " --> pdb=" O LYS H 23 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N VAL H 28 " --> pdb=" O VAL H 24 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N THR H 39 " --> pdb=" O LEU H 35 " (cutoff:3.500A) Processing helix chain 'H' and resid 60 through 70 removed outlier: 3.763A pdb=" N ASP H 67 " --> pdb=" O ASN H 63 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LYS H 68 " --> pdb=" O VAL H 64 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER H 69 " --> pdb=" O CYS H 65 " (cutoff:3.500A) Processing helix chain 'H' and resid 73 through 105 removed outlier: 3.747A pdb=" N PHE H 84 " --> pdb=" O LEU H 80 " (cutoff:3.500A) Proline residue: H 88 - end of helix removed outlier: 3.584A pdb=" N TYR H 98 " --> pdb=" O ALA H 94 " (cutoff:3.500A) Processing helix chain 'H' and resid 151 through 177 removed outlier: 3.500A pdb=" N TYR H 155 " --> pdb=" O LEU H 151 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE H 159 " --> pdb=" O TYR H 155 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS H 162 " --> pdb=" O SER H 158 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE H 172 " --> pdb=" O ALA H 168 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLN H 173 " --> pdb=" O PHE H 169 " (cutoff:3.500A) Processing helix chain 'H' and resid 202 through 233 removed outlier: 3.690A pdb=" N PHE H 209 " --> pdb=" O GLU H 205 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N SER H 217 " --> pdb=" O MET H 213 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N GLU H 227 " --> pdb=" O LEU H 223 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE H 232 " --> pdb=" O LEU H 228 " (cutoff:3.500A) Processing helix chain 'I' and resid 4 through 14 removed outlier: 3.728A pdb=" N LYS I 9 " --> pdb=" O SER I 5 " (cutoff:3.500A) Processing helix chain 'I' and resid 21 through 40 removed outlier: 4.107A pdb=" N SER I 27 " --> pdb=" O LYS I 23 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N VAL I 28 " --> pdb=" O VAL I 24 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N THR I 39 " --> pdb=" O LEU I 35 " (cutoff:3.500A) Processing helix chain 'I' and resid 60 through 70 removed outlier: 3.763A pdb=" N ASP I 67 " --> pdb=" O ASN I 63 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LYS I 68 " --> pdb=" O VAL I 64 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER I 69 " --> pdb=" O CYS I 65 " (cutoff:3.500A) Processing helix chain 'I' and resid 73 through 105 removed outlier: 3.747A pdb=" N PHE I 84 " --> pdb=" O LEU I 80 " (cutoff:3.500A) Proline residue: I 88 - end of helix removed outlier: 3.584A pdb=" N TYR I 98 " --> pdb=" O ALA I 94 " (cutoff:3.500A) Processing helix chain 'I' and resid 151 through 177 removed outlier: 3.560A pdb=" N ILE I 159 " --> pdb=" O TYR I 155 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYS I 162 " --> pdb=" O SER I 158 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE I 172 " --> pdb=" O ALA I 168 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLN I 173 " --> pdb=" O PHE I 169 " (cutoff:3.500A) Processing helix chain 'I' and resid 202 through 233 removed outlier: 3.688A pdb=" N PHE I 209 " --> pdb=" O GLU I 205 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER I 217 " --> pdb=" O MET I 213 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLU I 227 " --> pdb=" O LEU I 223 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE I 232 " --> pdb=" O LEU I 228 " (cutoff:3.500A) Processing helix chain 'J' and resid 4 through 14 removed outlier: 3.728A pdb=" N LYS J 9 " --> pdb=" O SER J 5 " (cutoff:3.500A) Processing helix chain 'J' and resid 21 through 40 removed outlier: 4.107A pdb=" N SER J 27 " --> pdb=" O LYS J 23 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N VAL J 28 " --> pdb=" O VAL J 24 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N THR J 39 " --> pdb=" O LEU J 35 " (cutoff:3.500A) Processing helix chain 'J' and resid 60 through 70 removed outlier: 3.764A pdb=" N ASP J 67 " --> pdb=" O ASN J 63 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LYS J 68 " --> pdb=" O VAL J 64 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER J 69 " --> pdb=" O CYS J 65 " (cutoff:3.500A) Processing helix chain 'J' and resid 73 through 105 removed outlier: 3.747A pdb=" N PHE J 84 " --> pdb=" O LEU J 80 " (cutoff:3.500A) Proline residue: J 88 - end of helix removed outlier: 3.584A pdb=" N TYR J 98 " --> pdb=" O ALA J 94 " (cutoff:3.500A) Processing helix chain 'J' and resid 151 through 177 removed outlier: 3.560A pdb=" N ILE J 159 " --> pdb=" O TYR J 155 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LYS J 162 " --> pdb=" O SER J 158 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE J 172 " --> pdb=" O ALA J 168 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN J 173 " --> pdb=" O PHE J 169 " (cutoff:3.500A) Processing helix chain 'J' and resid 202 through 233 removed outlier: 3.689A pdb=" N PHE J 209 " --> pdb=" O GLU J 205 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER J 217 " --> pdb=" O MET J 213 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLU J 227 " --> pdb=" O LEU J 223 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE J 232 " --> pdb=" O LEU J 228 " (cutoff:3.500A) Processing helix chain 'K' and resid 4 through 14 removed outlier: 3.728A pdb=" N LYS K 9 " --> pdb=" O SER K 5 " (cutoff:3.500A) Processing helix chain 'K' and resid 21 through 40 removed outlier: 4.107A pdb=" N SER K 27 " --> pdb=" O LYS K 23 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N VAL K 28 " --> pdb=" O VAL K 24 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N THR K 39 " --> pdb=" O LEU K 35 " (cutoff:3.500A) Processing helix chain 'K' and resid 60 through 70 removed outlier: 3.763A pdb=" N ASP K 67 " --> pdb=" O ASN K 63 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LYS K 68 " --> pdb=" O VAL K 64 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER K 69 " --> pdb=" O CYS K 65 " (cutoff:3.500A) Processing helix chain 'K' and resid 73 through 105 removed outlier: 3.747A pdb=" N PHE K 84 " --> pdb=" O LEU K 80 " (cutoff:3.500A) Proline residue: K 88 - end of helix removed outlier: 3.582A pdb=" N TYR K 98 " --> pdb=" O ALA K 94 " (cutoff:3.500A) Processing helix chain 'K' and resid 151 through 177 removed outlier: 3.561A pdb=" N ILE K 159 " --> pdb=" O TYR K 155 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS K 162 " --> pdb=" O SER K 158 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE K 172 " --> pdb=" O ALA K 168 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLN K 173 " --> pdb=" O PHE K 169 " (cutoff:3.500A) Processing helix chain 'K' and resid 202 through 233 removed outlier: 3.689A pdb=" N PHE K 209 " --> pdb=" O GLU K 205 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER K 217 " --> pdb=" O MET K 213 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLU K 227 " --> pdb=" O LEU K 223 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE K 232 " --> pdb=" O LEU K 228 " (cutoff:3.500A) Processing helix chain 'L' and resid 4 through 14 removed outlier: 3.728A pdb=" N LYS L 9 " --> pdb=" O SER L 5 " (cutoff:3.500A) Processing helix chain 'L' and resid 21 through 40 removed outlier: 4.108A pdb=" N SER L 27 " --> pdb=" O LYS L 23 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N VAL L 28 " --> pdb=" O VAL L 24 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N THR L 39 " --> pdb=" O LEU L 35 " (cutoff:3.500A) Processing helix chain 'L' and resid 60 through 70 removed outlier: 3.763A pdb=" N ASP L 67 " --> pdb=" O ASN L 63 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LYS L 68 " --> pdb=" O VAL L 64 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER L 69 " --> pdb=" O CYS L 65 " (cutoff:3.500A) Processing helix chain 'L' and resid 73 through 105 removed outlier: 3.748A pdb=" N PHE L 84 " --> pdb=" O LEU L 80 " (cutoff:3.500A) Proline residue: L 88 - end of helix removed outlier: 3.583A pdb=" N TYR L 98 " --> pdb=" O ALA L 94 " (cutoff:3.500A) Processing helix chain 'L' and resid 151 through 177 removed outlier: 3.560A pdb=" N ILE L 159 " --> pdb=" O TYR L 155 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYS L 162 " --> pdb=" O SER L 158 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE L 172 " --> pdb=" O ALA L 168 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLN L 173 " --> pdb=" O PHE L 169 " (cutoff:3.500A) Processing helix chain 'L' and resid 202 through 233 removed outlier: 3.688A pdb=" N PHE L 209 " --> pdb=" O GLU L 205 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER L 217 " --> pdb=" O MET L 213 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N GLU L 227 " --> pdb=" O LEU L 223 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE L 232 " --> pdb=" O LEU L 228 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 53 through 54 removed outlier: 3.659A pdb=" N ARG A 53 " --> pdb=" O PHE A 199 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 53 through 54 removed outlier: 3.660A pdb=" N ARG B 53 " --> pdb=" O PHE B 199 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 53 through 54 removed outlier: 3.660A pdb=" N ARG C 53 " --> pdb=" O PHE C 199 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 53 through 54 removed outlier: 3.659A pdb=" N ARG D 53 " --> pdb=" O PHE D 199 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 53 through 54 removed outlier: 3.660A pdb=" N ARG E 53 " --> pdb=" O PHE E 199 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 53 through 54 removed outlier: 3.659A pdb=" N ARG F 53 " --> pdb=" O PHE F 199 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 53 through 54 removed outlier: 3.659A pdb=" N ARG G 53 " --> pdb=" O PHE G 199 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 53 through 54 removed outlier: 3.659A pdb=" N ARG H 53 " --> pdb=" O PHE H 199 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 53 through 54 removed outlier: 3.660A pdb=" N ARG I 53 " --> pdb=" O PHE I 199 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 53 through 54 removed outlier: 3.660A pdb=" N ARG J 53 " --> pdb=" O PHE J 199 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 53 through 54 removed outlier: 3.659A pdb=" N ARG K 53 " --> pdb=" O PHE K 199 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 53 through 54 removed outlier: 3.659A pdb=" N ARG L 53 " --> pdb=" O PHE L 199 " (cutoff:3.500A) 1139 hydrogen bonds defined for protein. 3345 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.29 Time building geometry restraints manager: 1.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5590 1.34 - 1.46: 4875 1.46 - 1.58: 10619 1.58 - 1.69: 0 1.69 - 1.81: 120 Bond restraints: 21204 Sorted by residual: bond pdb=" C VAL L 87 " pdb=" N PRO L 88 " ideal model delta sigma weight residual 1.336 1.360 -0.024 1.25e-02 6.40e+03 3.60e+00 bond pdb=" C VAL J 87 " pdb=" N PRO J 88 " ideal model delta sigma weight residual 1.336 1.359 -0.023 1.23e-02 6.61e+03 3.58e+00 bond pdb=" C VAL E 87 " pdb=" N PRO E 88 " ideal model delta sigma weight residual 1.336 1.359 -0.023 1.23e-02 6.61e+03 3.57e+00 bond pdb=" C VAL B 87 " pdb=" N PRO B 88 " ideal model delta sigma weight residual 1.336 1.359 -0.023 1.23e-02 6.61e+03 3.52e+00 bond pdb=" C VAL A 87 " pdb=" N PRO A 88 " ideal model delta sigma weight residual 1.336 1.359 -0.023 1.23e-02 6.61e+03 3.49e+00 ... (remaining 21199 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.25: 25835 2.25 - 4.51: 1874 4.51 - 6.76: 323 6.76 - 9.01: 12 9.01 - 11.27: 12 Bond angle restraints: 28056 Sorted by residual: angle pdb=" CA PRO D 88 " pdb=" N PRO D 88 " pdb=" CD PRO D 88 " ideal model delta sigma weight residual 112.00 107.10 4.90 1.40e+00 5.10e-01 1.22e+01 angle pdb=" CA PRO K 88 " pdb=" N PRO K 88 " pdb=" CD PRO K 88 " ideal model delta sigma weight residual 112.00 107.13 4.87 1.40e+00 5.10e-01 1.21e+01 angle pdb=" CA PRO A 88 " pdb=" N PRO A 88 " pdb=" CD PRO A 88 " ideal model delta sigma weight residual 112.00 107.13 4.87 1.40e+00 5.10e-01 1.21e+01 angle pdb=" CA PRO J 88 " pdb=" N PRO J 88 " pdb=" CD PRO J 88 " ideal model delta sigma weight residual 112.00 107.14 4.86 1.40e+00 5.10e-01 1.21e+01 angle pdb=" CA PRO H 88 " pdb=" N PRO H 88 " pdb=" CD PRO H 88 " ideal model delta sigma weight residual 112.00 107.14 4.86 1.40e+00 5.10e-01 1.20e+01 ... (remaining 28051 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.56: 10630 16.56 - 33.11: 1538 33.11 - 49.67: 492 49.67 - 66.22: 96 66.22 - 82.78: 36 Dihedral angle restraints: 12792 sinusoidal: 5916 harmonic: 6876 Sorted by residual: dihedral pdb=" C VAL K 87 " pdb=" N VAL K 87 " pdb=" CA VAL K 87 " pdb=" CB VAL K 87 " ideal model delta harmonic sigma weight residual -122.00 -130.32 8.32 0 2.50e+00 1.60e-01 1.11e+01 dihedral pdb=" C VAL E 87 " pdb=" N VAL E 87 " pdb=" CA VAL E 87 " pdb=" CB VAL E 87 " ideal model delta harmonic sigma weight residual -122.00 -130.31 8.31 0 2.50e+00 1.60e-01 1.10e+01 dihedral pdb=" C VAL F 87 " pdb=" N VAL F 87 " pdb=" CA VAL F 87 " pdb=" CB VAL F 87 " ideal model delta harmonic sigma weight residual -122.00 -130.28 8.28 0 2.50e+00 1.60e-01 1.10e+01 ... (remaining 12789 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 2168 0.049 - 0.099: 729 0.099 - 0.148: 103 0.148 - 0.198: 7 0.198 - 0.247: 17 Chirality restraints: 3024 Sorted by residual: chirality pdb=" CB VAL F 87 " pdb=" CA VAL F 87 " pdb=" CG1 VAL F 87 " pdb=" CG2 VAL F 87 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.53e+00 chirality pdb=" CB VAL B 87 " pdb=" CA VAL B 87 " pdb=" CG1 VAL B 87 " pdb=" CG2 VAL B 87 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" CB VAL C 87 " pdb=" CA VAL C 87 " pdb=" CG1 VAL C 87 " pdb=" CG2 VAL C 87 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.51e+00 ... (remaining 3021 not shown) Planarity restraints: 3204 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS H 192 " 0.034 5.00e-02 4.00e+02 5.05e-02 4.08e+00 pdb=" N PRO H 193 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO H 193 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO H 193 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS F 192 " -0.033 5.00e-02 4.00e+02 5.03e-02 4.04e+00 pdb=" N PRO F 193 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO F 193 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO F 193 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS A 192 " -0.033 5.00e-02 4.00e+02 5.02e-02 4.02e+00 pdb=" N PRO A 193 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO A 193 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 193 " -0.028 5.00e-02 4.00e+02 ... (remaining 3201 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 6206 2.81 - 3.34: 16621 3.34 - 3.86: 31105 3.86 - 4.38: 34287 4.38 - 4.90: 60986 Nonbonded interactions: 149205 Sorted by model distance: nonbonded pdb=" O PRO A 203 " pdb=" OG1 THR A 207 " model vdw 2.293 3.040 nonbonded pdb=" O PRO G 203 " pdb=" OG1 THR G 207 " model vdw 2.293 3.040 nonbonded pdb=" O PRO F 203 " pdb=" OG1 THR F 207 " model vdw 2.293 3.040 nonbonded pdb=" O PRO K 203 " pdb=" OG1 THR K 207 " model vdw 2.293 3.040 nonbonded pdb=" O PRO C 203 " pdb=" OG1 THR C 207 " model vdw 2.293 3.040 ... (remaining 149200 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'L' } ncs_group { reference = chain 'D' selection = chain 'J' } ncs_group { reference = chain 'E' selection = chain 'K' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 12.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.670 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 17.610 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 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 : 0.007 0.051 21240 Z= 0.325 Angle : 1.261 11.268 28128 Z= 0.576 Chirality : 0.050 0.247 3024 Planarity : 0.006 0.051 3204 Dihedral : 16.993 82.776 8244 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 4.00 % Allowed : 10.29 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.48 (0.11), residues: 2304 helix: -3.98 (0.05), residues: 1548 sheet: 1.37 (0.48), residues: 132 loop : -3.13 (0.20), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 33 TYR 0.008 0.002 TYR A 155 PHE 0.020 0.002 PHE F 52 TRP 0.010 0.002 TRP K 45 HIS 0.004 0.001 HIS H 95 Details of bonding type rmsd covalent geometry : bond 0.00735 (21204) covalent geometry : angle 1.26144 (28056) SS BOND : bond 0.00349 ( 36) SS BOND : angle 0.88144 ( 72) hydrogen bonds : bond 0.28787 ( 1139) hydrogen bonds : angle 8.87897 ( 3345) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 636 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 552 time to evaluate : 0.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 ASP cc_start: 0.7816 (t0) cc_final: 0.7502 (t70) REVERT: A 47 ASP cc_start: 0.9174 (p0) cc_final: 0.8857 (p0) REVERT: A 185 TYR cc_start: 0.9025 (t80) cc_final: 0.8666 (t80) REVERT: A 213 MET cc_start: 0.8445 (mmm) cc_final: 0.7182 (mmm) REVERT: B 3 ASP cc_start: 0.7643 (t0) cc_final: 0.7186 (t70) REVERT: B 42 GLU cc_start: 0.7786 (tp30) cc_final: 0.7579 (tp30) REVERT: B 55 ASN cc_start: 0.9229 (t0) cc_final: 0.8792 (t0) REVERT: B 206 LYS cc_start: 0.9157 (mttt) cc_final: 0.8490 (mttp) REVERT: C 55 ASN cc_start: 0.9171 (t0) cc_final: 0.8957 (t0) REVERT: D 3 ASP cc_start: 0.7910 (t0) cc_final: 0.7571 (t70) REVERT: D 42 GLU cc_start: 0.7925 (tp30) cc_final: 0.7612 (tp30) REVERT: D 47 ASP cc_start: 0.9156 (p0) cc_final: 0.8767 (p0) REVERT: D 185 TYR cc_start: 0.9027 (t80) cc_final: 0.8677 (t80) REVERT: D 213 MET cc_start: 0.8437 (mmm) cc_final: 0.7133 (mmm) REVERT: E 3 ASP cc_start: 0.7933 (t0) cc_final: 0.7444 (t70) REVERT: E 47 ASP cc_start: 0.8919 (p0) cc_final: 0.8542 (p0) REVERT: E 185 TYR cc_start: 0.9033 (t80) cc_final: 0.8547 (t80) REVERT: F 3 ASP cc_start: 0.7997 (t0) cc_final: 0.7537 (t70) REVERT: F 55 ASN cc_start: 0.9145 (t0) cc_final: 0.8797 (t0) REVERT: G 3 ASP cc_start: 0.7458 (t0) cc_final: 0.7063 (t70) REVERT: G 47 ASP cc_start: 0.9128 (p0) cc_final: 0.8893 (p0) REVERT: G 53 ARG cc_start: 0.8290 (mtt90) cc_final: 0.8046 (mtt90) REVERT: G 55 ASN cc_start: 0.9159 (t0) cc_final: 0.8915 (t0) REVERT: H 3 ASP cc_start: 0.7598 (t0) cc_final: 0.7286 (t70) REVERT: H 47 ASP cc_start: 0.9167 (p0) cc_final: 0.8830 (p0) REVERT: H 55 ASN cc_start: 0.9288 (t0) cc_final: 0.8933 (t0) REVERT: H 82 ILE cc_start: 0.8754 (tt) cc_final: 0.8515 (tp) REVERT: H 98 TYR cc_start: 0.8748 (m-80) cc_final: 0.8450 (m-80) REVERT: I 3 ASP cc_start: 0.7672 (t0) cc_final: 0.7070 (t70) REVERT: I 98 TYR cc_start: 0.8740 (m-80) cc_final: 0.8479 (m-10) REVERT: I 206 LYS cc_start: 0.9088 (mttt) cc_final: 0.8452 (mttp) REVERT: J 3 ASP cc_start: 0.7983 (t0) cc_final: 0.7597 (t70) REVERT: J 55 ASN cc_start: 0.9155 (t0) cc_final: 0.8824 (t0) REVERT: K 3 ASP cc_start: 0.7937 (t0) cc_final: 0.7514 (t70) REVERT: K 47 ASP cc_start: 0.9073 (p0) cc_final: 0.8717 (p0) REVERT: K 82 ILE cc_start: 0.8806 (tt) cc_final: 0.8590 (tp) REVERT: K 104 GLU cc_start: 0.8612 (mt-10) cc_final: 0.8410 (mt-10) REVERT: K 185 TYR cc_start: 0.9049 (t80) cc_final: 0.8578 (t80) REVERT: K 213 MET cc_start: 0.8397 (mmm) cc_final: 0.7038 (mmm) REVERT: L 3 ASP cc_start: 0.7685 (t0) cc_final: 0.7173 (t70) REVERT: L 55 ASN cc_start: 0.9257 (t0) cc_final: 0.8844 (t0) REVERT: L 206 LYS cc_start: 0.9150 (mttt) cc_final: 0.8474 (mttp) REVERT: L 224 ASN cc_start: 0.9087 (m-40) cc_final: 0.8876 (m110) outliers start: 84 outliers final: 43 residues processed: 609 average time/residue: 0.1477 time to fit residues: 135.0240 Evaluate side-chains 518 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 475 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 SER Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain B residue 5 SER Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain C residue 5 SER Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain D residue 5 SER Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain E residue 5 SER Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain F residue 5 SER Chi-restraints excluded: chain F residue 50 SER Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain G residue 5 SER Chi-restraints excluded: chain G residue 50 SER Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 226 ILE Chi-restraints excluded: chain H residue 5 SER Chi-restraints excluded: chain H residue 50 SER Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 226 ILE Chi-restraints excluded: chain I residue 5 SER Chi-restraints excluded: chain I residue 50 SER Chi-restraints excluded: chain I residue 89 THR Chi-restraints excluded: chain I residue 226 ILE Chi-restraints excluded: chain J residue 5 SER Chi-restraints excluded: chain J residue 50 SER Chi-restraints excluded: chain J residue 89 THR Chi-restraints excluded: chain K residue 5 SER Chi-restraints excluded: chain K residue 50 SER Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 226 ILE Chi-restraints excluded: chain L residue 5 SER Chi-restraints excluded: chain L residue 50 SER Chi-restraints excluded: chain L residue 89 THR Chi-restraints excluded: chain L residue 226 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 216 optimal weight: 5.9990 chunk 98 optimal weight: 0.7980 chunk 194 optimal weight: 2.9990 chunk 227 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 0.9980 chunk 200 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 GLN A 58 GLN A 224 ASN B 49 GLN B 58 GLN B 81 GLN C 49 GLN C 58 GLN C 81 GLN D 49 GLN D 224 ASN E 49 GLN F 49 GLN F 58 GLN F 81 GLN F 224 ASN G 49 GLN G 58 GLN H 49 GLN H 58 GLN I 49 GLN I 58 GLN I 81 GLN J 49 GLN J 81 GLN J 224 ASN K 49 GLN K 224 ASN L 49 GLN L 58 GLN L 81 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.131572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.110675 restraints weight = 35700.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.114288 restraints weight = 14626.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.116655 restraints weight = 8016.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.118148 restraints weight = 5382.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.118984 restraints weight = 4202.996| |-----------------------------------------------------------------------------| r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 21240 Z= 0.129 Angle : 0.589 9.023 28128 Z= 0.296 Chirality : 0.038 0.199 3024 Planarity : 0.005 0.037 3204 Dihedral : 10.567 58.444 3903 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.10 % Allowed : 16.81 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.05 (0.15), residues: 2304 helix: -0.89 (0.11), residues: 1572 sheet: 1.54 (0.47), residues: 132 loop : -3.02 (0.20), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 53 TYR 0.019 0.001 TYR D 230 PHE 0.017 0.001 PHE H 30 TRP 0.006 0.001 TRP K 45 HIS 0.002 0.001 HIS D 95 Details of bonding type rmsd covalent geometry : bond 0.00280 (21204) covalent geometry : angle 0.58833 (28056) SS BOND : bond 0.00135 ( 36) SS BOND : angle 0.83467 ( 72) hydrogen bonds : bond 0.04958 ( 1139) hydrogen bonds : angle 3.89693 ( 3345) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 616 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 551 time to evaluate : 0.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 ASP cc_start: 0.7652 (t0) cc_final: 0.7089 (t70) REVERT: A 47 ASP cc_start: 0.9127 (p0) cc_final: 0.8847 (p0) REVERT: A 55 ASN cc_start: 0.9135 (t0) cc_final: 0.8651 (t0) REVERT: B 3 ASP cc_start: 0.7514 (t0) cc_final: 0.6760 (t70) REVERT: B 55 ASN cc_start: 0.9092 (t0) cc_final: 0.8670 (t0) REVERT: B 213 MET cc_start: 0.8330 (mmm) cc_final: 0.6905 (mmm) REVERT: C 55 ASN cc_start: 0.9025 (t0) cc_final: 0.8644 (t0) REVERT: D 3 ASP cc_start: 0.7820 (t0) cc_final: 0.7328 (t70) REVERT: D 47 ASP cc_start: 0.9087 (p0) cc_final: 0.8676 (p0) REVERT: D 55 ASN cc_start: 0.9150 (t0) cc_final: 0.8854 (t0) REVERT: E 47 ASP cc_start: 0.9048 (p0) cc_final: 0.8748 (p0) REVERT: E 55 ASN cc_start: 0.9189 (t0) cc_final: 0.8841 (t0) REVERT: E 185 TYR cc_start: 0.9040 (t80) cc_final: 0.8244 (t80) REVERT: E 213 MET cc_start: 0.8296 (mmm) cc_final: 0.7096 (mmm) REVERT: F 3 ASP cc_start: 0.7846 (t0) cc_final: 0.7225 (t70) REVERT: F 55 ASN cc_start: 0.9108 (t0) cc_final: 0.8808 (t0) REVERT: F 76 ARG cc_start: 0.8853 (mtt90) cc_final: 0.8613 (mtt90) REVERT: G 3 ASP cc_start: 0.7293 (t0) cc_final: 0.6790 (t70) REVERT: G 47 ASP cc_start: 0.9084 (p0) cc_final: 0.8882 (p0) REVERT: G 55 ASN cc_start: 0.9118 (t0) cc_final: 0.8834 (t0) REVERT: H 3 ASP cc_start: 0.7472 (t0) cc_final: 0.6833 (t70) REVERT: H 47 ASP cc_start: 0.9128 (p0) cc_final: 0.8867 (p0) REVERT: H 55 ASN cc_start: 0.9143 (t0) cc_final: 0.8827 (t0) REVERT: I 55 ASN cc_start: 0.9103 (t0) cc_final: 0.8752 (t0) REVERT: J 3 ASP cc_start: 0.7858 (t0) cc_final: 0.7153 (t70) REVERT: J 55 ASN cc_start: 0.9109 (t0) cc_final: 0.8778 (t0) REVERT: K 3 ASP cc_start: 0.7815 (t0) cc_final: 0.7260 (t70) REVERT: K 47 ASP cc_start: 0.9041 (p0) cc_final: 0.8641 (p0) REVERT: K 55 ASN cc_start: 0.9173 (t0) cc_final: 0.8716 (t0) REVERT: L 3 ASP cc_start: 0.7569 (t0) cc_final: 0.6720 (t70) REVERT: L 55 ASN cc_start: 0.9123 (t0) cc_final: 0.8712 (t0) REVERT: L 76 ARG cc_start: 0.8959 (mtt90) cc_final: 0.8544 (mtt90) REVERT: L 213 MET cc_start: 0.8312 (mmm) cc_final: 0.6887 (mmm) outliers start: 65 outliers final: 47 residues processed: 580 average time/residue: 0.1361 time to fit residues: 121.2892 Evaluate side-chains 542 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 495 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 SER Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain B residue 5 SER Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain C residue 5 SER Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 224 ASN Chi-restraints excluded: chain D residue 5 SER Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain E residue 5 SER Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain F residue 5 SER Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 63 ASN Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain G residue 5 SER Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 232 PHE Chi-restraints excluded: chain H residue 5 SER Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain I residue 5 SER Chi-restraints excluded: chain I residue 41 VAL Chi-restraints excluded: chain I residue 89 THR Chi-restraints excluded: chain J residue 5 SER Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 62 GLU Chi-restraints excluded: chain J residue 63 ASN Chi-restraints excluded: chain J residue 89 THR Chi-restraints excluded: chain K residue 5 SER Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain L residue 5 SER Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 41 VAL Chi-restraints excluded: chain L residue 67 ASP Chi-restraints excluded: chain L residue 89 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 200 optimal weight: 0.0370 chunk 191 optimal weight: 0.4980 chunk 121 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 187 optimal weight: 0.9990 chunk 116 optimal weight: 2.9990 chunk 83 optimal weight: 0.7980 chunk 219 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 145 optimal weight: 4.9990 overall best weight: 0.6662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 ASN B 63 ASN B 81 GLN C 63 ASN C 81 GLN D 81 GLN E 58 GLN E 81 GLN F 63 ASN F 81 GLN G 63 ASN G 81 GLN H 63 ASN I 81 GLN J 58 GLN J 63 ASN J 81 GLN K 63 ASN L 81 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.135295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.114250 restraints weight = 35224.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.117913 restraints weight = 14485.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.120278 restraints weight = 7951.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.121684 restraints weight = 5370.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.122627 restraints weight = 4262.295| |-----------------------------------------------------------------------------| r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.3014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 21240 Z= 0.101 Angle : 0.539 9.669 28128 Z= 0.265 Chirality : 0.037 0.154 3024 Planarity : 0.004 0.031 3204 Dihedral : 9.158 58.085 3876 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.95 % Allowed : 19.76 % Favored : 77.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.17), residues: 2304 helix: 0.54 (0.13), residues: 1572 sheet: 1.60 (0.48), residues: 132 loop : -2.65 (0.21), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 53 TYR 0.014 0.001 TYR L 230 PHE 0.016 0.001 PHE H 30 TRP 0.009 0.001 TRP D 45 HIS 0.001 0.000 HIS L 194 Details of bonding type rmsd covalent geometry : bond 0.00212 (21204) covalent geometry : angle 0.53897 (28056) SS BOND : bond 0.00162 ( 36) SS BOND : angle 0.56162 ( 72) hydrogen bonds : bond 0.03960 ( 1139) hydrogen bonds : angle 3.45288 ( 3345) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 601 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 539 time to evaluate : 0.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 ASP cc_start: 0.7530 (t0) cc_final: 0.7210 (t70) REVERT: A 47 ASP cc_start: 0.9083 (p0) cc_final: 0.8639 (p0) REVERT: A 55 ASN cc_start: 0.9079 (t0) cc_final: 0.8622 (t0) REVERT: B 3 ASP cc_start: 0.7424 (t0) cc_final: 0.6649 (t70) REVERT: B 55 ASN cc_start: 0.9057 (t0) cc_final: 0.8642 (t0) REVERT: C 55 ASN cc_start: 0.8989 (t0) cc_final: 0.8656 (t0) REVERT: C 152 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8752 (mt) REVERT: D 3 ASP cc_start: 0.7725 (t0) cc_final: 0.7189 (t70) REVERT: D 47 ASP cc_start: 0.9001 (p0) cc_final: 0.8604 (p0) REVERT: D 55 ASN cc_start: 0.9094 (t0) cc_final: 0.8842 (t0) REVERT: E 47 ASP cc_start: 0.9052 (p0) cc_final: 0.8751 (p0) REVERT: E 55 ASN cc_start: 0.9110 (t0) cc_final: 0.8751 (t0) REVERT: E 152 LEU cc_start: 0.9097 (OUTLIER) cc_final: 0.8752 (mt) REVERT: E 213 MET cc_start: 0.8314 (mmm) cc_final: 0.6989 (mmm) REVERT: F 3 ASP cc_start: 0.7755 (t0) cc_final: 0.7104 (t70) REVERT: F 55 ASN cc_start: 0.9050 (t0) cc_final: 0.8787 (t0) REVERT: F 103 GLU cc_start: 0.8887 (mt-10) cc_final: 0.8059 (mp0) REVERT: F 166 GLU cc_start: 0.8535 (tp30) cc_final: 0.8285 (tp30) REVERT: F 213 MET cc_start: 0.8509 (mmm) cc_final: 0.7546 (mmm) REVERT: G 3 ASP cc_start: 0.7221 (t0) cc_final: 0.6661 (t70) REVERT: G 47 ASP cc_start: 0.9075 (p0) cc_final: 0.8699 (p0) REVERT: G 55 ASN cc_start: 0.9075 (t0) cc_final: 0.8831 (t0) REVERT: H 3 ASP cc_start: 0.7413 (t0) cc_final: 0.6739 (t70) REVERT: H 47 ASP cc_start: 0.9083 (p0) cc_final: 0.8812 (p0) REVERT: H 55 ASN cc_start: 0.9094 (t0) cc_final: 0.8820 (t0) REVERT: I 55 ASN cc_start: 0.9052 (t0) cc_final: 0.8679 (t0) REVERT: I 152 LEU cc_start: 0.9062 (OUTLIER) cc_final: 0.8716 (mt) REVERT: J 3 ASP cc_start: 0.7737 (t0) cc_final: 0.7298 (t70) REVERT: J 55 ASN cc_start: 0.9088 (t0) cc_final: 0.8809 (t0) REVERT: J 213 MET cc_start: 0.8507 (mmm) cc_final: 0.7509 (mmm) REVERT: K 3 ASP cc_start: 0.7695 (t0) cc_final: 0.7104 (t70) REVERT: K 47 ASP cc_start: 0.8968 (p0) cc_final: 0.8575 (p0) REVERT: K 55 ASN cc_start: 0.9108 (t0) cc_final: 0.8665 (t0) REVERT: L 3 ASP cc_start: 0.7472 (t0) cc_final: 0.6624 (t70) REVERT: L 55 ASN cc_start: 0.9093 (t0) cc_final: 0.8694 (t0) outliers start: 62 outliers final: 43 residues processed: 560 average time/residue: 0.1469 time to fit residues: 125.2539 Evaluate side-chains 542 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 496 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 63 ASN Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 232 PHE Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 63 ASN Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 232 PHE Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 232 PHE Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 90 LEU Chi-restraints excluded: chain H residue 232 PHE Chi-restraints excluded: chain I residue 41 VAL Chi-restraints excluded: chain I residue 89 THR Chi-restraints excluded: chain I residue 152 LEU Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 63 ASN Chi-restraints excluded: chain J residue 89 THR Chi-restraints excluded: chain J residue 232 PHE Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 41 VAL Chi-restraints excluded: chain L residue 62 GLU Chi-restraints excluded: chain L residue 64 VAL Chi-restraints excluded: chain L residue 89 THR Chi-restraints excluded: chain L residue 232 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 87 optimal weight: 9.9990 chunk 76 optimal weight: 5.9990 chunk 153 optimal weight: 2.9990 chunk 81 optimal weight: 0.8980 chunk 143 optimal weight: 0.0000 chunk 139 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 167 optimal weight: 0.4980 chunk 53 optimal weight: 30.0000 chunk 51 optimal weight: 0.3980 chunk 41 optimal weight: 3.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 63 ASN C 63 ASN C 81 GLN D 58 GLN E 81 GLN F 81 GLN G 81 GLN J 63 ASN J 81 GLN K 58 GLN K 63 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.135278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.114334 restraints weight = 35341.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.118031 restraints weight = 14437.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.120411 restraints weight = 7856.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.121894 restraints weight = 5278.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.122741 restraints weight = 4132.081| |-----------------------------------------------------------------------------| r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.3244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 21240 Z= 0.103 Angle : 0.531 9.392 28128 Z= 0.262 Chirality : 0.038 0.294 3024 Planarity : 0.004 0.031 3204 Dihedral : 8.810 59.488 3864 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.10 % Allowed : 21.95 % Favored : 74.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.17), residues: 2304 helix: 1.19 (0.13), residues: 1572 sheet: 1.58 (0.48), residues: 132 loop : -2.42 (0.22), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 53 TYR 0.017 0.001 TYR F 230 PHE 0.012 0.001 PHE G 161 TRP 0.006 0.001 TRP K 45 HIS 0.002 0.000 HIS J 95 Details of bonding type rmsd covalent geometry : bond 0.00228 (21204) covalent geometry : angle 0.53137 (28056) SS BOND : bond 0.00131 ( 36) SS BOND : angle 0.50996 ( 72) hydrogen bonds : bond 0.03553 ( 1139) hydrogen bonds : angle 3.33393 ( 3345) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 589 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 524 time to evaluate : 0.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 ASP cc_start: 0.7476 (t0) cc_final: 0.7161 (t70) REVERT: A 55 ASN cc_start: 0.9075 (t0) cc_final: 0.8627 (t0) REVERT: B 3 ASP cc_start: 0.7429 (t0) cc_final: 0.6664 (t70) REVERT: B 55 ASN cc_start: 0.9048 (t0) cc_final: 0.8659 (t0) REVERT: B 218 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8712 (mm) REVERT: C 47 ASP cc_start: 0.8969 (p0) cc_final: 0.8639 (p0) REVERT: C 55 ASN cc_start: 0.8995 (t0) cc_final: 0.8696 (t0) REVERT: C 76 ARG cc_start: 0.8936 (mtt90) cc_final: 0.8543 (mtt90) REVERT: C 152 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8748 (mt) REVERT: C 162 LYS cc_start: 0.7468 (mtpt) cc_final: 0.7259 (mtpp) REVERT: D 3 ASP cc_start: 0.7654 (t0) cc_final: 0.7107 (t70) REVERT: D 47 ASP cc_start: 0.8970 (p0) cc_final: 0.8570 (p0) REVERT: D 55 ASN cc_start: 0.9071 (t0) cc_final: 0.8848 (t0) REVERT: D 213 MET cc_start: 0.8464 (mmm) cc_final: 0.7667 (mmm) REVERT: E 47 ASP cc_start: 0.9052 (p0) cc_final: 0.8711 (p0) REVERT: E 55 ASN cc_start: 0.9089 (t0) cc_final: 0.8728 (t0) REVERT: E 152 LEU cc_start: 0.9096 (OUTLIER) cc_final: 0.8756 (mt) REVERT: E 213 MET cc_start: 0.8364 (mmm) cc_final: 0.6977 (mmm) REVERT: F 3 ASP cc_start: 0.7697 (t0) cc_final: 0.7030 (t70) REVERT: F 55 ASN cc_start: 0.9052 (t0) cc_final: 0.8573 (t0) REVERT: F 76 ARG cc_start: 0.8891 (mtt90) cc_final: 0.8615 (mtt90) REVERT: F 166 GLU cc_start: 0.8543 (tp30) cc_final: 0.8287 (tp30) REVERT: G 3 ASP cc_start: 0.7209 (t0) cc_final: 0.6641 (t70) REVERT: G 55 ASN cc_start: 0.9033 (t0) cc_final: 0.8809 (t0) REVERT: G 230 TYR cc_start: 0.8275 (t80) cc_final: 0.8064 (t80) REVERT: H 3 ASP cc_start: 0.7437 (t0) cc_final: 0.6768 (t70) REVERT: H 55 ASN cc_start: 0.9067 (t0) cc_final: 0.8576 (t0) REVERT: I 55 ASN cc_start: 0.9035 (t0) cc_final: 0.8669 (t0) REVERT: I 152 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8711 (mt) REVERT: J 3 ASP cc_start: 0.7702 (t0) cc_final: 0.7281 (t70) REVERT: J 55 ASN cc_start: 0.9083 (t0) cc_final: 0.8823 (t0) REVERT: J 76 ARG cc_start: 0.8884 (mtt90) cc_final: 0.8614 (mtt90) REVERT: K 3 ASP cc_start: 0.7638 (t0) cc_final: 0.7061 (t70) REVERT: K 55 ASN cc_start: 0.9106 (t0) cc_final: 0.8571 (t0) REVERT: L 3 ASP cc_start: 0.7459 (t0) cc_final: 0.6625 (t70) REVERT: L 55 ASN cc_start: 0.9083 (t0) cc_final: 0.8690 (t0) outliers start: 65 outliers final: 36 residues processed: 554 average time/residue: 0.1377 time to fit residues: 117.4375 Evaluate side-chains 540 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 500 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 232 PHE Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 224 ASN Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 232 PHE Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 232 PHE Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 232 PHE Chi-restraints excluded: chain I residue 41 VAL Chi-restraints excluded: chain I residue 89 THR Chi-restraints excluded: chain I residue 152 LEU Chi-restraints excluded: chain I residue 232 PHE Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 89 THR Chi-restraints excluded: chain J residue 232 PHE Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 232 PHE Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 41 VAL Chi-restraints excluded: chain L residue 62 GLU Chi-restraints excluded: chain L residue 64 VAL Chi-restraints excluded: chain L residue 89 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 7 optimal weight: 5.9990 chunk 204 optimal weight: 0.8980 chunk 145 optimal weight: 0.8980 chunk 87 optimal weight: 9.9990 chunk 61 optimal weight: 0.0060 chunk 45 optimal weight: 5.9990 chunk 128 optimal weight: 4.9990 chunk 142 optimal weight: 1.9990 chunk 38 optimal weight: 6.9990 chunk 139 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 overall best weight: 1.3600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 81 GLN E 81 GLN F 63 ASN G 81 GLN J 63 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.134233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.113686 restraints weight = 34879.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.117362 restraints weight = 14172.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.119740 restraints weight = 7651.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.121160 restraints weight = 5096.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.122027 restraints weight = 3996.195| |-----------------------------------------------------------------------------| r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.3376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 21240 Z= 0.113 Angle : 0.528 8.771 28128 Z= 0.262 Chirality : 0.038 0.128 3024 Planarity : 0.003 0.029 3204 Dihedral : 8.737 59.834 3863 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.62 % Allowed : 22.86 % Favored : 74.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.18), residues: 2304 helix: 1.54 (0.13), residues: 1572 sheet: 1.63 (0.47), residues: 132 loop : -1.95 (0.24), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 53 TYR 0.025 0.001 TYR F 230 PHE 0.014 0.001 PHE I 30 TRP 0.007 0.001 TRP D 45 HIS 0.002 0.001 HIS J 95 Details of bonding type rmsd covalent geometry : bond 0.00261 (21204) covalent geometry : angle 0.52802 (28056) SS BOND : bond 0.00129 ( 36) SS BOND : angle 0.54103 ( 72) hydrogen bonds : bond 0.03459 ( 1139) hydrogen bonds : angle 3.29689 ( 3345) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 594 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 539 time to evaluate : 0.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 ASP cc_start: 0.7466 (t0) cc_final: 0.6895 (t70) REVERT: A 47 ASP cc_start: 0.8983 (p0) cc_final: 0.8529 (p0) REVERT: A 55 ASN cc_start: 0.9081 (t0) cc_final: 0.8652 (t0) REVERT: B 3 ASP cc_start: 0.7456 (t0) cc_final: 0.6695 (t70) REVERT: B 55 ASN cc_start: 0.9052 (t0) cc_final: 0.8661 (t0) REVERT: B 152 LEU cc_start: 0.9121 (OUTLIER) cc_final: 0.8751 (mt) REVERT: B 213 MET cc_start: 0.8387 (mmm) cc_final: 0.7546 (mmm) REVERT: C 3 ASP cc_start: 0.7536 (t0) cc_final: 0.6791 (t70) REVERT: C 47 ASP cc_start: 0.8969 (p0) cc_final: 0.8193 (p0) REVERT: C 55 ASN cc_start: 0.9019 (t0) cc_final: 0.8746 (t0) REVERT: C 76 ARG cc_start: 0.8922 (mtt90) cc_final: 0.8473 (mtt90) REVERT: C 152 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8603 (mt) REVERT: C 162 LYS cc_start: 0.7474 (mtpt) cc_final: 0.7247 (mtpp) REVERT: C 213 MET cc_start: 0.8229 (mmm) cc_final: 0.7319 (mmm) REVERT: D 3 ASP cc_start: 0.7638 (t0) cc_final: 0.7083 (t70) REVERT: D 47 ASP cc_start: 0.8962 (p0) cc_final: 0.8330 (p0) REVERT: D 55 ASN cc_start: 0.9076 (t0) cc_final: 0.8619 (t0) REVERT: E 47 ASP cc_start: 0.9057 (p0) cc_final: 0.8664 (p0) REVERT: E 55 ASN cc_start: 0.9074 (t0) cc_final: 0.8733 (t0) REVERT: E 152 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8761 (mt) REVERT: F 3 ASP cc_start: 0.7652 (t0) cc_final: 0.7039 (t70) REVERT: F 47 ASP cc_start: 0.8984 (p0) cc_final: 0.8545 (p0) REVERT: F 55 ASN cc_start: 0.9050 (t0) cc_final: 0.8575 (t0) REVERT: F 76 ARG cc_start: 0.8892 (mtt90) cc_final: 0.8512 (mtt90) REVERT: F 103 GLU cc_start: 0.8822 (mm-30) cc_final: 0.8203 (mp0) REVERT: F 161 PHE cc_start: 0.8771 (m-80) cc_final: 0.8548 (m-80) REVERT: F 166 GLU cc_start: 0.8566 (tp30) cc_final: 0.8305 (tp30) REVERT: F 213 MET cc_start: 0.8393 (mmm) cc_final: 0.7371 (mmm) REVERT: G 3 ASP cc_start: 0.7289 (t0) cc_final: 0.6695 (t70) REVERT: G 47 ASP cc_start: 0.8969 (p0) cc_final: 0.8479 (p0) REVERT: G 55 ASN cc_start: 0.9050 (t0) cc_final: 0.8832 (t0) REVERT: G 200 LEU cc_start: 0.9009 (mp) cc_final: 0.8761 (mt) REVERT: H 3 ASP cc_start: 0.7418 (t0) cc_final: 0.6766 (t70) REVERT: H 47 ASP cc_start: 0.8976 (p0) cc_final: 0.8502 (p0) REVERT: H 55 ASN cc_start: 0.9081 (t0) cc_final: 0.8607 (t0) REVERT: I 3 ASP cc_start: 0.7539 (t0) cc_final: 0.6797 (t70) REVERT: I 47 ASP cc_start: 0.8720 (p0) cc_final: 0.8270 (p0) REVERT: I 55 ASN cc_start: 0.9032 (t0) cc_final: 0.8678 (t0) REVERT: I 152 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8721 (mt) REVERT: J 3 ASP cc_start: 0.7637 (t0) cc_final: 0.6927 (t70) REVERT: J 47 ASP cc_start: 0.8971 (p0) cc_final: 0.8540 (p0) REVERT: J 55 ASN cc_start: 0.9078 (t0) cc_final: 0.8841 (t0) REVERT: J 76 ARG cc_start: 0.8875 (mtt90) cc_final: 0.8521 (mtt90) REVERT: J 161 PHE cc_start: 0.8769 (m-80) cc_final: 0.8546 (m-80) REVERT: J 166 GLU cc_start: 0.8561 (tp30) cc_final: 0.8306 (tp30) REVERT: J 213 MET cc_start: 0.8390 (mmm) cc_final: 0.7317 (mmm) REVERT: K 3 ASP cc_start: 0.7591 (t0) cc_final: 0.7048 (t70) REVERT: K 47 ASP cc_start: 0.8895 (p0) cc_final: 0.8465 (p0) REVERT: K 55 ASN cc_start: 0.9110 (t0) cc_final: 0.8682 (t0) REVERT: K 152 LEU cc_start: 0.9135 (OUTLIER) cc_final: 0.8750 (mt) REVERT: K 213 MET cc_start: 0.8485 (mmm) cc_final: 0.7561 (mmm) REVERT: L 3 ASP cc_start: 0.7514 (t0) cc_final: 0.6668 (t70) REVERT: L 55 ASN cc_start: 0.9080 (t0) cc_final: 0.8704 (t0) REVERT: L 152 LEU cc_start: 0.9137 (OUTLIER) cc_final: 0.8765 (mt) REVERT: L 213 MET cc_start: 0.8459 (mmm) cc_final: 0.7577 (mmm) REVERT: L 218 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8611 (mm) outliers start: 55 outliers final: 24 residues processed: 555 average time/residue: 0.1355 time to fit residues: 116.4764 Evaluate side-chains 547 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 516 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 224 ASN Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 232 PHE Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 232 PHE Chi-restraints excluded: chain I residue 41 VAL Chi-restraints excluded: chain I residue 152 LEU Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 232 PHE Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 152 LEU Chi-restraints excluded: chain L residue 41 VAL Chi-restraints excluded: chain L residue 62 GLU Chi-restraints excluded: chain L residue 152 LEU Chi-restraints excluded: chain L residue 218 LEU Chi-restraints excluded: chain L residue 232 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 56 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 192 optimal weight: 5.9990 chunk 102 optimal weight: 3.9990 chunk 202 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 216 optimal weight: 6.9990 chunk 101 optimal weight: 4.9990 chunk 115 optimal weight: 0.0970 chunk 47 optimal weight: 6.9990 chunk 191 optimal weight: 4.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 81 GLN D 63 ASN E 81 GLN F 63 ASN G 81 GLN I 81 GLN L 81 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.133600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.113113 restraints weight = 34809.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.116764 restraints weight = 14184.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.119122 restraints weight = 7668.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.120581 restraints weight = 5113.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.121368 restraints weight = 3986.417| |-----------------------------------------------------------------------------| r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.3502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 21240 Z= 0.122 Angle : 0.542 8.993 28128 Z= 0.270 Chirality : 0.039 0.282 3024 Planarity : 0.003 0.030 3204 Dihedral : 8.676 59.983 3852 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.62 % Allowed : 23.67 % Favored : 73.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.18), residues: 2304 helix: 1.68 (0.13), residues: 1572 sheet: 1.63 (0.47), residues: 132 loop : -1.72 (0.25), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 76 TYR 0.018 0.001 TYR G 230 PHE 0.020 0.001 PHE I 30 TRP 0.006 0.001 TRP K 45 HIS 0.002 0.001 HIS J 95 Details of bonding type rmsd covalent geometry : bond 0.00286 (21204) covalent geometry : angle 0.54174 (28056) SS BOND : bond 0.00191 ( 36) SS BOND : angle 0.67368 ( 72) hydrogen bonds : bond 0.03479 ( 1139) hydrogen bonds : angle 3.34362 ( 3345) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 578 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 523 time to evaluate : 0.710 Fit side-chains revert: symmetry clash REVERT: A 3 ASP cc_start: 0.7438 (t0) cc_final: 0.6859 (t70) REVERT: A 47 ASP cc_start: 0.8951 (p0) cc_final: 0.8483 (p0) REVERT: A 55 ASN cc_start: 0.9086 (t0) cc_final: 0.8571 (t0) REVERT: A 213 MET cc_start: 0.8514 (mmm) cc_final: 0.7488 (mmm) REVERT: B 3 ASP cc_start: 0.7470 (t0) cc_final: 0.6701 (t70) REVERT: B 42 GLU cc_start: 0.7848 (tp30) cc_final: 0.7636 (tp30) REVERT: B 55 ASN cc_start: 0.9046 (t0) cc_final: 0.8687 (t0) REVERT: B 152 LEU cc_start: 0.9130 (OUTLIER) cc_final: 0.8743 (mt) REVERT: B 213 MET cc_start: 0.8373 (mmm) cc_final: 0.7372 (mmm) REVERT: B 218 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8678 (mm) REVERT: C 3 ASP cc_start: 0.7539 (t0) cc_final: 0.6828 (t70) REVERT: C 47 ASP cc_start: 0.8944 (p0) cc_final: 0.8234 (p0) REVERT: C 55 ASN cc_start: 0.9047 (t0) cc_final: 0.8779 (t0) REVERT: C 152 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8724 (mt) REVERT: D 3 ASP cc_start: 0.7616 (t0) cc_final: 0.7055 (t70) REVERT: D 47 ASP cc_start: 0.8945 (p0) cc_final: 0.8312 (p0) REVERT: D 55 ASN cc_start: 0.9072 (t0) cc_final: 0.8613 (t0) REVERT: D 213 MET cc_start: 0.8492 (mmm) cc_final: 0.7463 (mmm) REVERT: E 3 ASP cc_start: 0.7659 (t0) cc_final: 0.7264 (t70) REVERT: E 47 ASP cc_start: 0.9081 (p0) cc_final: 0.8677 (p0) REVERT: E 55 ASN cc_start: 0.9062 (t0) cc_final: 0.8728 (t0) REVERT: E 152 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8748 (mt) REVERT: F 3 ASP cc_start: 0.7595 (t0) cc_final: 0.6908 (t70) REVERT: F 47 ASP cc_start: 0.8976 (p0) cc_final: 0.8570 (p0) REVERT: F 55 ASN cc_start: 0.9055 (t0) cc_final: 0.8584 (t0) REVERT: F 152 LEU cc_start: 0.9137 (OUTLIER) cc_final: 0.8725 (mt) REVERT: F 161 PHE cc_start: 0.8789 (m-80) cc_final: 0.8553 (m-80) REVERT: F 166 GLU cc_start: 0.8573 (tp30) cc_final: 0.8310 (tp30) REVERT: G 3 ASP cc_start: 0.7335 (t0) cc_final: 0.6758 (t70) REVERT: G 47 ASP cc_start: 0.8918 (p0) cc_final: 0.8424 (p0) REVERT: G 55 ASN cc_start: 0.9054 (t0) cc_final: 0.8839 (t0) REVERT: H 3 ASP cc_start: 0.7417 (t0) cc_final: 0.6765 (t70) REVERT: H 42 GLU cc_start: 0.7585 (tp30) cc_final: 0.7278 (tp30) REVERT: H 47 ASP cc_start: 0.8961 (p0) cc_final: 0.8465 (p0) REVERT: H 55 ASN cc_start: 0.9073 (t0) cc_final: 0.8534 (t0) REVERT: I 3 ASP cc_start: 0.7555 (t0) cc_final: 0.6814 (t70) REVERT: I 42 GLU cc_start: 0.7992 (tp30) cc_final: 0.7777 (tp30) REVERT: I 55 ASN cc_start: 0.9059 (t0) cc_final: 0.8742 (t0) REVERT: I 152 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8717 (mt) REVERT: J 3 ASP cc_start: 0.7602 (t0) cc_final: 0.6886 (t70) REVERT: J 47 ASP cc_start: 0.8958 (p0) cc_final: 0.8568 (p0) REVERT: J 55 ASN cc_start: 0.9096 (t0) cc_final: 0.8863 (t0) REVERT: J 161 PHE cc_start: 0.8782 (m-80) cc_final: 0.8544 (m-80) REVERT: J 166 GLU cc_start: 0.8575 (tp30) cc_final: 0.8322 (tp30) REVERT: K 3 ASP cc_start: 0.7563 (t0) cc_final: 0.6982 (t70) REVERT: K 47 ASP cc_start: 0.8893 (p0) cc_final: 0.8459 (p0) REVERT: K 55 ASN cc_start: 0.9114 (t0) cc_final: 0.8669 (t0) REVERT: L 3 ASP cc_start: 0.7539 (t0) cc_final: 0.6706 (t70) REVERT: L 55 ASN cc_start: 0.9078 (t0) cc_final: 0.8714 (t0) REVERT: L 152 LEU cc_start: 0.9144 (OUTLIER) cc_final: 0.8760 (mt) REVERT: L 213 MET cc_start: 0.8391 (mmm) cc_final: 0.7480 (mmm) outliers start: 55 outliers final: 26 residues processed: 537 average time/residue: 0.1381 time to fit residues: 114.3105 Evaluate side-chains 538 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 505 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 224 ASN Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 152 LEU Chi-restraints excluded: chain F residue 218 LEU Chi-restraints excluded: chain F residue 232 PHE Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 232 PHE Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain I residue 41 VAL Chi-restraints excluded: chain I residue 152 LEU Chi-restraints excluded: chain I residue 232 PHE Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 232 PHE Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain L residue 41 VAL Chi-restraints excluded: chain L residue 62 GLU Chi-restraints excluded: chain L residue 152 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 82 optimal weight: 3.9990 chunk 174 optimal weight: 5.9990 chunk 124 optimal weight: 1.9990 chunk 198 optimal weight: 0.7980 chunk 200 optimal weight: 0.8980 chunk 85 optimal weight: 0.9990 chunk 196 optimal weight: 2.9990 chunk 105 optimal weight: 8.9990 chunk 207 optimal weight: 6.9990 chunk 92 optimal weight: 3.9990 chunk 154 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 81 GLN E 81 GLN G 81 GLN I 81 GLN L 81 GLN L 224 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.132373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.112111 restraints weight = 35126.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.115728 restraints weight = 14331.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.118099 restraints weight = 7749.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.119562 restraints weight = 5151.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.120437 restraints weight = 4004.685| |-----------------------------------------------------------------------------| r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.3624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 21240 Z= 0.113 Angle : 0.542 10.790 28128 Z= 0.268 Chirality : 0.039 0.324 3024 Planarity : 0.003 0.028 3204 Dihedral : 8.519 59.901 3852 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.43 % Allowed : 24.24 % Favored : 73.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.17), residues: 2304 helix: 1.71 (0.13), residues: 1584 sheet: 1.60 (0.47), residues: 132 loop : -2.02 (0.24), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 76 TYR 0.019 0.001 TYR H 230 PHE 0.041 0.001 PHE H 30 TRP 0.006 0.001 TRP K 45 HIS 0.002 0.001 HIS J 95 Details of bonding type rmsd covalent geometry : bond 0.00265 (21204) covalent geometry : angle 0.54187 (28056) SS BOND : bond 0.00151 ( 36) SS BOND : angle 0.60523 ( 72) hydrogen bonds : bond 0.03367 ( 1139) hydrogen bonds : angle 3.34192 ( 3345) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 571 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 520 time to evaluate : 0.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 ASP cc_start: 0.7460 (t0) cc_final: 0.6877 (t70) REVERT: A 47 ASP cc_start: 0.8927 (p0) cc_final: 0.8455 (p0) REVERT: A 55 ASN cc_start: 0.9059 (t0) cc_final: 0.8542 (t0) REVERT: A 223 LEU cc_start: 0.8826 (mt) cc_final: 0.8623 (mt) REVERT: B 3 ASP cc_start: 0.7456 (t0) cc_final: 0.6672 (t70) REVERT: B 55 ASN cc_start: 0.9031 (t0) cc_final: 0.8674 (t0) REVERT: B 152 LEU cc_start: 0.9116 (OUTLIER) cc_final: 0.8733 (mt) REVERT: B 161 PHE cc_start: 0.8637 (m-80) cc_final: 0.8420 (m-80) REVERT: B 213 MET cc_start: 0.8314 (mmm) cc_final: 0.7253 (mmm) REVERT: B 218 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8717 (mm) REVERT: C 3 ASP cc_start: 0.7547 (t0) cc_final: 0.6830 (t70) REVERT: C 55 ASN cc_start: 0.9021 (t0) cc_final: 0.8765 (t0) REVERT: C 152 LEU cc_start: 0.9076 (OUTLIER) cc_final: 0.8706 (mt) REVERT: D 3 ASP cc_start: 0.7602 (t0) cc_final: 0.7024 (t70) REVERT: D 47 ASP cc_start: 0.8883 (p0) cc_final: 0.8223 (p0) REVERT: D 55 ASN cc_start: 0.9048 (t0) cc_final: 0.8585 (t0) REVERT: E 3 ASP cc_start: 0.7653 (t0) cc_final: 0.7243 (t70) REVERT: E 47 ASP cc_start: 0.9073 (p0) cc_final: 0.8646 (p0) REVERT: E 55 ASN cc_start: 0.9040 (t0) cc_final: 0.8712 (t0) REVERT: E 152 LEU cc_start: 0.9102 (OUTLIER) cc_final: 0.8735 (mt) REVERT: E 218 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8638 (mm) REVERT: F 3 ASP cc_start: 0.7580 (t0) cc_final: 0.6863 (t70) REVERT: F 47 ASP cc_start: 0.8951 (p0) cc_final: 0.8249 (p0) REVERT: F 55 ASN cc_start: 0.9030 (t0) cc_final: 0.8807 (t0) REVERT: F 76 ARG cc_start: 0.8937 (mtt90) cc_final: 0.8598 (mtt90) REVERT: F 103 GLU cc_start: 0.8851 (mm-30) cc_final: 0.8153 (mp0) REVERT: F 152 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8772 (mt) REVERT: F 166 GLU cc_start: 0.8557 (tp30) cc_final: 0.8298 (tp30) REVERT: F 213 MET cc_start: 0.8324 (mmm) cc_final: 0.7485 (mmm) REVERT: G 3 ASP cc_start: 0.7311 (t0) cc_final: 0.6691 (t70) REVERT: G 47 ASP cc_start: 0.8902 (p0) cc_final: 0.8406 (p0) REVERT: G 55 ASN cc_start: 0.9048 (t0) cc_final: 0.8838 (t0) REVERT: G 213 MET cc_start: 0.8335 (mmm) cc_final: 0.7572 (mmm) REVERT: H 3 ASP cc_start: 0.7380 (t0) cc_final: 0.6843 (t70) REVERT: H 42 GLU cc_start: 0.7567 (tp30) cc_final: 0.7266 (tp30) REVERT: H 47 ASP cc_start: 0.8935 (p0) cc_final: 0.8271 (p0) REVERT: H 55 ASN cc_start: 0.9057 (t0) cc_final: 0.8517 (t0) REVERT: H 161 PHE cc_start: 0.8626 (m-80) cc_final: 0.8372 (m-80) REVERT: I 3 ASP cc_start: 0.7566 (t0) cc_final: 0.6818 (t70) REVERT: I 55 ASN cc_start: 0.9041 (t0) cc_final: 0.8707 (t0) REVERT: I 152 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8692 (mt) REVERT: J 3 ASP cc_start: 0.7562 (t0) cc_final: 0.6844 (t70) REVERT: J 47 ASP cc_start: 0.8942 (p0) cc_final: 0.8264 (p0) REVERT: J 55 ASN cc_start: 0.9078 (t0) cc_final: 0.8851 (t0) REVERT: J 76 ARG cc_start: 0.8926 (mtt90) cc_final: 0.8565 (mtt90) REVERT: J 166 GLU cc_start: 0.8557 (tp30) cc_final: 0.8308 (tp30) REVERT: J 213 MET cc_start: 0.8334 (mmm) cc_final: 0.7513 (mmm) REVERT: K 3 ASP cc_start: 0.7534 (t0) cc_final: 0.6954 (t70) REVERT: K 47 ASP cc_start: 0.8864 (p0) cc_final: 0.8247 (p0) REVERT: K 55 ASN cc_start: 0.9091 (t0) cc_final: 0.8633 (t0) REVERT: K 200 LEU cc_start: 0.9112 (mp) cc_final: 0.8864 (mt) REVERT: K 213 MET cc_start: 0.8424 (mmm) cc_final: 0.7434 (mmm) REVERT: L 3 ASP cc_start: 0.7518 (t0) cc_final: 0.6705 (t70) REVERT: L 55 ASN cc_start: 0.9054 (t0) cc_final: 0.8691 (t0) REVERT: L 152 LEU cc_start: 0.9122 (OUTLIER) cc_final: 0.8747 (mt) REVERT: L 161 PHE cc_start: 0.8632 (m-80) cc_final: 0.8422 (m-80) REVERT: L 213 MET cc_start: 0.8378 (mmm) cc_final: 0.7366 (mmm) outliers start: 51 outliers final: 30 residues processed: 531 average time/residue: 0.1375 time to fit residues: 112.3507 Evaluate side-chains 543 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 505 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 232 PHE Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 232 PHE Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 152 LEU Chi-restraints excluded: chain F residue 232 PHE Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 12 ASP Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 232 PHE Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 232 PHE Chi-restraints excluded: chain I residue 41 VAL Chi-restraints excluded: chain I residue 152 LEU Chi-restraints excluded: chain I residue 232 PHE Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 62 GLU Chi-restraints excluded: chain J residue 232 PHE Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 232 PHE Chi-restraints excluded: chain L residue 41 VAL Chi-restraints excluded: chain L residue 62 GLU Chi-restraints excluded: chain L residue 152 LEU Chi-restraints excluded: chain L residue 232 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 189 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 143 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 chunk 90 optimal weight: 0.2980 chunk 184 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 131 optimal weight: 0.7980 chunk 112 optimal weight: 5.9990 chunk 14 optimal weight: 4.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 81 GLN E 81 GLN F 81 GLN G 81 GLN G 224 ASN I 81 GLN J 81 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.135886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.115653 restraints weight = 35051.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.119362 restraints weight = 14303.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.121765 restraints weight = 7697.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.123220 restraints weight = 5095.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.124160 restraints weight = 3966.669| |-----------------------------------------------------------------------------| r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.3860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 21240 Z= 0.097 Angle : 0.540 12.204 28128 Z= 0.263 Chirality : 0.038 0.355 3024 Planarity : 0.003 0.028 3204 Dihedral : 8.029 58.989 3852 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.33 % Allowed : 24.62 % Favored : 73.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.17), residues: 2304 helix: 1.88 (0.13), residues: 1572 sheet: 1.67 (0.47), residues: 132 loop : -2.04 (0.22), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 76 TYR 0.028 0.001 TYR L 155 PHE 0.032 0.001 PHE H 30 TRP 0.005 0.001 TRP K 45 HIS 0.002 0.000 HIS J 95 Details of bonding type rmsd covalent geometry : bond 0.00217 (21204) covalent geometry : angle 0.53971 (28056) SS BOND : bond 0.00107 ( 36) SS BOND : angle 0.47403 ( 72) hydrogen bonds : bond 0.03096 ( 1139) hydrogen bonds : angle 3.29752 ( 3345) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 600 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 551 time to evaluate : 0.571 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 3 ASP cc_start: 0.7418 (t0) cc_final: 0.6807 (t70) REVERT: A 47 ASP cc_start: 0.8871 (p0) cc_final: 0.8224 (p0) REVERT: A 55 ASN cc_start: 0.9003 (t0) cc_final: 0.8466 (t0) REVERT: A 161 PHE cc_start: 0.8564 (m-80) cc_final: 0.8304 (m-80) REVERT: A 212 PHE cc_start: 0.8864 (OUTLIER) cc_final: 0.8517 (t80) REVERT: A 213 MET cc_start: 0.8482 (mmm) cc_final: 0.7422 (mmm) REVERT: B 3 ASP cc_start: 0.7418 (t0) cc_final: 0.6642 (t70) REVERT: B 55 ASN cc_start: 0.8985 (t0) cc_final: 0.8626 (t0) REVERT: B 103 GLU cc_start: 0.8728 (mm-30) cc_final: 0.8170 (mp0) REVERT: B 152 LEU cc_start: 0.9092 (OUTLIER) cc_final: 0.8734 (mt) REVERT: C 3 ASP cc_start: 0.7501 (t0) cc_final: 0.6782 (t70) REVERT: C 47 ASP cc_start: 0.8813 (p0) cc_final: 0.8201 (p0) REVERT: C 55 ASN cc_start: 0.8963 (t0) cc_final: 0.8701 (t0) REVERT: C 152 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8694 (mt) REVERT: C 162 LYS cc_start: 0.7391 (mtpt) cc_final: 0.7147 (mtpp) REVERT: D 3 ASP cc_start: 0.7572 (t0) cc_final: 0.6956 (t70) REVERT: D 55 ASN cc_start: 0.8984 (t0) cc_final: 0.8465 (t0) REVERT: D 213 MET cc_start: 0.8508 (mmm) cc_final: 0.7490 (mmm) REVERT: E 3 ASP cc_start: 0.7595 (t0) cc_final: 0.6897 (t70) REVERT: E 47 ASP cc_start: 0.9043 (p0) cc_final: 0.8585 (p0) REVERT: E 55 ASN cc_start: 0.8982 (t0) cc_final: 0.8654 (t0) REVERT: E 152 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8717 (mt) REVERT: E 218 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8617 (mm) REVERT: F 3 ASP cc_start: 0.7536 (t0) cc_final: 0.6798 (t70) REVERT: F 47 ASP cc_start: 0.8898 (p0) cc_final: 0.8256 (p0) REVERT: F 55 ASN cc_start: 0.8975 (t0) cc_final: 0.8758 (t0) REVERT: F 152 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8741 (mt) REVERT: F 166 GLU cc_start: 0.8547 (tp30) cc_final: 0.8310 (tp30) REVERT: G 3 ASP cc_start: 0.7325 (t0) cc_final: 0.6664 (t70) REVERT: G 47 ASP cc_start: 0.8844 (p0) cc_final: 0.8217 (p0) REVERT: G 55 ASN cc_start: 0.8988 (t0) cc_final: 0.8765 (t0) REVERT: G 103 GLU cc_start: 0.8875 (mm-30) cc_final: 0.8269 (mp0) REVERT: G 213 MET cc_start: 0.8391 (mmm) cc_final: 0.7577 (mmm) REVERT: H 3 ASP cc_start: 0.7373 (t0) cc_final: 0.6803 (t70) REVERT: H 47 ASP cc_start: 0.8885 (p0) cc_final: 0.8366 (p0) REVERT: H 55 ASN cc_start: 0.8997 (t0) cc_final: 0.8465 (t0) REVERT: I 3 ASP cc_start: 0.7540 (t0) cc_final: 0.6760 (t70) REVERT: I 55 ASN cc_start: 0.8999 (t0) cc_final: 0.8672 (t0) REVERT: I 152 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8691 (mt) REVERT: I 161 PHE cc_start: 0.8543 (m-80) cc_final: 0.8327 (m-80) REVERT: I 162 LYS cc_start: 0.7414 (mtpt) cc_final: 0.7144 (mtpp) REVERT: J 3 ASP cc_start: 0.7489 (t0) cc_final: 0.6756 (t70) REVERT: J 47 ASP cc_start: 0.8892 (p0) cc_final: 0.8267 (p0) REVERT: J 55 ASN cc_start: 0.9024 (t0) cc_final: 0.8794 (t0) REVERT: J 152 LEU cc_start: 0.9030 (tt) cc_final: 0.8732 (mt) REVERT: J 166 GLU cc_start: 0.8533 (tp30) cc_final: 0.8309 (tp30) REVERT: K 3 ASP cc_start: 0.7513 (t0) cc_final: 0.6897 (t70) REVERT: K 47 ASP cc_start: 0.8812 (p0) cc_final: 0.8242 (p0) REVERT: K 55 ASN cc_start: 0.9031 (t0) cc_final: 0.8493 (t0) REVERT: K 161 PHE cc_start: 0.8593 (m-80) cc_final: 0.8332 (m-80) REVERT: K 213 MET cc_start: 0.8391 (mmm) cc_final: 0.7272 (mmm) REVERT: L 3 ASP cc_start: 0.7487 (t0) cc_final: 0.6681 (t70) REVERT: L 55 ASN cc_start: 0.9000 (t0) cc_final: 0.8633 (t0) REVERT: L 103 GLU cc_start: 0.8795 (mm-30) cc_final: 0.8224 (mp0) REVERT: L 152 LEU cc_start: 0.9086 (OUTLIER) cc_final: 0.8736 (mt) REVERT: L 213 MET cc_start: 0.8284 (mmm) cc_final: 0.7168 (mmm) outliers start: 49 outliers final: 28 residues processed: 562 average time/residue: 0.1382 time to fit residues: 119.8129 Evaluate side-chains 549 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 513 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 232 PHE Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 232 PHE Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 152 LEU Chi-restraints excluded: chain F residue 232 PHE Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 232 PHE Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 232 PHE Chi-restraints excluded: chain I residue 41 VAL Chi-restraints excluded: chain I residue 152 LEU Chi-restraints excluded: chain I residue 232 PHE Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 62 GLU Chi-restraints excluded: chain J residue 232 PHE Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 232 PHE Chi-restraints excluded: chain L residue 41 VAL Chi-restraints excluded: chain L residue 62 GLU Chi-restraints excluded: chain L residue 152 LEU Chi-restraints excluded: chain L residue 232 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 126 optimal weight: 0.9980 chunk 42 optimal weight: 7.9990 chunk 8 optimal weight: 0.9990 chunk 226 optimal weight: 1.9990 chunk 148 optimal weight: 7.9990 chunk 52 optimal weight: 10.0000 chunk 111 optimal weight: 6.9990 chunk 146 optimal weight: 3.9990 chunk 78 optimal weight: 0.9990 chunk 68 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 81 GLN F 81 GLN G 81 GLN H 224 ASN I 81 GLN J 81 GLN L 81 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.133918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.113833 restraints weight = 35157.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.117435 restraints weight = 14320.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.119848 restraints weight = 7708.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.121252 restraints weight = 5108.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.122178 restraints weight = 3999.091| |-----------------------------------------------------------------------------| r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.3851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 21240 Z= 0.125 Angle : 0.583 11.559 28128 Z= 0.285 Chirality : 0.041 0.361 3024 Planarity : 0.003 0.028 3204 Dihedral : 8.246 57.166 3852 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.43 % Allowed : 25.19 % Favored : 72.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.17), residues: 2304 helix: 1.74 (0.13), residues: 1584 sheet: 1.62 (0.47), residues: 132 loop : -1.99 (0.23), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 53 TYR 0.029 0.001 TYR H 155 PHE 0.027 0.001 PHE H 30 TRP 0.006 0.001 TRP K 45 HIS 0.002 0.001 HIS D 74 Details of bonding type rmsd covalent geometry : bond 0.00298 (21204) covalent geometry : angle 0.58288 (28056) SS BOND : bond 0.00177 ( 36) SS BOND : angle 0.64060 ( 72) hydrogen bonds : bond 0.03403 ( 1139) hydrogen bonds : angle 3.52308 ( 3345) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 582 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 531 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 3 ASP cc_start: 0.7473 (t0) cc_final: 0.6855 (t70) REVERT: A 47 ASP cc_start: 0.8900 (p0) cc_final: 0.8223 (p0) REVERT: A 55 ASN cc_start: 0.9061 (t0) cc_final: 0.8618 (t0) REVERT: A 213 MET cc_start: 0.8431 (mmm) cc_final: 0.7372 (mmm) REVERT: B 3 ASP cc_start: 0.7483 (t0) cc_final: 0.6709 (t70) REVERT: B 55 ASN cc_start: 0.9036 (t0) cc_final: 0.8693 (t0) REVERT: B 103 GLU cc_start: 0.8769 (mm-30) cc_final: 0.8156 (mp0) REVERT: B 152 LEU cc_start: 0.9115 (OUTLIER) cc_final: 0.8769 (mt) REVERT: B 213 MET cc_start: 0.8453 (mmm) cc_final: 0.7353 (mmm) REVERT: B 218 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8672 (mm) REVERT: C 3 ASP cc_start: 0.7550 (t0) cc_final: 0.6836 (t70) REVERT: C 47 ASP cc_start: 0.8833 (p0) cc_final: 0.8205 (p0) REVERT: C 55 ASN cc_start: 0.9037 (t0) cc_final: 0.8781 (t0) REVERT: C 152 LEU cc_start: 0.9095 (OUTLIER) cc_final: 0.8724 (mt) REVERT: C 162 LYS cc_start: 0.7457 (mtpt) cc_final: 0.7237 (mtpp) REVERT: D 3 ASP cc_start: 0.7569 (t0) cc_final: 0.6994 (t70) REVERT: D 47 ASP cc_start: 0.8857 (p0) cc_final: 0.8207 (p0) REVERT: D 55 ASN cc_start: 0.9063 (t0) cc_final: 0.8610 (t0) REVERT: D 98 TYR cc_start: 0.8707 (m-80) cc_final: 0.8381 (m-80) REVERT: D 161 PHE cc_start: 0.8661 (m-80) cc_final: 0.8424 (m-80) REVERT: D 213 MET cc_start: 0.8450 (mmm) cc_final: 0.7416 (mmm) REVERT: E 3 ASP cc_start: 0.7601 (t0) cc_final: 0.7176 (t70) REVERT: E 47 ASP cc_start: 0.9021 (p0) cc_final: 0.8543 (p0) REVERT: E 55 ASN cc_start: 0.9048 (t0) cc_final: 0.8718 (t0) REVERT: E 152 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8734 (mt) REVERT: E 218 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8646 (mm) REVERT: F 3 ASP cc_start: 0.7572 (t0) cc_final: 0.6837 (t70) REVERT: F 47 ASP cc_start: 0.8920 (p0) cc_final: 0.8263 (p0) REVERT: F 55 ASN cc_start: 0.9041 (t0) cc_final: 0.8583 (t0) REVERT: F 76 ARG cc_start: 0.8928 (mtt90) cc_final: 0.8670 (mtt90) REVERT: F 152 LEU cc_start: 0.9115 (OUTLIER) cc_final: 0.8773 (mt) REVERT: G 3 ASP cc_start: 0.7402 (t0) cc_final: 0.6776 (t70) REVERT: G 47 ASP cc_start: 0.8865 (p0) cc_final: 0.8217 (p0) REVERT: G 55 ASN cc_start: 0.9037 (t0) cc_final: 0.8822 (t0) REVERT: G 213 MET cc_start: 0.8399 (mmm) cc_final: 0.7555 (mmm) REVERT: H 3 ASP cc_start: 0.7462 (t0) cc_final: 0.6880 (t70) REVERT: H 47 ASP cc_start: 0.8926 (p0) cc_final: 0.8408 (p0) REVERT: H 55 ASN cc_start: 0.9068 (t0) cc_final: 0.8610 (t0) REVERT: H 213 MET cc_start: 0.8430 (mmm) cc_final: 0.7630 (mmm) REVERT: I 3 ASP cc_start: 0.7562 (t0) cc_final: 0.6827 (t70) REVERT: I 55 ASN cc_start: 0.9062 (t0) cc_final: 0.8743 (t0) REVERT: I 152 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8707 (mt) REVERT: I 162 LYS cc_start: 0.7445 (mtpt) cc_final: 0.7177 (mtpp) REVERT: J 3 ASP cc_start: 0.7542 (t0) cc_final: 0.6803 (t70) REVERT: J 47 ASP cc_start: 0.8906 (p0) cc_final: 0.8278 (p0) REVERT: J 55 ASN cc_start: 0.9082 (t0) cc_final: 0.8863 (t0) REVERT: J 76 ARG cc_start: 0.8917 (mtt90) cc_final: 0.8658 (mtt90) REVERT: J 152 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8702 (mt) REVERT: J 213 MET cc_start: 0.8341 (mmm) cc_final: 0.7569 (mmm) REVERT: K 3 ASP cc_start: 0.7522 (t0) cc_final: 0.6947 (t70) REVERT: K 47 ASP cc_start: 0.8858 (p0) cc_final: 0.8242 (p0) REVERT: K 55 ASN cc_start: 0.9083 (t0) cc_final: 0.8613 (t0) REVERT: K 213 MET cc_start: 0.8369 (mmm) cc_final: 0.7246 (mmm) REVERT: L 3 ASP cc_start: 0.7525 (t0) cc_final: 0.6735 (t70) REVERT: L 47 ASP cc_start: 0.8896 (p0) cc_final: 0.8194 (p0) REVERT: L 55 ASN cc_start: 0.9057 (t0) cc_final: 0.8692 (t0) REVERT: L 103 GLU cc_start: 0.8830 (mm-30) cc_final: 0.8176 (mp0) REVERT: L 152 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8734 (mt) REVERT: L 213 MET cc_start: 0.8300 (mmm) cc_final: 0.7147 (mmm) outliers start: 51 outliers final: 32 residues processed: 544 average time/residue: 0.1356 time to fit residues: 113.9424 Evaluate side-chains 561 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 520 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 232 PHE Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 232 PHE Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 152 LEU Chi-restraints excluded: chain F residue 232 PHE Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 232 PHE Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 232 PHE Chi-restraints excluded: chain I residue 41 VAL Chi-restraints excluded: chain I residue 152 LEU Chi-restraints excluded: chain I residue 232 PHE Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 56 THR Chi-restraints excluded: chain J residue 62 GLU Chi-restraints excluded: chain J residue 152 LEU Chi-restraints excluded: chain J residue 218 LEU Chi-restraints excluded: chain J residue 232 PHE Chi-restraints excluded: chain K residue 34 ILE Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 232 PHE Chi-restraints excluded: chain L residue 41 VAL Chi-restraints excluded: chain L residue 62 GLU Chi-restraints excluded: chain L residue 152 LEU Chi-restraints excluded: chain L residue 232 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 53 optimal weight: 30.0000 chunk 164 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 158 optimal weight: 4.9990 chunk 167 optimal weight: 0.0370 chunk 32 optimal weight: 9.9990 chunk 118 optimal weight: 3.9990 chunk 57 optimal weight: 10.0000 chunk 87 optimal weight: 6.9990 chunk 63 optimal weight: 2.9990 chunk 129 optimal weight: 5.9990 overall best weight: 2.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 81 GLN G 81 GLN I 81 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.130196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.110335 restraints weight = 35497.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.113885 restraints weight = 14529.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.116215 restraints weight = 7866.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.117661 restraints weight = 5226.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.118468 restraints weight = 4058.092| |-----------------------------------------------------------------------------| r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.3783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 21240 Z= 0.150 Angle : 0.609 11.116 28128 Z= 0.299 Chirality : 0.042 0.354 3024 Planarity : 0.003 0.029 3204 Dihedral : 8.666 59.409 3852 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.19 % Allowed : 26.24 % Favored : 71.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.17), residues: 2304 helix: 1.69 (0.13), residues: 1584 sheet: 1.56 (0.47), residues: 132 loop : -2.00 (0.23), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 76 TYR 0.035 0.001 TYR I 155 PHE 0.026 0.001 PHE H 30 TRP 0.007 0.001 TRP K 45 HIS 0.002 0.001 HIS D 74 Details of bonding type rmsd covalent geometry : bond 0.00362 (21204) covalent geometry : angle 0.60887 (28056) SS BOND : bond 0.00225 ( 36) SS BOND : angle 0.77662 ( 72) hydrogen bonds : bond 0.03625 ( 1139) hydrogen bonds : angle 3.60884 ( 3345) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 558 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 512 time to evaluate : 0.683 Fit side-chains revert: symmetry clash REVERT: A 3 ASP cc_start: 0.7509 (t0) cc_final: 0.6885 (t70) REVERT: A 47 ASP cc_start: 0.8931 (p0) cc_final: 0.8240 (p0) REVERT: A 55 ASN cc_start: 0.9094 (t0) cc_final: 0.8637 (t0) REVERT: A 161 PHE cc_start: 0.8640 (m-80) cc_final: 0.8408 (m-80) REVERT: A 213 MET cc_start: 0.8434 (mmm) cc_final: 0.7364 (mmm) REVERT: B 3 ASP cc_start: 0.7472 (t0) cc_final: 0.6702 (t70) REVERT: B 47 ASP cc_start: 0.8839 (p0) cc_final: 0.8068 (p0) REVERT: B 55 ASN cc_start: 0.9084 (t0) cc_final: 0.8729 (t0) REVERT: B 103 GLU cc_start: 0.8830 (mm-30) cc_final: 0.8163 (mp0) REVERT: B 152 LEU cc_start: 0.9140 (OUTLIER) cc_final: 0.8746 (mt) REVERT: B 213 MET cc_start: 0.8437 (mmm) cc_final: 0.7333 (mmm) REVERT: B 218 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8678 (mm) REVERT: C 3 ASP cc_start: 0.7566 (t0) cc_final: 0.6850 (t70) REVERT: C 47 ASP cc_start: 0.8857 (p0) cc_final: 0.8212 (p0) REVERT: C 55 ASN cc_start: 0.9062 (t0) cc_final: 0.8802 (t0) REVERT: C 103 GLU cc_start: 0.8742 (mm-30) cc_final: 0.8031 (mp0) REVERT: C 152 LEU cc_start: 0.9132 (OUTLIER) cc_final: 0.8737 (mt) REVERT: C 162 LYS cc_start: 0.7506 (mtpt) cc_final: 0.7262 (mtpp) REVERT: D 3 ASP cc_start: 0.7582 (t0) cc_final: 0.6976 (t70) REVERT: D 47 ASP cc_start: 0.8902 (p0) cc_final: 0.8224 (p0) REVERT: D 55 ASN cc_start: 0.9110 (t0) cc_final: 0.8650 (t0) REVERT: D 98 TYR cc_start: 0.8693 (m-80) cc_final: 0.8425 (m-80) REVERT: D 213 MET cc_start: 0.8443 (mmm) cc_final: 0.7407 (mmm) REVERT: E 3 ASP cc_start: 0.7584 (t0) cc_final: 0.7144 (t70) REVERT: E 47 ASP cc_start: 0.9065 (p0) cc_final: 0.8581 (p0) REVERT: E 55 ASN cc_start: 0.9063 (t0) cc_final: 0.8758 (t0) REVERT: E 152 LEU cc_start: 0.9119 (OUTLIER) cc_final: 0.8727 (mt) REVERT: E 161 PHE cc_start: 0.8727 (m-80) cc_final: 0.8512 (m-80) REVERT: E 213 MET cc_start: 0.8462 (mmm) cc_final: 0.7116 (mmm) REVERT: E 218 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8661 (mm) REVERT: F 3 ASP cc_start: 0.7583 (t0) cc_final: 0.6840 (t70) REVERT: F 42 GLU cc_start: 0.7990 (tp30) cc_final: 0.7764 (tp30) REVERT: F 47 ASP cc_start: 0.8969 (p0) cc_final: 0.8286 (p0) REVERT: F 55 ASN cc_start: 0.9076 (t0) cc_final: 0.8847 (t0) REVERT: F 76 ARG cc_start: 0.8959 (mtt90) cc_final: 0.8643 (mtt90) REVERT: F 152 LEU cc_start: 0.9135 (OUTLIER) cc_final: 0.8711 (mt) REVERT: F 213 MET cc_start: 0.8405 (mmm) cc_final: 0.7521 (mmm) REVERT: G 3 ASP cc_start: 0.7475 (t0) cc_final: 0.6822 (t70) REVERT: G 47 ASP cc_start: 0.8893 (p0) cc_final: 0.8235 (p0) REVERT: G 55 ASN cc_start: 0.9069 (t0) cc_final: 0.8852 (t0) REVERT: G 213 MET cc_start: 0.8397 (mmm) cc_final: 0.7523 (mmm) REVERT: H 3 ASP cc_start: 0.7518 (t0) cc_final: 0.6902 (t70) REVERT: H 47 ASP cc_start: 0.8948 (p0) cc_final: 0.8437 (p0) REVERT: H 55 ASN cc_start: 0.9115 (t0) cc_final: 0.8669 (t0) REVERT: H 213 MET cc_start: 0.8457 (mmm) cc_final: 0.7626 (mmm) REVERT: I 3 ASP cc_start: 0.7605 (t0) cc_final: 0.6858 (t70) REVERT: I 47 ASP cc_start: 0.8739 (p0) cc_final: 0.8008 (p0) REVERT: I 55 ASN cc_start: 0.9085 (t0) cc_final: 0.8785 (t0) REVERT: I 152 LEU cc_start: 0.9141 (OUTLIER) cc_final: 0.8779 (mt) REVERT: I 218 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8735 (mm) REVERT: J 3 ASP cc_start: 0.7545 (t0) cc_final: 0.6797 (t70) REVERT: J 47 ASP cc_start: 0.8937 (p0) cc_final: 0.8296 (p0) REVERT: J 55 ASN cc_start: 0.9112 (t0) cc_final: 0.8885 (t0) REVERT: J 76 ARG cc_start: 0.8938 (mtt90) cc_final: 0.8630 (mtt90) REVERT: J 152 LEU cc_start: 0.9101 (OUTLIER) cc_final: 0.8689 (mt) REVERT: J 213 MET cc_start: 0.8349 (mmm) cc_final: 0.7595 (mmm) REVERT: K 3 ASP cc_start: 0.7561 (t0) cc_final: 0.6972 (t70) REVERT: K 47 ASP cc_start: 0.8905 (p0) cc_final: 0.8283 (p0) REVERT: K 55 ASN cc_start: 0.9128 (t0) cc_final: 0.8650 (t0) REVERT: K 161 PHE cc_start: 0.8672 (m-80) cc_final: 0.8439 (m-80) REVERT: L 3 ASP cc_start: 0.7549 (t0) cc_final: 0.6771 (t70) REVERT: L 47 ASP cc_start: 0.8948 (p0) cc_final: 0.8242 (p0) REVERT: L 55 ASN cc_start: 0.9097 (t0) cc_final: 0.8758 (t0) REVERT: L 152 LEU cc_start: 0.9133 (OUTLIER) cc_final: 0.8751 (mt) REVERT: L 213 MET cc_start: 0.8303 (mmm) cc_final: 0.7195 (mmm) outliers start: 46 outliers final: 24 residues processed: 526 average time/residue: 0.1385 time to fit residues: 112.2703 Evaluate side-chains 544 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 510 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 152 LEU Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain I residue 41 VAL Chi-restraints excluded: chain I residue 152 LEU Chi-restraints excluded: chain I residue 218 LEU Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 56 THR Chi-restraints excluded: chain J residue 62 GLU Chi-restraints excluded: chain J residue 152 LEU Chi-restraints excluded: chain J residue 218 LEU Chi-restraints excluded: chain J residue 232 PHE Chi-restraints excluded: chain K residue 34 ILE Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain L residue 41 VAL Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 62 GLU Chi-restraints excluded: chain L residue 152 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 34 optimal weight: 20.0000 chunk 210 optimal weight: 10.0000 chunk 46 optimal weight: 0.6980 chunk 154 optimal weight: 0.9990 chunk 156 optimal weight: 0.9980 chunk 205 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 133 optimal weight: 1.9990 chunk 204 optimal weight: 0.9980 chunk 172 optimal weight: 4.9990 chunk 200 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 81 GLN E 63 ASN E 81 GLN G 81 GLN I 63 ASN I 81 GLN J 81 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.135043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.115188 restraints weight = 34982.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.118854 restraints weight = 14185.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.121228 restraints weight = 7613.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.122696 restraints weight = 5021.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.123618 restraints weight = 3887.109| |-----------------------------------------------------------------------------| r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.4013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 21240 Z= 0.107 Angle : 0.582 11.829 28128 Z= 0.281 Chirality : 0.041 0.375 3024 Planarity : 0.003 0.027 3204 Dihedral : 8.074 56.887 3852 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.67 % Allowed : 26.76 % Favored : 71.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.17), residues: 2304 helix: 1.80 (0.13), residues: 1572 sheet: 1.61 (0.47), residues: 132 loop : -2.07 (0.21), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 76 TYR 0.033 0.001 TYR I 155 PHE 0.023 0.001 PHE H 30 TRP 0.005 0.001 TRP K 45 HIS 0.002 0.001 HIS J 95 Details of bonding type rmsd covalent geometry : bond 0.00244 (21204) covalent geometry : angle 0.58240 (28056) SS BOND : bond 0.00126 ( 36) SS BOND : angle 0.55931 ( 72) hydrogen bonds : bond 0.03297 ( 1139) hydrogen bonds : angle 3.51281 ( 3345) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3772.02 seconds wall clock time: 65 minutes 37.92 seconds (3937.92 seconds total)