Starting phenix.real_space_refine on Wed Jan 14 20:31:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bd4_15974/01_2026/8bd4_15974_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bd4_15974/01_2026/8bd4_15974.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8bd4_15974/01_2026/8bd4_15974_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bd4_15974/01_2026/8bd4_15974_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8bd4_15974/01_2026/8bd4_15974.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bd4_15974/01_2026/8bd4_15974.map" } resolution = 3.44 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 6 6.06 5 P 53 5.49 5 Mg 7 5.21 5 S 98 5.16 5 C 11814 2.51 5 N 3481 2.21 5 O 3543 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 49 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19002 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 2060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2060 Classifications: {'peptide': 260} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 9, 'TRANS': 250} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 2060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2060 Classifications: {'peptide': 260} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 9, 'TRANS': 250} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "C" Number of atoms: 2060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2060 Classifications: {'peptide': 260} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 9, 'TRANS': 250} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "D" Number of atoms: 2060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2060 Classifications: {'peptide': 260} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 9, 'TRANS': 250} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "E" Number of atoms: 2060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2060 Classifications: {'peptide': 260} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 9, 'TRANS': 250} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "F" Number of atoms: 2060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2060 Classifications: {'peptide': 260} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 9, 'TRANS': 250} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "G" Number of atoms: 2060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2060 Classifications: {'peptide': 260} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 9, 'TRANS': 250} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "R" Number of atoms: 1232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1232 Classifications: {'peptide': 155} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 143} Chain: "S" Number of atoms: 1232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1232 Classifications: {'peptide': 155} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 143} Chain: "T" Number of atoms: 1232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1232 Classifications: {'peptide': 155} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 143} Chain: "U" Number of atoms: 328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 328 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Chain: "V" Number of atoms: 328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 328 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 16621 SG CYS S 133 51.815 93.107 30.604 1.00 30.00 S ATOM 16642 SG CYS S 136 55.020 92.672 32.790 1.00 30.00 S ATOM 16758 SG CYS S 151 52.366 90.200 33.003 1.00 30.00 S ATOM 16785 SG CYS S 154 51.583 93.699 34.264 1.00 30.00 S ATOM 15389 SG CYS R 133 92.843 67.172 54.516 1.00 30.00 S ATOM 15410 SG CYS R 136 90.970 64.717 56.904 1.00 30.00 S ATOM 15526 SG CYS R 151 90.317 68.282 57.143 1.00 30.00 S ATOM 15553 SG CYS R 154 93.795 67.087 58.105 1.00 30.00 S ATOM 15114 SG CYS R 100 95.296 76.297 43.807 1.00 30.00 S ATOM 15129 SG CYS R 103 94.230 79.959 43.196 1.00 30.00 S ATOM 15298 SG CYS R 122 95.044 78.001 40.238 1.00 30.00 S ATOM 16346 SG CYS S 100 42.192 91.060 20.250 1.00 30.00 S ATOM 16361 SG CYS S 103 39.629 88.249 19.581 1.00 30.00 S ATOM 16530 SG CYS S 122 40.686 90.191 16.688 1.00 30.00 S ATOM 17853 SG CYS T 133 50.765 46.267 42.986 1.00 30.00 S ATOM 17874 SG CYS T 136 49.732 49.139 45.421 1.00 30.00 S ATOM 17990 SG CYS T 151 53.179 47.992 45.373 1.00 30.00 S ATOM 18017 SG CYS T 154 50.554 45.543 46.623 1.00 30.00 S ATOM 17578 SG CYS T 100 56.600 39.506 31.840 1.00 30.00 S ATOM 17593 SG CYS T 103 60.254 38.659 30.918 1.00 30.00 S ATOM 17762 SG CYS T 122 57.890 38.835 28.154 1.00 30.00 S Time building chain proxies: 3.81, per 1000 atoms: 0.20 Number of scatterers: 19002 At special positions: 0 Unit cell: (132.6, 137.8, 131.95, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 6 29.99 S 98 16.00 P 53 15.00 Mg 7 11.99 O 3543 8.00 N 3481 7.00 C 11814 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=33, symmetry=0 Number of additional bonds: simple=33, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.03 Conformation dependent library (CDL) restraints added in 783.6 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 303 " pdb="ZN ZN A 303 " - pdb=" SG CYS S 154 " pdb="ZN ZN A 303 " - pdb=" SG CYS S 151 " pdb="ZN ZN A 303 " - pdb=" SG CYS S 136 " pdb="ZN ZN A 303 " - pdb=" SG CYS S 133 " pdb=" ZN E 303 " pdb="ZN ZN E 303 " - pdb=" SG CYS R 154 " pdb="ZN ZN E 303 " - pdb=" SG CYS R 151 " pdb="ZN ZN E 303 " - pdb=" SG CYS R 136 " pdb="ZN ZN E 303 " - pdb=" SG CYS R 133 " pdb=" ZN R 201 " pdb="ZN ZN R 201 " - pdb=" ND1 HIS R 125 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 103 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 122 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 100 " pdb=" ZN S 201 " pdb="ZN ZN S 201 " - pdb=" ND1 HIS S 125 " pdb="ZN ZN S 201 " - pdb=" SG CYS S 103 " pdb="ZN ZN S 201 " - pdb=" SG CYS S 122 " pdb="ZN ZN S 201 " - pdb=" SG CYS S 100 " pdb=" ZN T 201 " pdb="ZN ZN T 201 " - pdb=" SG CYS T 154 " pdb="ZN ZN T 201 " - pdb=" SG CYS T 151 " pdb="ZN ZN T 201 " - pdb=" SG CYS T 136 " pdb="ZN ZN T 201 " - pdb=" SG CYS T 133 " pdb=" ZN T 202 " pdb="ZN ZN T 202 " - pdb=" ND1 HIS T 125 " pdb="ZN ZN T 202 " - pdb=" SG CYS T 103 " pdb="ZN ZN T 202 " - pdb=" SG CYS T 122 " pdb="ZN ZN T 202 " - pdb=" SG CYS T 100 " Number of angles added : 27 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4286 Finding SS restraints... Secondary structure from input PDB file: 114 helices and 10 sheets defined 60.5% alpha, 3.0% beta 16 base pairs and 30 stacking pairs defined. Time for finding SS restraints: 2.09 Creating SS restraints... Processing helix chain 'A' and resid 17 through 30 Processing helix chain 'A' and resid 36 through 52 removed outlier: 3.728A pdb=" N ALA A 52 " --> pdb=" O GLY A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 77 removed outlier: 3.752A pdb=" N ALA A 69 " --> pdb=" O GLY A 65 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N HIS A 77 " --> pdb=" O TYR A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 113 Processing helix chain 'A' and resid 121 through 136 Processing helix chain 'A' and resid 150 through 164 removed outlier: 3.641A pdb=" N PHE A 154 " --> pdb=" O LYS A 150 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ALA A 155 " --> pdb=" O PRO A 151 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ASP A 156 " --> pdb=" O GLU A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 182 removed outlier: 4.065A pdb=" N ASP A 177 " --> pdb=" O THR A 173 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA A 178 " --> pdb=" O ASP A 174 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG A 182 " --> pdb=" O ALA A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 190 removed outlier: 3.662A pdb=" N GLU A 188 " --> pdb=" O GLU A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 215 Processing helix chain 'A' and resid 226 through 238 Processing helix chain 'A' and resid 240 through 258 Processing helix chain 'A' and resid 264 through 276 removed outlier: 3.822A pdb=" N LEU A 268 " --> pdb=" O ASP A 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 30 Processing helix chain 'B' and resid 36 through 52 removed outlier: 3.727A pdb=" N ALA B 52 " --> pdb=" O GLY B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 77 removed outlier: 3.752A pdb=" N ALA B 69 " --> pdb=" O GLY B 65 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N HIS B 77 " --> pdb=" O TYR B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 113 Processing helix chain 'B' and resid 121 through 136 Processing helix chain 'B' and resid 150 through 164 removed outlier: 3.641A pdb=" N PHE B 154 " --> pdb=" O LYS B 150 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ALA B 155 " --> pdb=" O PRO B 151 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N ASP B 156 " --> pdb=" O GLU B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 182 removed outlier: 4.066A pdb=" N ASP B 177 " --> pdb=" O THR B 173 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA B 178 " --> pdb=" O ASP B 174 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG B 182 " --> pdb=" O ALA B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 190 removed outlier: 3.662A pdb=" N GLU B 188 " --> pdb=" O GLU B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 215 Processing helix chain 'B' and resid 226 through 238 Processing helix chain 'B' and resid 240 through 258 Processing helix chain 'B' and resid 264 through 276 removed outlier: 3.822A pdb=" N LEU B 268 " --> pdb=" O ASP B 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 30 Processing helix chain 'C' and resid 36 through 52 removed outlier: 3.728A pdb=" N ALA C 52 " --> pdb=" O GLY C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 77 removed outlier: 3.751A pdb=" N ALA C 69 " --> pdb=" O GLY C 65 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N HIS C 77 " --> pdb=" O TYR C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 113 Processing helix chain 'C' and resid 121 through 136 Processing helix chain 'C' and resid 150 through 164 removed outlier: 3.641A pdb=" N PHE C 154 " --> pdb=" O LYS C 150 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ALA C 155 " --> pdb=" O PRO C 151 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N ASP C 156 " --> pdb=" O GLU C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 182 removed outlier: 4.065A pdb=" N ASP C 177 " --> pdb=" O THR C 173 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA C 178 " --> pdb=" O ASP C 174 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG C 182 " --> pdb=" O ALA C 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 190 removed outlier: 3.663A pdb=" N GLU C 188 " --> pdb=" O GLU C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 215 Processing helix chain 'C' and resid 226 through 238 Processing helix chain 'C' and resid 240 through 258 Processing helix chain 'C' and resid 264 through 276 removed outlier: 3.822A pdb=" N LEU C 268 " --> pdb=" O ASP C 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 30 Processing helix chain 'D' and resid 36 through 52 removed outlier: 3.728A pdb=" N ALA D 52 " --> pdb=" O GLY D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 77 removed outlier: 3.752A pdb=" N ALA D 69 " --> pdb=" O GLY D 65 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N HIS D 77 " --> pdb=" O TYR D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 113 Processing helix chain 'D' and resid 121 through 136 Processing helix chain 'D' and resid 150 through 164 removed outlier: 3.641A pdb=" N PHE D 154 " --> pdb=" O LYS D 150 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ALA D 155 " --> pdb=" O PRO D 151 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N ASP D 156 " --> pdb=" O GLU D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 182 removed outlier: 4.065A pdb=" N ASP D 177 " --> pdb=" O THR D 173 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA D 178 " --> pdb=" O ASP D 174 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG D 182 " --> pdb=" O ALA D 178 " (cutoff:3.500A) Processing helix chain 'D' and resid 184 through 190 removed outlier: 3.662A pdb=" N GLU D 188 " --> pdb=" O GLU D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 201 through 215 Processing helix chain 'D' and resid 226 through 238 Processing helix chain 'D' and resid 240 through 258 Processing helix chain 'D' and resid 264 through 276 removed outlier: 3.822A pdb=" N LEU D 268 " --> pdb=" O ASP D 264 " (cutoff:3.500A) Processing helix chain 'E' and resid 18 through 30 Processing helix chain 'E' and resid 36 through 52 removed outlier: 3.728A pdb=" N ALA E 52 " --> pdb=" O GLY E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 77 removed outlier: 3.752A pdb=" N ALA E 69 " --> pdb=" O GLY E 65 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N HIS E 77 " --> pdb=" O TYR E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 101 through 113 Processing helix chain 'E' and resid 121 through 136 Processing helix chain 'E' and resid 150 through 164 removed outlier: 3.642A pdb=" N PHE E 154 " --> pdb=" O LYS E 150 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ALA E 155 " --> pdb=" O PRO E 151 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N ASP E 156 " --> pdb=" O GLU E 152 " (cutoff:3.500A) Processing helix chain 'E' and resid 173 through 182 removed outlier: 4.066A pdb=" N ASP E 177 " --> pdb=" O THR E 173 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA E 178 " --> pdb=" O ASP E 174 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG E 182 " --> pdb=" O ALA E 178 " (cutoff:3.500A) Processing helix chain 'E' and resid 184 through 190 removed outlier: 3.663A pdb=" N GLU E 188 " --> pdb=" O GLU E 184 " (cutoff:3.500A) Processing helix chain 'E' and resid 201 through 215 Processing helix chain 'E' and resid 226 through 238 Processing helix chain 'E' and resid 240 through 258 Processing helix chain 'E' and resid 264 through 276 removed outlier: 3.822A pdb=" N LEU E 268 " --> pdb=" O ASP E 264 " (cutoff:3.500A) Processing helix chain 'F' and resid 18 through 30 Processing helix chain 'F' and resid 36 through 52 removed outlier: 3.729A pdb=" N ALA F 52 " --> pdb=" O GLY F 48 " (cutoff:3.500A) Processing helix chain 'F' and resid 65 through 77 removed outlier: 3.752A pdb=" N ALA F 69 " --> pdb=" O GLY F 65 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N HIS F 77 " --> pdb=" O TYR F 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 101 through 113 Processing helix chain 'F' and resid 121 through 136 Processing helix chain 'F' and resid 150 through 164 removed outlier: 3.641A pdb=" N PHE F 154 " --> pdb=" O LYS F 150 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ALA F 155 " --> pdb=" O PRO F 151 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N ASP F 156 " --> pdb=" O GLU F 152 " (cutoff:3.500A) Processing helix chain 'F' and resid 173 through 182 removed outlier: 4.066A pdb=" N ASP F 177 " --> pdb=" O THR F 173 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA F 178 " --> pdb=" O ASP F 174 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG F 182 " --> pdb=" O ALA F 178 " (cutoff:3.500A) Processing helix chain 'F' and resid 184 through 190 removed outlier: 3.662A pdb=" N GLU F 188 " --> pdb=" O GLU F 184 " (cutoff:3.500A) Processing helix chain 'F' and resid 201 through 215 Processing helix chain 'F' and resid 226 through 238 Processing helix chain 'F' and resid 240 through 258 Processing helix chain 'F' and resid 264 through 276 removed outlier: 3.822A pdb=" N LEU F 268 " --> pdb=" O ASP F 264 " (cutoff:3.500A) Processing helix chain 'G' and resid 18 through 30 Processing helix chain 'G' and resid 36 through 52 removed outlier: 3.728A pdb=" N ALA G 52 " --> pdb=" O GLY G 48 " (cutoff:3.500A) Processing helix chain 'G' and resid 65 through 77 removed outlier: 3.752A pdb=" N ALA G 69 " --> pdb=" O GLY G 65 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N HIS G 77 " --> pdb=" O TYR G 73 " (cutoff:3.500A) Processing helix chain 'G' and resid 101 through 113 Processing helix chain 'G' and resid 121 through 136 Processing helix chain 'G' and resid 150 through 164 removed outlier: 3.642A pdb=" N PHE G 154 " --> pdb=" O LYS G 150 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ALA G 155 " --> pdb=" O PRO G 151 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N ASP G 156 " --> pdb=" O GLU G 152 " (cutoff:3.500A) Processing helix chain 'G' and resid 173 through 182 removed outlier: 4.066A pdb=" N ASP G 177 " --> pdb=" O THR G 173 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA G 178 " --> pdb=" O ASP G 174 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG G 182 " --> pdb=" O ALA G 178 " (cutoff:3.500A) Processing helix chain 'G' and resid 184 through 190 removed outlier: 3.663A pdb=" N GLU G 188 " --> pdb=" O GLU G 184 " (cutoff:3.500A) Processing helix chain 'G' and resid 201 through 215 Processing helix chain 'G' and resid 226 through 238 Processing helix chain 'G' and resid 240 through 258 Processing helix chain 'G' and resid 264 through 276 removed outlier: 3.822A pdb=" N LEU G 268 " --> pdb=" O ASP G 264 " (cutoff:3.500A) Processing helix chain 'R' and resid 21 through 33 Processing helix chain 'R' and resid 36 through 44 Processing helix chain 'R' and resid 48 through 55 Processing helix chain 'R' and resid 63 through 75 removed outlier: 3.627A pdb=" N VAL R 73 " --> pdb=" O ALA R 69 " (cutoff:3.500A) Processing helix chain 'R' and resid 77 through 83 Processing helix chain 'R' and resid 100 through 107 Processing helix chain 'R' and resid 111 through 116 Processing helix chain 'R' and resid 142 through 146 Processing helix chain 'R' and resid 157 through 162 removed outlier: 3.779A pdb=" N ALA R 162 " --> pdb=" O PHE R 158 " (cutoff:3.500A) Processing helix chain 'R' and resid 163 through 165 No H-bonds generated for 'chain 'R' and resid 163 through 165' Processing helix chain 'S' and resid 21 through 33 Processing helix chain 'S' and resid 36 through 44 Processing helix chain 'S' and resid 48 through 55 Processing helix chain 'S' and resid 63 through 75 removed outlier: 3.629A pdb=" N VAL S 73 " --> pdb=" O ALA S 69 " (cutoff:3.500A) Processing helix chain 'S' and resid 77 through 83 Processing helix chain 'S' and resid 100 through 107 Processing helix chain 'S' and resid 111 through 116 Processing helix chain 'S' and resid 142 through 146 Processing helix chain 'S' and resid 157 through 162 removed outlier: 3.779A pdb=" N ALA S 162 " --> pdb=" O PHE S 158 " (cutoff:3.500A) Processing helix chain 'S' and resid 163 through 165 No H-bonds generated for 'chain 'S' and resid 163 through 165' Processing helix chain 'T' and resid 21 through 33 Processing helix chain 'T' and resid 36 through 44 Processing helix chain 'T' and resid 48 through 55 Processing helix chain 'T' and resid 63 through 75 removed outlier: 3.628A pdb=" N VAL T 73 " --> pdb=" O ALA T 69 " (cutoff:3.500A) Processing helix chain 'T' and resid 77 through 83 Processing helix chain 'T' and resid 100 through 107 Processing helix chain 'T' and resid 111 through 116 Processing helix chain 'T' and resid 142 through 146 Processing helix chain 'T' and resid 157 through 162 removed outlier: 3.779A pdb=" N ALA T 162 " --> pdb=" O PHE T 158 " (cutoff:3.500A) Processing helix chain 'T' and resid 163 through 165 No H-bonds generated for 'chain 'T' and resid 163 through 165' Processing sheet with id=AA1, first strand: chain 'A' and resid 91 through 94 removed outlier: 6.524A pdb=" N VAL A 92 " --> pdb=" O ILE A 142 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 91 through 94 removed outlier: 6.525A pdb=" N VAL B 92 " --> pdb=" O ILE B 142 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 91 through 94 removed outlier: 6.525A pdb=" N VAL C 92 " --> pdb=" O ILE C 142 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 91 through 94 removed outlier: 6.524A pdb=" N VAL D 92 " --> pdb=" O ILE D 142 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 91 through 94 removed outlier: 6.525A pdb=" N VAL E 92 " --> pdb=" O ILE E 142 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 91 through 94 removed outlier: 6.525A pdb=" N VAL F 92 " --> pdb=" O ILE F 142 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 91 through 94 removed outlier: 6.525A pdb=" N VAL G 92 " --> pdb=" O ILE G 142 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'R' and resid 121 through 122 removed outlier: 3.607A pdb=" N LEU R 127 " --> pdb=" O CYS R 122 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 121 through 122 removed outlier: 3.608A pdb=" N LEU S 127 " --> pdb=" O CYS S 122 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'T' and resid 121 through 122 removed outlier: 3.606A pdb=" N LEU T 127 " --> pdb=" O CYS T 122 " (cutoff:3.500A) 877 hydrogen bonds defined for protein. 2586 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 40 hydrogen bonds 80 hydrogen bond angles 0 basepair planarities 16 basepair parallelities 30 stacking parallelities Total time for adding SS restraints: 2.84 Time building geometry restraints manager: 2.57 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: 6251 1.34 - 1.47: 4282 1.47 - 1.59: 8647 1.59 - 1.71: 75 1.71 - 1.84: 141 Bond restraints: 19396 Sorted by residual: bond pdb=" C ARG D 85 " pdb=" N PRO D 86 " ideal model delta sigma weight residual 1.331 1.370 -0.039 8.70e-03 1.32e+04 2.01e+01 bond pdb=" C ARG E 85 " pdb=" N PRO E 86 " ideal model delta sigma weight residual 1.331 1.369 -0.038 8.70e-03 1.32e+04 1.92e+01 bond pdb=" C ARG C 85 " pdb=" N PRO C 86 " ideal model delta sigma weight residual 1.331 1.369 -0.038 8.70e-03 1.32e+04 1.92e+01 bond pdb=" C ARG B 85 " pdb=" N PRO B 86 " ideal model delta sigma weight residual 1.331 1.369 -0.038 8.70e-03 1.32e+04 1.89e+01 bond pdb=" C ARG G 85 " pdb=" N PRO G 86 " ideal model delta sigma weight residual 1.331 1.369 -0.038 8.70e-03 1.32e+04 1.89e+01 ... (remaining 19391 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.14: 25753 2.14 - 4.28: 459 4.28 - 6.42: 72 6.42 - 8.56: 10 8.56 - 10.70: 12 Bond angle restraints: 26306 Sorted by residual: angle pdb=" C ARG D 85 " pdb=" N PRO D 86 " pdb=" CA PRO D 86 " ideal model delta sigma weight residual 119.66 114.52 5.14 7.30e-01 1.88e+00 4.96e+01 angle pdb=" C ARG B 85 " pdb=" N PRO B 86 " pdb=" CA PRO B 86 " ideal model delta sigma weight residual 119.66 114.53 5.13 7.30e-01 1.88e+00 4.93e+01 angle pdb=" C ARG G 85 " pdb=" N PRO G 86 " pdb=" CA PRO G 86 " ideal model delta sigma weight residual 119.66 114.55 5.11 7.30e-01 1.88e+00 4.89e+01 angle pdb=" C ARG E 85 " pdb=" N PRO E 86 " pdb=" CA PRO E 86 " ideal model delta sigma weight residual 119.66 114.56 5.10 7.30e-01 1.88e+00 4.88e+01 angle pdb=" C ARG C 85 " pdb=" N PRO C 86 " pdb=" CA PRO C 86 " ideal model delta sigma weight residual 119.66 114.58 5.08 7.30e-01 1.88e+00 4.85e+01 ... (remaining 26301 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.75: 9955 16.75 - 33.50: 1198 33.50 - 50.25: 617 50.25 - 67.00: 155 67.00 - 83.75: 53 Dihedral angle restraints: 11978 sinusoidal: 5359 harmonic: 6619 Sorted by residual: dihedral pdb=" CA LEU T 99 " pdb=" C LEU T 99 " pdb=" N CYS T 100 " pdb=" CA CYS T 100 " ideal model delta harmonic sigma weight residual 180.00 158.17 21.83 0 5.00e+00 4.00e-02 1.91e+01 dihedral pdb=" CA LEU S 99 " pdb=" C LEU S 99 " pdb=" N CYS S 100 " pdb=" CA CYS S 100 " ideal model delta harmonic sigma weight residual 180.00 158.18 21.82 0 5.00e+00 4.00e-02 1.91e+01 dihedral pdb=" CA LEU R 99 " pdb=" C LEU R 99 " pdb=" N CYS R 100 " pdb=" CA CYS R 100 " ideal model delta harmonic sigma weight residual 180.00 158.23 21.77 0 5.00e+00 4.00e-02 1.90e+01 ... (remaining 11975 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 2424 0.066 - 0.132: 387 0.132 - 0.198: 76 0.198 - 0.264: 8 0.264 - 0.330: 6 Chirality restraints: 2901 Sorted by residual: chirality pdb=" CA GLN R 137 " pdb=" N GLN R 137 " pdb=" C GLN R 137 " pdb=" CB GLN R 137 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.73e+00 chirality pdb=" CA GLN T 137 " pdb=" N GLN T 137 " pdb=" C GLN T 137 " pdb=" CB GLN T 137 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.71e+00 chirality pdb=" CA GLN S 137 " pdb=" N GLN S 137 " pdb=" C GLN S 137 " pdb=" CB GLN S 137 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.67e+00 ... (remaining 2898 not shown) Planarity restraints: 3238 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET T 142 " -0.031 5.00e-02 4.00e+02 4.71e-02 3.55e+00 pdb=" N PRO T 143 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO T 143 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO T 143 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET S 142 " 0.031 5.00e-02 4.00e+02 4.70e-02 3.53e+00 pdb=" N PRO S 143 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO S 143 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO S 143 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET R 142 " 0.031 5.00e-02 4.00e+02 4.69e-02 3.51e+00 pdb=" N PRO R 143 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO R 143 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO R 143 " 0.026 5.00e-02 4.00e+02 ... (remaining 3235 not shown) Histogram of nonbonded interaction distances: 0.31 - 1.23: 68 1.23 - 2.15: 399 2.15 - 3.06: 13841 3.06 - 3.98: 54081 3.98 - 4.90: 95276 Warning: very small nonbonded interaction distances. Nonbonded interactions: 163665 Sorted by model distance: nonbonded pdb=" CG TYR A 115 " pdb=" C ARG S 155 " model vdw 0.311 2.792 nonbonded pdb=" OG1 THR C 110 " pdb=" CG ARG T 155 " model vdw 0.390 3.440 nonbonded pdb=" CG1 VAL C 132 " pdb=" O CYS T 154 " model vdw 0.402 3.460 nonbonded pdb=" CG ARG A 128 " pdb=" CA ARG S 153 " model vdw 0.474 3.870 nonbonded pdb=" CD GLU A 131 " pdb=" CB CYS S 136 " model vdw 0.476 3.670 ... (remaining 163660 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 17 through 302) selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = (chain 'E' and resid 17 through 302) selection = chain 'F' selection = chain 'G' } ncs_group { reference = chain 'R' selection = chain 'S' selection = (chain 'T' and resid 12 through 201) } ncs_group { reference = chain 'U' selection = chain 'V' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 15.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.420 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 20.660 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2314 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 : 0.016 1.007 19453 Z= 1.588 Angle : 0.762 10.696 26333 Z= 0.450 Chirality : 0.052 0.330 2901 Planarity : 0.005 0.047 3238 Dihedral : 19.225 83.754 7692 Min Nonbonded Distance : 0.311 Molprobity Statistics. All-atom Clashscore : 36.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.48 % Allowed : 18.58 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.09 (0.18), residues: 2265 helix: 0.92 (0.15), residues: 1231 sheet: -1.55 (0.37), residues: 189 loop : -0.73 (0.20), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG S 98 TYR 0.020 0.003 TYR C 112 PHE 0.018 0.002 PHE T 25 TRP 0.020 0.003 TRP R 120 HIS 0.007 0.002 HIS R 57 Details of bonding type rmsd covalent geometry : bond 0.00405 (19396) covalent geometry : angle 0.74842 (26306) hydrogen bonds : bond 0.12400 ( 917) hydrogen bonds : angle 5.39590 ( 2666) metal coordination : bond 0.01849 ( 24) metal coordination : angle 4.59560 ( 27) Misc. bond : bond 0.38193 ( 33) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 684 residues out of total 1973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 656 time to evaluate : 0.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 212 GLU cc_start: 0.4797 (tt0) cc_final: 0.3954 (mt-10) REVERT: B 73 TYR cc_start: 0.6997 (t80) cc_final: 0.6077 (t80) REVERT: B 80 GLN cc_start: 0.7075 (OUTLIER) cc_final: 0.6346 (mm-40) REVERT: B 111 GLU cc_start: 0.8337 (tm-30) cc_final: 0.7881 (mt-10) REVERT: B 125 PHE cc_start: 0.7341 (m-80) cc_final: 0.6715 (m-80) REVERT: B 179 VAL cc_start: 0.8476 (t) cc_final: 0.8270 (m) REVERT: B 240 TYR cc_start: 0.6328 (m-80) cc_final: 0.5620 (m-10) REVERT: C 183 ASP cc_start: 0.8102 (t0) cc_final: 0.7674 (t0) REVERT: C 187 LEU cc_start: 0.7400 (tp) cc_final: 0.7086 (tp) REVERT: C 195 ARG cc_start: 0.6399 (ttt90) cc_final: 0.5794 (ttt180) REVERT: D 73 TYR cc_start: 0.5897 (t80) cc_final: 0.5571 (t80) REVERT: D 114 LYS cc_start: 0.8239 (mmtt) cc_final: 0.7698 (ptmt) REVERT: D 124 ASP cc_start: 0.8130 (m-30) cc_final: 0.7444 (t0) REVERT: D 216 LEU cc_start: 0.8375 (mt) cc_final: 0.8059 (mt) REVERT: E 121 THR cc_start: 0.6456 (t) cc_final: 0.6128 (t) REVERT: E 162 GLU cc_start: 0.5343 (tp30) cc_final: 0.5108 (tt0) REVERT: E 187 LEU cc_start: 0.6820 (tp) cc_final: 0.6586 (tp) REVERT: E 195 ARG cc_start: 0.6973 (ttt90) cc_final: 0.5092 (ptt90) REVERT: E 241 ILE cc_start: 0.6818 (mm) cc_final: 0.6519 (tp) REVERT: E 248 LEU cc_start: 0.5314 (mt) cc_final: 0.4980 (mt) REVERT: F 73 TYR cc_start: 0.6265 (t80) cc_final: 0.5127 (t80) REVERT: F 88 THR cc_start: 0.6296 (OUTLIER) cc_final: 0.5995 (t) REVERT: F 104 ASP cc_start: 0.7819 (m-30) cc_final: 0.7382 (t0) REVERT: F 174 ASP cc_start: 0.5929 (m-30) cc_final: 0.5724 (m-30) REVERT: F 194 LEU cc_start: 0.6567 (tt) cc_final: 0.6331 (tt) REVERT: F 195 ARG cc_start: 0.7506 (ttt90) cc_final: 0.7028 (ttt180) REVERT: F 210 MET cc_start: 0.7263 (tpp) cc_final: 0.6834 (ttm) REVERT: F 229 MET cc_start: 0.7016 (mmt) cc_final: 0.6556 (ttt) REVERT: F 261 LYS cc_start: 0.7904 (tttt) cc_final: 0.7610 (tmtt) REVERT: G 38 GLN cc_start: 0.6345 (tt0) cc_final: 0.6025 (tp-100) REVERT: G 73 TYR cc_start: 0.5942 (t80) cc_final: 0.5041 (t80) REVERT: G 81 GLN cc_start: 0.7804 (pt0) cc_final: 0.7263 (tt0) REVERT: G 124 ASP cc_start: 0.8773 (m-30) cc_final: 0.8455 (t0) REVERT: G 148 ARG cc_start: 0.5537 (mtt180) cc_final: 0.5158 (mtp85) REVERT: G 159 ASP cc_start: 0.5555 (m-30) cc_final: 0.5299 (m-30) REVERT: G 188 GLU cc_start: 0.5534 (mm-30) cc_final: 0.5207 (mm-30) REVERT: G 195 ARG cc_start: 0.7658 (ttt90) cc_final: 0.5478 (ptt-90) REVERT: G 248 LEU cc_start: 0.5175 (mt) cc_final: 0.4869 (mt) REVERT: G 261 LYS cc_start: 0.7276 (tttt) cc_final: 0.7049 (tptp) REVERT: G 274 GLU cc_start: 0.7159 (tt0) cc_final: 0.6764 (tp30) outliers start: 28 outliers final: 3 residues processed: 672 average time/residue: 0.1978 time to fit residues: 182.1990 Evaluate side-chains 324 residues out of total 1973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 319 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 80 GLN Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain E residue 88 THR Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain G residue 88 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 216 optimal weight: 0.9980 chunk 98 optimal weight: 30.0000 chunk 194 optimal weight: 7.9990 chunk 227 optimal weight: 10.0000 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.8980 chunk 200 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 80 GLN ** B 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 GLN ** D 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 38 GLN ** F 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 77 HIS F 81 GLN G 37 GLN G 81 GLN R 24 HIS R 59 ASN R 135 ASN ** R 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 34 HIS ** T 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4584 r_free = 0.4584 target = 0.191655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.146022 restraints weight = 40227.724| |-----------------------------------------------------------------------------| r_work (start): 0.3936 rms_B_bonded: 4.07 r_work: 0.3751 rms_B_bonded: 4.88 restraints_weight: 0.5000 r_work (final): 0.3751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7134 moved from start: 0.4026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.431 19453 Z= 0.390 Angle : 1.125 60.538 26333 Z= 0.534 Chirality : 0.052 0.469 2901 Planarity : 0.017 0.460 3238 Dihedral : 18.191 173.057 3136 Min Nonbonded Distance : 1.670 Molprobity Statistics. All-atom Clashscore : 20.81 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.83 % Favored : 97.00 % Rotamer: Outliers : 5.82 % Allowed : 18.42 % Favored : 75.75 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: 0.11 (0.18), residues: 2265 helix: 0.69 (0.15), residues: 1244 sheet: -2.00 (0.66), residues: 70 loop : -0.47 (0.20), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.055 0.002 ARG S 153 TYR 0.060 0.003 TYR E 115 PHE 0.020 0.002 PHE G 204 TRP 0.020 0.002 TRP A 45 HIS 0.020 0.002 HIS E 43 Details of bonding type rmsd covalent geometry : bond 0.00771 (19396) covalent geometry : angle 0.94617 (26306) hydrogen bonds : bond 0.05139 ( 917) hydrogen bonds : angle 4.62775 ( 2666) metal coordination : bond 0.02633 ( 24) metal coordination : angle 19.05185 ( 27) Misc. bond : bond 0.01393 ( 33) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 1973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 332 time to evaluate : 0.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 GLU cc_start: 0.7642 (tp30) cc_final: 0.7112 (tt0) REVERT: A 229 MET cc_start: 0.4098 (mpp) cc_final: 0.3815 (mpp) REVERT: B 37 GLN cc_start: 0.8542 (mp10) cc_final: 0.8244 (mp10) REVERT: B 111 GLU cc_start: 0.8350 (tm-30) cc_final: 0.8067 (mt-10) REVERT: B 128 ARG cc_start: 0.6153 (ptp-170) cc_final: 0.5124 (tpt170) REVERT: C 45 TRP cc_start: 0.8265 (OUTLIER) cc_final: 0.7838 (t-100) REVERT: C 73 TYR cc_start: 0.8115 (t80) cc_final: 0.7744 (t80) REVERT: C 124 ASP cc_start: 0.8965 (OUTLIER) cc_final: 0.8276 (t70) REVERT: C 195 ARG cc_start: 0.7749 (ttt90) cc_final: 0.6381 (ttt180) REVERT: C 205 LYS cc_start: 0.9032 (ttmt) cc_final: 0.8530 (tptp) REVERT: D 45 TRP cc_start: 0.7163 (t-100) cc_final: 0.6002 (t-100) REVERT: D 114 LYS cc_start: 0.8033 (mmtt) cc_final: 0.7778 (ptmt) REVERT: D 275 TYR cc_start: 0.6485 (m-10) cc_final: 0.6172 (m-80) REVERT: E 81 GLN cc_start: 0.6790 (mt0) cc_final: 0.6469 (mp10) REVERT: E 131 GLU cc_start: 0.8699 (mm-30) cc_final: 0.8472 (mt-10) REVERT: E 195 ARG cc_start: 0.8296 (ttt90) cc_final: 0.6620 (ptt-90) REVERT: E 229 MET cc_start: 0.6736 (mmt) cc_final: 0.5798 (ttt) REVERT: E 275 TYR cc_start: 0.7359 (m-80) cc_final: 0.7118 (m-80) REVERT: F 89 VAL cc_start: 0.8979 (t) cc_final: 0.8770 (m) REVERT: F 188 GLU cc_start: 0.8056 (mm-30) cc_final: 0.6827 (mm-30) REVERT: F 195 ARG cc_start: 0.8249 (ttt90) cc_final: 0.7005 (ttt180) REVERT: F 229 MET cc_start: 0.7382 (mmt) cc_final: 0.6867 (ttt) REVERT: G 106 PHE cc_start: 0.9064 (m-80) cc_final: 0.8142 (m-80) REVERT: G 176 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8518 (tp) REVERT: G 195 ARG cc_start: 0.8181 (ttt90) cc_final: 0.6612 (ptt-90) REVERT: G 205 LYS cc_start: 0.8698 (ttmt) cc_final: 0.8113 (tptt) REVERT: G 274 GLU cc_start: 0.7634 (tt0) cc_final: 0.6812 (tp30) REVERT: S 84 MET cc_start: -0.0118 (mpp) cc_final: -0.0751 (mmm) REVERT: T 92 MET cc_start: 0.5712 (pmm) cc_final: 0.4458 (ttt) REVERT: T 142 MET cc_start: 0.3824 (ptt) cc_final: 0.3314 (mmt) outliers start: 110 outliers final: 52 residues processed: 411 average time/residue: 0.1824 time to fit residues: 106.0250 Evaluate side-chains 297 residues out of total 1973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 242 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 115 TYR Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 128 ARG Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain B residue 29 LYS Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 43 HIS Chi-restraints excluded: chain C residue 45 TRP Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 124 ASP Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 71 ASP Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain E residue 174 ASP Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 63 ARG Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain F residue 153 THR Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 43 HIS Chi-restraints excluded: chain G residue 88 THR Chi-restraints excluded: chain G residue 113 LEU Chi-restraints excluded: chain G residue 173 THR Chi-restraints excluded: chain G residue 176 LEU Chi-restraints excluded: chain G residue 200 SER Chi-restraints excluded: chain R residue 42 THR Chi-restraints excluded: chain R residue 58 PHE Chi-restraints excluded: chain R residue 161 MET Chi-restraints excluded: chain T residue 148 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 24 optimal weight: 0.0970 chunk 9 optimal weight: 9.9990 chunk 224 optimal weight: 30.0000 chunk 175 optimal weight: 2.9990 chunk 182 optimal weight: 5.9990 chunk 203 optimal weight: 4.9990 chunk 78 optimal weight: 9.9990 chunk 105 optimal weight: 3.9990 chunk 88 optimal weight: 0.8980 chunk 215 optimal weight: 20.0000 chunk 5 optimal weight: 20.0000 overall best weight: 2.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 GLN A 193 HIS ** B 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 GLN C 38 GLN ** C 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 213 GLN G 38 GLN ** R 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4494 r_free = 0.4494 target = 0.183746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.133153 restraints weight = 38691.972| |-----------------------------------------------------------------------------| r_work (start): 0.3790 rms_B_bonded: 3.33 r_work: 0.3638 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.5284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.123 19453 Z= 0.299 Angle : 1.005 36.646 26333 Z= 0.487 Chirality : 0.051 0.566 2901 Planarity : 0.011 0.238 3238 Dihedral : 18.666 173.022 3129 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 19.19 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.66 % Favored : 96.20 % Rotamer: Outliers : 5.72 % Allowed : 19.53 % Favored : 74.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: 0.17 (0.18), residues: 2265 helix: 0.80 (0.15), residues: 1202 sheet: -1.62 (0.69), residues: 70 loop : -0.52 (0.20), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.043 0.001 ARG E 63 TYR 0.071 0.003 TYR A 115 PHE 0.017 0.002 PHE G 106 TRP 0.020 0.002 TRP S 146 HIS 0.024 0.002 HIS S 152 Details of bonding type rmsd covalent geometry : bond 0.00675 (19396) covalent geometry : angle 0.89540 (26306) hydrogen bonds : bond 0.04720 ( 917) hydrogen bonds : angle 4.47492 ( 2666) metal coordination : bond 0.02680 ( 24) metal coordination : angle 14.28854 ( 27) Misc. bond : bond 0.01212 ( 33) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 1973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 264 time to evaluate : 0.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 THR cc_start: 0.6893 (OUTLIER) cc_final: 0.6684 (p) REVERT: A 131 GLU cc_start: 0.7967 (tp30) cc_final: 0.7574 (tt0) REVERT: B 37 GLN cc_start: 0.8557 (mp10) cc_final: 0.8240 (mp10) REVERT: B 111 GLU cc_start: 0.8379 (tm-30) cc_final: 0.8130 (mt-10) REVERT: B 128 ARG cc_start: 0.6287 (ptp-170) cc_final: 0.5617 (tpt170) REVERT: C 45 TRP cc_start: 0.8354 (OUTLIER) cc_final: 0.7779 (t-100) REVERT: C 73 TYR cc_start: 0.8485 (t80) cc_final: 0.8230 (t80) REVERT: C 124 ASP cc_start: 0.9049 (OUTLIER) cc_final: 0.8430 (t70) REVERT: C 205 LYS cc_start: 0.8937 (ttmt) cc_final: 0.8708 (tptp) REVERT: D 114 LYS cc_start: 0.8112 (mmtt) cc_final: 0.7796 (ptmt) REVERT: E 31 LYS cc_start: 0.7393 (OUTLIER) cc_final: 0.7135 (mtpt) REVERT: E 188 GLU cc_start: 0.8481 (mm-30) cc_final: 0.7524 (tp30) REVERT: E 208 VAL cc_start: 0.8813 (t) cc_final: 0.8468 (m) REVERT: E 246 GLU cc_start: 0.8099 (mm-30) cc_final: 0.7808 (mt-10) REVERT: E 262 LYS cc_start: 0.3793 (tptm) cc_final: 0.3475 (tppt) REVERT: F 229 MET cc_start: 0.7447 (mmt) cc_final: 0.7049 (ttt) REVERT: G 176 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8528 (tp) REVERT: G 205 LYS cc_start: 0.8820 (ttmt) cc_final: 0.8285 (tptp) REVERT: G 274 GLU cc_start: 0.7752 (tt0) cc_final: 0.6974 (tp30) REVERT: R 92 MET cc_start: 0.0701 (tmm) cc_final: -0.0399 (pmm) REVERT: T 92 MET cc_start: 0.5684 (pmm) cc_final: 0.4385 (ttt) REVERT: T 142 MET cc_start: 0.3997 (ptt) cc_final: 0.3432 (mmt) outliers start: 108 outliers final: 63 residues processed: 348 average time/residue: 0.1645 time to fit residues: 82.7016 Evaluate side-chains 289 residues out of total 1973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 221 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 128 ARG Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain B residue 29 LYS Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 43 HIS Chi-restraints excluded: chain C residue 45 TRP Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 124 ASP Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain E residue 31 LYS Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 88 THR Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 116 ARG Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain F residue 31 LYS Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 63 ARG Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain F residue 153 THR Chi-restraints excluded: chain F residue 256 LEU Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 43 HIS Chi-restraints excluded: chain G residue 55 SER Chi-restraints excluded: chain G residue 62 SER Chi-restraints excluded: chain G residue 88 THR Chi-restraints excluded: chain G residue 113 LEU Chi-restraints excluded: chain G residue 125 PHE Chi-restraints excluded: chain G residue 173 THR Chi-restraints excluded: chain G residue 176 LEU Chi-restraints excluded: chain G residue 248 LEU Chi-restraints excluded: chain R residue 42 THR Chi-restraints excluded: chain R residue 117 LYS Chi-restraints excluded: chain T residue 148 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 170 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 150 optimal weight: 10.0000 chunk 156 optimal weight: 6.9990 chunk 122 optimal weight: 0.7980 chunk 55 optimal weight: 0.6980 chunk 209 optimal weight: 30.0000 chunk 117 optimal weight: 5.9990 chunk 114 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 GLN ** C 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 97 HIS ** E 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 97 HIS ** R 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 135 ASN T 93 GLN ** T 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4482 r_free = 0.4482 target = 0.183024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.132315 restraints weight = 38743.783| |-----------------------------------------------------------------------------| r_work (start): 0.3778 rms_B_bonded: 3.34 r_work: 0.3622 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.5865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.118 19453 Z= 0.229 Angle : 0.900 30.356 26333 Z= 0.435 Chirality : 0.047 0.543 2901 Planarity : 0.013 0.367 3238 Dihedral : 17.709 174.099 3129 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 16.62 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.80 % Favored : 96.11 % Rotamer: Outliers : 5.82 % Allowed : 21.02 % Favored : 73.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: 0.16 (0.18), residues: 2265 helix: 0.71 (0.15), residues: 1265 sheet: -1.48 (0.70), residues: 70 loop : -0.48 (0.21), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.049 0.001 ARG B 63 TYR 0.056 0.003 TYR A 115 PHE 0.014 0.002 PHE G 204 TRP 0.025 0.002 TRP A 45 HIS 0.014 0.002 HIS S 152 Details of bonding type rmsd covalent geometry : bond 0.00506 (19396) covalent geometry : angle 0.80036 (26306) hydrogen bonds : bond 0.04087 ( 917) hydrogen bonds : angle 4.27630 ( 2666) metal coordination : bond 0.02101 ( 24) metal coordination : angle 12.88537 ( 27) Misc. bond : bond 0.01298 ( 33) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 231 time to evaluate : 0.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 GLU cc_start: 0.8025 (tp30) cc_final: 0.7715 (tt0) REVERT: A 212 GLU cc_start: 0.4576 (OUTLIER) cc_final: 0.3349 (mt-10) REVERT: B 37 GLN cc_start: 0.8473 (mp10) cc_final: 0.8139 (mp10) REVERT: B 93 TYR cc_start: 0.8837 (t80) cc_final: 0.8584 (t80) REVERT: B 111 GLU cc_start: 0.8427 (tm-30) cc_final: 0.8157 (mt-10) REVERT: C 45 TRP cc_start: 0.8358 (OUTLIER) cc_final: 0.7727 (t-100) REVERT: C 73 TYR cc_start: 0.8551 (t80) cc_final: 0.8181 (t80) REVERT: C 124 ASP cc_start: 0.9061 (OUTLIER) cc_final: 0.8344 (t0) REVERT: C 214 MET cc_start: 0.8486 (tpp) cc_final: 0.7872 (mtm) REVERT: D 114 LYS cc_start: 0.8154 (mmtt) cc_final: 0.7841 (ptmt) REVERT: D 275 TYR cc_start: 0.6717 (m-80) cc_final: 0.6443 (m-80) REVERT: E 31 LYS cc_start: 0.7599 (OUTLIER) cc_final: 0.7353 (mtpt) REVERT: E 208 VAL cc_start: 0.8800 (t) cc_final: 0.8459 (m) REVERT: E 229 MET cc_start: 0.7138 (mmt) cc_final: 0.6064 (ttt) REVERT: E 246 GLU cc_start: 0.8178 (mm-30) cc_final: 0.7856 (mt-10) REVERT: E 262 LYS cc_start: 0.3776 (tptm) cc_final: 0.3461 (tppt) REVERT: F 148 ARG cc_start: 0.8422 (OUTLIER) cc_final: 0.7532 (mtt180) REVERT: F 174 ASP cc_start: 0.8678 (m-30) cc_final: 0.8462 (m-30) REVERT: F 229 MET cc_start: 0.7459 (mmt) cc_final: 0.7064 (ttt) REVERT: G 176 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8549 (tp) REVERT: G 205 LYS cc_start: 0.8801 (ttmt) cc_final: 0.8263 (tptp) REVERT: G 274 GLU cc_start: 0.7750 (tt0) cc_final: 0.6945 (tp30) REVERT: T 92 MET cc_start: 0.5745 (pmm) cc_final: 0.4459 (ttt) REVERT: T 142 MET cc_start: 0.3809 (ptt) cc_final: 0.3347 (mmm) outliers start: 110 outliers final: 68 residues processed: 313 average time/residue: 0.1753 time to fit residues: 78.4627 Evaluate side-chains 270 residues out of total 1973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 196 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain B residue 29 LYS Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 43 HIS Chi-restraints excluded: chain C residue 45 TRP Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 124 ASP Chi-restraints excluded: chain C residue 127 ASP Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain D residue 43 HIS Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain E residue 31 LYS Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 88 THR Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain F residue 21 LEU Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 43 HIS Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 63 ARG Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain F residue 148 ARG Chi-restraints excluded: chain F residue 153 THR Chi-restraints excluded: chain F residue 256 LEU Chi-restraints excluded: chain F residue 268 LEU Chi-restraints excluded: chain F residue 269 GLN Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 43 HIS Chi-restraints excluded: chain G residue 55 SER Chi-restraints excluded: chain G residue 88 THR Chi-restraints excluded: chain G residue 164 LEU Chi-restraints excluded: chain G residue 176 LEU Chi-restraints excluded: chain G residue 248 LEU Chi-restraints excluded: chain R residue 42 THR Chi-restraints excluded: chain R residue 50 VAL Chi-restraints excluded: chain R residue 117 LYS Chi-restraints excluded: chain T residue 148 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 161 optimal weight: 0.6980 chunk 97 optimal weight: 4.9990 chunk 74 optimal weight: 4.9990 chunk 193 optimal weight: 20.0000 chunk 154 optimal weight: 0.8980 chunk 131 optimal weight: 3.9990 chunk 18 optimal weight: 10.0000 chunk 66 optimal weight: 4.9990 chunk 22 optimal weight: 9.9990 chunk 146 optimal weight: 0.0070 chunk 55 optimal weight: 2.9990 overall best weight: 1.7202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 HIS ** B 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 GLN C 38 GLN C 97 HIS ** E 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.180798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.130195 restraints weight = 38279.160| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 3.75 r_work: 0.3553 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.6352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 19453 Z= 0.227 Angle : 0.881 30.875 26333 Z= 0.423 Chirality : 0.047 0.520 2901 Planarity : 0.012 0.331 3238 Dihedral : 17.694 167.131 3129 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 15.91 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.15 % Favored : 95.72 % Rotamer: Outliers : 6.35 % Allowed : 21.33 % Favored : 72.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % 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: 0.20 (0.18), residues: 2265 helix: 0.78 (0.15), residues: 1258 sheet: -1.45 (0.72), residues: 70 loop : -0.53 (0.21), residues: 937 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.049 0.001 ARG B 63 TYR 0.052 0.003 TYR A 115 PHE 0.011 0.001 PHE D 190 TRP 0.017 0.002 TRP C 45 HIS 0.018 0.001 HIS S 152 Details of bonding type rmsd covalent geometry : bond 0.00503 (19396) covalent geometry : angle 0.78014 (26306) hydrogen bonds : bond 0.04009 ( 917) hydrogen bonds : angle 4.22085 ( 2666) metal coordination : bond 0.02021 ( 24) metal coordination : angle 12.81304 ( 27) Misc. bond : bond 0.01244 ( 33) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 1973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 217 time to evaluate : 0.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 GLU cc_start: 0.8011 (tp30) cc_final: 0.7662 (tt0) REVERT: A 212 GLU cc_start: 0.4666 (OUTLIER) cc_final: 0.3374 (mt-10) REVERT: B 37 GLN cc_start: 0.8459 (mp10) cc_final: 0.8080 (mp10) REVERT: B 111 GLU cc_start: 0.8511 (tm-30) cc_final: 0.8180 (mt-10) REVERT: C 45 TRP cc_start: 0.8419 (OUTLIER) cc_final: 0.7730 (t-100) REVERT: C 73 TYR cc_start: 0.8708 (t80) cc_final: 0.8490 (t80) REVERT: C 124 ASP cc_start: 0.9255 (OUTLIER) cc_final: 0.8792 (t70) REVERT: C 126 ARG cc_start: 0.7650 (OUTLIER) cc_final: 0.5629 (ttm-80) REVERT: C 210 MET cc_start: 0.8785 (OUTLIER) cc_final: 0.8074 (tpt) REVERT: C 247 ILE cc_start: 0.8741 (mm) cc_final: 0.8521 (mt) REVERT: D 114 LYS cc_start: 0.8196 (mmtt) cc_final: 0.7845 (ptmt) REVERT: D 260 LEU cc_start: 0.8443 (mt) cc_final: 0.7758 (tp) REVERT: E 128 ARG cc_start: 0.8271 (mmt90) cc_final: 0.7906 (mmt180) REVERT: E 208 VAL cc_start: 0.8857 (t) cc_final: 0.8501 (m) REVERT: E 229 MET cc_start: 0.7235 (mmt) cc_final: 0.6171 (ttt) REVERT: E 246 GLU cc_start: 0.8262 (mm-30) cc_final: 0.7961 (mt-10) REVERT: E 262 LYS cc_start: 0.3979 (tptm) cc_final: 0.3644 (tppt) REVERT: F 97 HIS cc_start: 0.8018 (OUTLIER) cc_final: 0.7229 (m-70) REVERT: F 148 ARG cc_start: 0.8517 (OUTLIER) cc_final: 0.7644 (mtt180) REVERT: F 174 ASP cc_start: 0.8707 (m-30) cc_final: 0.8498 (m-30) REVERT: F 229 MET cc_start: 0.7481 (mmt) cc_final: 0.7072 (ttt) REVERT: F 269 GLN cc_start: 0.8177 (OUTLIER) cc_final: 0.7965 (mp10) REVERT: G 75 TYR cc_start: 0.8054 (m-80) cc_final: 0.7792 (m-10) REVERT: G 205 LYS cc_start: 0.8841 (ttmt) cc_final: 0.8267 (tptt) REVERT: G 249 ARG cc_start: 0.8515 (tpp80) cc_final: 0.8303 (tpp80) REVERT: S 161 MET cc_start: -0.2077 (mmm) cc_final: -0.2423 (mmm) REVERT: T 92 MET cc_start: 0.5742 (pmm) cc_final: 0.4463 (ttt) REVERT: T 142 MET cc_start: 0.3879 (ptt) cc_final: 0.3341 (mmm) outliers start: 120 outliers final: 79 residues processed: 304 average time/residue: 0.1740 time to fit residues: 76.0908 Evaluate side-chains 278 residues out of total 1973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 191 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 128 ARG Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain B residue 29 LYS Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 38 GLN Chi-restraints excluded: chain C residue 43 HIS Chi-restraints excluded: chain C residue 45 TRP Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 124 ASP Chi-restraints excluded: chain C residue 126 ARG Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain D residue 43 HIS Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 88 THR Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain F residue 21 LEU Chi-restraints excluded: chain F residue 31 LYS Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 43 HIS Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 63 ARG Chi-restraints excluded: chain F residue 97 HIS Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 148 ARG Chi-restraints excluded: chain F residue 153 THR Chi-restraints excluded: chain F residue 241 ILE Chi-restraints excluded: chain F residue 268 LEU Chi-restraints excluded: chain F residue 269 GLN Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 43 HIS Chi-restraints excluded: chain G residue 55 SER Chi-restraints excluded: chain G residue 88 THR Chi-restraints excluded: chain G residue 97 HIS Chi-restraints excluded: chain G residue 113 LEU Chi-restraints excluded: chain G residue 125 PHE Chi-restraints excluded: chain G residue 164 LEU Chi-restraints excluded: chain G residue 166 ILE Chi-restraints excluded: chain G residue 248 LEU Chi-restraints excluded: chain R residue 42 THR Chi-restraints excluded: chain R residue 99 LEU Chi-restraints excluded: chain R residue 117 LYS Chi-restraints excluded: chain R residue 155 ARG Chi-restraints excluded: chain R residue 156 MET Chi-restraints excluded: chain T residue 148 ASP Chi-restraints excluded: chain T residue 151 CYS Chi-restraints excluded: chain T residue 155 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 127 optimal weight: 6.9990 chunk 4 optimal weight: 10.0000 chunk 5 optimal weight: 6.9990 chunk 218 optimal weight: 6.9990 chunk 112 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 79 optimal weight: 8.9990 chunk 75 optimal weight: 0.9980 chunk 27 optimal weight: 10.0000 chunk 93 optimal weight: 0.8980 chunk 101 optimal weight: 0.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 HIS ** B 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 GLN D 38 GLN F 77 HIS R 59 ASN ** R 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.181374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.131105 restraints weight = 38280.612| |-----------------------------------------------------------------------------| r_work (start): 0.3753 rms_B_bonded: 3.72 r_work: 0.3587 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.6620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.135 19453 Z= 0.201 Angle : 0.872 30.060 26333 Z= 0.419 Chirality : 0.046 0.520 2901 Planarity : 0.013 0.463 3238 Dihedral : 17.430 166.917 3129 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 16.01 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.84 % Favored : 96.07 % Rotamer: Outliers : 5.93 % Allowed : 21.49 % Favored : 72.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: 0.30 (0.18), residues: 2265 helix: 0.88 (0.15), residues: 1258 sheet: -1.42 (0.72), residues: 70 loop : -0.50 (0.21), residues: 937 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.032 0.001 ARG F 63 TYR 0.051 0.003 TYR A 115 PHE 0.022 0.001 PHE D 190 TRP 0.016 0.001 TRP C 45 HIS 0.013 0.002 HIS S 152 Details of bonding type rmsd covalent geometry : bond 0.00434 (19396) covalent geometry : angle 0.77020 (26306) hydrogen bonds : bond 0.03933 ( 917) hydrogen bonds : angle 4.13331 ( 2666) metal coordination : bond 0.02001 ( 24) metal coordination : angle 12.79071 ( 27) Misc. bond : bond 0.01274 ( 33) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 1973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 223 time to evaluate : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 THR cc_start: 0.4171 (OUTLIER) cc_final: 0.3910 (p) REVERT: A 131 GLU cc_start: 0.8041 (tp30) cc_final: 0.7730 (tt0) REVERT: A 212 GLU cc_start: 0.4720 (OUTLIER) cc_final: 0.3451 (mt-10) REVERT: B 37 GLN cc_start: 0.8425 (mp10) cc_final: 0.8045 (mp10) REVERT: B 111 GLU cc_start: 0.8519 (tm-30) cc_final: 0.8191 (mt-10) REVERT: C 45 TRP cc_start: 0.8425 (OUTLIER) cc_final: 0.7677 (t-100) REVERT: C 73 TYR cc_start: 0.8717 (t80) cc_final: 0.8496 (t80) REVERT: C 124 ASP cc_start: 0.9160 (OUTLIER) cc_final: 0.8691 (t70) REVERT: C 159 ASP cc_start: 0.8234 (m-30) cc_final: 0.7923 (m-30) REVERT: C 205 LYS cc_start: 0.8919 (ttmt) cc_final: 0.8486 (tptp) REVERT: C 210 MET cc_start: 0.8818 (OUTLIER) cc_final: 0.8108 (tpt) REVERT: C 247 ILE cc_start: 0.8769 (OUTLIER) cc_final: 0.8558 (mt) REVERT: D 114 LYS cc_start: 0.8223 (mmtt) cc_final: 0.7855 (ptmt) REVERT: D 260 LEU cc_start: 0.8436 (mt) cc_final: 0.7775 (tp) REVERT: D 275 TYR cc_start: 0.6869 (m-80) cc_final: 0.6654 (m-80) REVERT: E 189 ARG cc_start: 0.7731 (OUTLIER) cc_final: 0.6655 (mtm-85) REVERT: E 208 VAL cc_start: 0.8840 (t) cc_final: 0.8489 (m) REVERT: E 229 MET cc_start: 0.7198 (mmt) cc_final: 0.6170 (ttt) REVERT: E 262 LYS cc_start: 0.3979 (tptm) cc_final: 0.3576 (tttp) REVERT: F 156 ASP cc_start: 0.8053 (OUTLIER) cc_final: 0.7732 (m-30) REVERT: F 229 MET cc_start: 0.7424 (mmt) cc_final: 0.7021 (ttt) REVERT: F 246 GLU cc_start: 0.7378 (mm-30) cc_final: 0.7047 (mt-10) REVERT: G 75 TYR cc_start: 0.8002 (m-80) cc_final: 0.7745 (m-10) REVERT: G 205 LYS cc_start: 0.8840 (ttmt) cc_final: 0.8330 (tptp) REVERT: G 249 ARG cc_start: 0.8479 (tpp80) cc_final: 0.8251 (tpp80) REVERT: S 99 LEU cc_start: 0.1637 (OUTLIER) cc_final: 0.1203 (tp) REVERT: T 92 MET cc_start: 0.5776 (pmm) cc_final: 0.4516 (ttt) REVERT: T 142 MET cc_start: 0.3891 (ptt) cc_final: 0.3348 (mmm) outliers start: 112 outliers final: 71 residues processed: 302 average time/residue: 0.1636 time to fit residues: 71.6514 Evaluate side-chains 278 residues out of total 1973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 198 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 128 ARG Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 43 HIS Chi-restraints excluded: chain C residue 45 TRP Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 124 ASP Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain D residue 43 HIS Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 88 THR Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 189 ARG Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain F residue 21 LEU Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 43 HIS Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 63 ARG Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 153 THR Chi-restraints excluded: chain F residue 156 ASP Chi-restraints excluded: chain F residue 241 ILE Chi-restraints excluded: chain F residue 268 LEU Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 43 HIS Chi-restraints excluded: chain G residue 55 SER Chi-restraints excluded: chain G residue 88 THR Chi-restraints excluded: chain G residue 97 HIS Chi-restraints excluded: chain G residue 125 PHE Chi-restraints excluded: chain G residue 164 LEU Chi-restraints excluded: chain G residue 248 LEU Chi-restraints excluded: chain R residue 42 THR Chi-restraints excluded: chain R residue 117 LYS Chi-restraints excluded: chain R residue 155 ARG Chi-restraints excluded: chain S residue 99 LEU Chi-restraints excluded: chain T residue 148 ASP Chi-restraints excluded: chain T residue 151 CYS Chi-restraints excluded: chain T residue 155 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 207 optimal weight: 0.8980 chunk 145 optimal weight: 0.9980 chunk 93 optimal weight: 3.9990 chunk 176 optimal weight: 4.9990 chunk 99 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 139 optimal weight: 0.6980 chunk 20 optimal weight: 20.0000 chunk 182 optimal weight: 0.9980 chunk 203 optimal weight: 9.9990 chunk 60 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 GLN G 22 GLN ** R 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.181601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.132824 restraints weight = 38435.115| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 4.02 r_work: 0.3588 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.6863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 19453 Z= 0.188 Angle : 0.907 38.408 26333 Z= 0.419 Chirality : 0.045 0.502 2901 Planarity : 0.012 0.341 3238 Dihedral : 17.289 165.387 3129 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 15.75 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.89 % Favored : 95.98 % Rotamer: Outliers : 4.76 % Allowed : 22.82 % Favored : 72.42 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: 0.28 (0.18), residues: 2265 helix: 0.90 (0.15), residues: 1276 sheet: -1.91 (0.46), residues: 133 loop : -0.40 (0.22), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.037 0.001 ARG B 63 TYR 0.069 0.003 TYR A 115 PHE 0.022 0.001 PHE D 190 TRP 0.016 0.002 TRP R 146 HIS 0.017 0.001 HIS C 43 Details of bonding type rmsd covalent geometry : bond 0.00394 (19396) covalent geometry : angle 0.76965 (26306) hydrogen bonds : bond 0.03728 ( 917) hydrogen bonds : angle 4.10407 ( 2666) metal coordination : bond 0.02052 ( 24) metal coordination : angle 14.99310 ( 27) Misc. bond : bond 0.01235 ( 33) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 218 time to evaluate : 0.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 GLU cc_start: 0.7947 (tp30) cc_final: 0.7683 (tt0) REVERT: A 212 GLU cc_start: 0.4650 (OUTLIER) cc_final: 0.3599 (mt-10) REVERT: B 111 GLU cc_start: 0.8531 (tm-30) cc_final: 0.8212 (mt-10) REVERT: C 73 TYR cc_start: 0.8734 (t80) cc_final: 0.8524 (t80) REVERT: C 124 ASP cc_start: 0.9168 (OUTLIER) cc_final: 0.8609 (t0) REVERT: C 159 ASP cc_start: 0.8136 (m-30) cc_final: 0.7792 (m-30) REVERT: C 205 LYS cc_start: 0.8928 (ttmt) cc_final: 0.8486 (tptp) REVERT: C 210 MET cc_start: 0.8813 (OUTLIER) cc_final: 0.8098 (tpt) REVERT: D 114 LYS cc_start: 0.8215 (mmtt) cc_final: 0.7850 (ptmt) REVERT: D 213 GLN cc_start: 0.8268 (tm-30) cc_final: 0.8035 (tm-30) REVERT: E 128 ARG cc_start: 0.8554 (mmm-85) cc_final: 0.7837 (mmm-85) REVERT: E 196 PHE cc_start: 0.8565 (OUTLIER) cc_final: 0.8328 (m-80) REVERT: E 229 MET cc_start: 0.7283 (mmt) cc_final: 0.6200 (ttt) REVERT: E 262 LYS cc_start: 0.3979 (tptm) cc_final: 0.3637 (tmtt) REVERT: F 229 MET cc_start: 0.7483 (mmt) cc_final: 0.7103 (ttt) REVERT: F 246 GLU cc_start: 0.7428 (mm-30) cc_final: 0.7105 (mt-10) REVERT: G 205 LYS cc_start: 0.8837 (ttmt) cc_final: 0.8337 (tptp) REVERT: G 249 ARG cc_start: 0.8515 (tpp80) cc_final: 0.8230 (tpp80) REVERT: R 156 MET cc_start: 0.3682 (OUTLIER) cc_final: 0.3384 (ppp) REVERT: S 99 LEU cc_start: 0.1652 (OUTLIER) cc_final: 0.1349 (tp) REVERT: T 92 MET cc_start: 0.5796 (pmm) cc_final: 0.4551 (ttt) REVERT: T 142 MET cc_start: 0.3844 (ptt) cc_final: 0.3365 (mmp) outliers start: 90 outliers final: 64 residues processed: 280 average time/residue: 0.1668 time to fit residues: 67.7189 Evaluate side-chains 250 residues out of total 1973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 180 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 43 HIS Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 128 ARG Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain B residue 29 LYS Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 124 ASP Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain D residue 43 HIS Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 88 THR Chi-restraints excluded: chain E residue 196 PHE Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain F residue 21 LEU Chi-restraints excluded: chain F residue 31 LYS Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 43 HIS Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 63 ARG Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 125 PHE Chi-restraints excluded: chain F residue 153 THR Chi-restraints excluded: chain F residue 268 LEU Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 43 HIS Chi-restraints excluded: chain G residue 88 THR Chi-restraints excluded: chain G residue 97 HIS Chi-restraints excluded: chain G residue 113 LEU Chi-restraints excluded: chain G residue 125 PHE Chi-restraints excluded: chain G residue 164 LEU Chi-restraints excluded: chain G residue 248 LEU Chi-restraints excluded: chain R residue 42 THR Chi-restraints excluded: chain R residue 155 ARG Chi-restraints excluded: chain R residue 156 MET Chi-restraints excluded: chain S residue 29 PHE Chi-restraints excluded: chain S residue 99 LEU Chi-restraints excluded: chain T residue 148 ASP Chi-restraints excluded: chain T residue 151 CYS Chi-restraints excluded: chain T residue 155 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 227 optimal weight: 9.9990 chunk 31 optimal weight: 1.9990 chunk 118 optimal weight: 0.8980 chunk 221 optimal weight: 7.9990 chunk 138 optimal weight: 0.9990 chunk 210 optimal weight: 9.9990 chunk 103 optimal weight: 0.9990 chunk 220 optimal weight: 0.7980 chunk 72 optimal weight: 9.9990 chunk 183 optimal weight: 9.9990 chunk 208 optimal weight: 7.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 33 ASN S 34 HIS ** T 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.184726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.134146 restraints weight = 38124.766| |-----------------------------------------------------------------------------| r_work (start): 0.3766 rms_B_bonded: 3.39 r_work: 0.3600 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.7118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 19453 Z= 0.196 Angle : 0.961 36.643 26333 Z= 0.453 Chirality : 0.046 0.478 2901 Planarity : 0.012 0.351 3238 Dihedral : 16.809 141.302 3129 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 15.51 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.02 % Favored : 95.89 % Rotamer: Outliers : 4.61 % Allowed : 23.19 % Favored : 72.21 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % 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: 0.30 (0.18), residues: 2265 helix: 0.94 (0.15), residues: 1276 sheet: -1.89 (0.46), residues: 133 loop : -0.46 (0.22), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.045 0.001 ARG B 63 TYR 0.070 0.003 TYR A 115 PHE 0.027 0.002 PHE R 158 TRP 0.015 0.001 TRP C 45 HIS 0.017 0.002 HIS C 43 Details of bonding type rmsd covalent geometry : bond 0.00421 (19396) covalent geometry : angle 0.85132 (26306) hydrogen bonds : bond 0.03753 ( 917) hydrogen bonds : angle 4.07392 ( 2666) metal coordination : bond 0.01979 ( 24) metal coordination : angle 13.94268 ( 27) Misc. bond : bond 0.01188 ( 33) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 195 time to evaluate : 0.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 GLU cc_start: 0.7899 (tp30) cc_final: 0.7654 (tt0) REVERT: A 212 GLU cc_start: 0.4662 (OUTLIER) cc_final: 0.3573 (mt-10) REVERT: B 111 GLU cc_start: 0.8486 (tm-30) cc_final: 0.8212 (mt-10) REVERT: C 73 TYR cc_start: 0.8774 (t80) cc_final: 0.8561 (t80) REVERT: C 124 ASP cc_start: 0.9156 (OUTLIER) cc_final: 0.8635 (t70) REVERT: C 159 ASP cc_start: 0.8183 (m-30) cc_final: 0.7948 (m-30) REVERT: C 205 LYS cc_start: 0.8951 (ttmt) cc_final: 0.8647 (tptt) REVERT: C 210 MET cc_start: 0.8787 (OUTLIER) cc_final: 0.8099 (tpt) REVERT: D 114 LYS cc_start: 0.8212 (mmtt) cc_final: 0.7852 (ptmt) REVERT: E 114 LYS cc_start: 0.7459 (mmtm) cc_final: 0.7038 (ttmt) REVERT: E 128 ARG cc_start: 0.8502 (mmm-85) cc_final: 0.7798 (mmm-85) REVERT: E 208 VAL cc_start: 0.8909 (t) cc_final: 0.8573 (p) REVERT: E 229 MET cc_start: 0.7254 (mmt) cc_final: 0.6226 (ttt) REVERT: F 229 MET cc_start: 0.7401 (mmt) cc_final: 0.7111 (ttt) REVERT: F 246 GLU cc_start: 0.7432 (mm-30) cc_final: 0.7145 (mt-10) REVERT: G 205 LYS cc_start: 0.8849 (ttmt) cc_final: 0.8329 (tptp) REVERT: G 249 ARG cc_start: 0.8540 (tpp80) cc_final: 0.8255 (tpp80) REVERT: R 156 MET cc_start: 0.3758 (OUTLIER) cc_final: 0.3431 (ppp) REVERT: S 99 LEU cc_start: 0.1729 (OUTLIER) cc_final: 0.1502 (tp) REVERT: S 156 MET cc_start: -0.0481 (ptm) cc_final: -0.0830 (mtt) REVERT: T 92 MET cc_start: 0.5838 (pmm) cc_final: 0.4537 (ttt) REVERT: T 142 MET cc_start: 0.3845 (ptt) cc_final: 0.3417 (mmp) outliers start: 87 outliers final: 68 residues processed: 258 average time/residue: 0.1676 time to fit residues: 62.6909 Evaluate side-chains 255 residues out of total 1973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 182 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 128 ARG Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain B residue 29 LYS Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 43 HIS Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 124 ASP Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain D residue 43 HIS Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 188 GLU Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 88 THR Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain F residue 21 LEU Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 43 HIS Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 63 ARG Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 125 PHE Chi-restraints excluded: chain F residue 153 THR Chi-restraints excluded: chain F residue 241 ILE Chi-restraints excluded: chain F residue 268 LEU Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 43 HIS Chi-restraints excluded: chain G residue 88 THR Chi-restraints excluded: chain G residue 113 LEU Chi-restraints excluded: chain G residue 125 PHE Chi-restraints excluded: chain G residue 164 LEU Chi-restraints excluded: chain G residue 200 SER Chi-restraints excluded: chain G residue 248 LEU Chi-restraints excluded: chain R residue 42 THR Chi-restraints excluded: chain R residue 156 MET Chi-restraints excluded: chain S residue 29 PHE Chi-restraints excluded: chain S residue 99 LEU Chi-restraints excluded: chain T residue 148 ASP Chi-restraints excluded: chain T residue 151 CYS Chi-restraints excluded: chain T residue 155 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 148 optimal weight: 3.9990 chunk 188 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 217 optimal weight: 7.9990 chunk 22 optimal weight: 20.0000 chunk 47 optimal weight: 0.7980 chunk 56 optimal weight: 4.9990 chunk 207 optimal weight: 3.9990 chunk 85 optimal weight: 0.0000 chunk 123 optimal weight: 2.9990 chunk 159 optimal weight: 1.9990 overall best weight: 1.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN ** B 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 38 GLN ** R 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.176061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.125088 restraints weight = 38190.195| |-----------------------------------------------------------------------------| r_work (start): 0.3742 rms_B_bonded: 3.41 r_work: 0.3595 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.7329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 19453 Z= 0.192 Angle : 0.930 34.009 26333 Z= 0.445 Chirality : 0.046 0.480 2901 Planarity : 0.013 0.380 3238 Dihedral : 16.718 142.425 3129 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 15.56 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.24 % Favored : 95.63 % Rotamer: Outliers : 4.29 % Allowed : 23.77 % Favored : 71.94 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % 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: 0.32 (0.18), residues: 2265 helix: 0.93 (0.15), residues: 1276 sheet: -1.87 (0.46), residues: 133 loop : -0.39 (0.22), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.052 0.001 ARG B 63 TYR 0.067 0.003 TYR A 115 PHE 0.018 0.001 PHE R 158 TRP 0.016 0.002 TRP C 45 HIS 0.010 0.001 HIS R 152 Details of bonding type rmsd covalent geometry : bond 0.00410 (19396) covalent geometry : angle 0.82846 (26306) hydrogen bonds : bond 0.03731 ( 917) hydrogen bonds : angle 4.10644 ( 2666) metal coordination : bond 0.01970 ( 24) metal coordination : angle 13.19814 ( 27) Misc. bond : bond 0.01198 ( 33) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 198 time to evaluate : 0.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 GLU cc_start: 0.7840 (tp30) cc_final: 0.7625 (tt0) REVERT: A 212 GLU cc_start: 0.4629 (tt0) cc_final: 0.3499 (mt-10) REVERT: B 111 GLU cc_start: 0.8475 (tm-30) cc_final: 0.8198 (mt-10) REVERT: B 199 LEU cc_start: 0.6305 (mp) cc_final: 0.5739 (tt) REVERT: B 210 MET cc_start: 0.8928 (ttt) cc_final: 0.8716 (ttt) REVERT: C 73 TYR cc_start: 0.8827 (t80) cc_final: 0.8586 (t80) REVERT: C 205 LYS cc_start: 0.8964 (ttmt) cc_final: 0.8656 (tptt) REVERT: C 210 MET cc_start: 0.8770 (OUTLIER) cc_final: 0.8102 (tpt) REVERT: D 114 LYS cc_start: 0.8219 (mmtt) cc_final: 0.7859 (ptmt) REVERT: D 173 THR cc_start: 0.8361 (OUTLIER) cc_final: 0.7945 (p) REVERT: E 128 ARG cc_start: 0.8490 (mmm-85) cc_final: 0.7167 (mmt180) REVERT: E 229 MET cc_start: 0.7287 (mmt) cc_final: 0.6208 (ttt) REVERT: F 229 MET cc_start: 0.7393 (mmt) cc_final: 0.7149 (ttt) REVERT: F 246 GLU cc_start: 0.7417 (mm-30) cc_final: 0.7136 (mt-10) REVERT: G 205 LYS cc_start: 0.8908 (ttmt) cc_final: 0.8274 (tptt) REVERT: G 249 ARG cc_start: 0.8555 (tpp80) cc_final: 0.8284 (tpp80) REVERT: R 155 ARG cc_start: 0.4219 (mmt180) cc_final: 0.3765 (mmt180) REVERT: R 156 MET cc_start: 0.3957 (OUTLIER) cc_final: 0.3652 (ppp) REVERT: T 142 MET cc_start: 0.3888 (ptt) cc_final: 0.3452 (mmp) REVERT: T 156 MET cc_start: 0.4558 (tpt) cc_final: 0.3605 (tmm) outliers start: 81 outliers final: 68 residues processed: 260 average time/residue: 0.1550 time to fit residues: 60.1053 Evaluate side-chains 261 residues out of total 1973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 190 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 128 ARG Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain B residue 29 LYS Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 43 HIS Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain D residue 43 HIS Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 88 THR Chi-restraints excluded: chain E residue 127 ASP Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 276 LYS Chi-restraints excluded: chain F residue 21 LEU Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 43 HIS Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 63 ARG Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 125 PHE Chi-restraints excluded: chain F residue 153 THR Chi-restraints excluded: chain F residue 241 ILE Chi-restraints excluded: chain F residue 268 LEU Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 43 HIS Chi-restraints excluded: chain G residue 88 THR Chi-restraints excluded: chain G residue 97 HIS Chi-restraints excluded: chain G residue 113 LEU Chi-restraints excluded: chain G residue 125 PHE Chi-restraints excluded: chain G residue 164 LEU Chi-restraints excluded: chain G residue 200 SER Chi-restraints excluded: chain G residue 248 LEU Chi-restraints excluded: chain R residue 42 THR Chi-restraints excluded: chain R residue 156 MET Chi-restraints excluded: chain S residue 29 PHE Chi-restraints excluded: chain T residue 148 ASP Chi-restraints excluded: chain T residue 151 CYS Chi-restraints excluded: chain T residue 155 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 163 optimal weight: 0.0970 chunk 97 optimal weight: 0.9990 chunk 194 optimal weight: 9.9990 chunk 40 optimal weight: 3.9990 chunk 0 optimal weight: 30.0000 chunk 100 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 137 optimal weight: 0.6980 chunk 9 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 132 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 93 GLN ** T 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.187215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.136872 restraints weight = 38378.458| |-----------------------------------------------------------------------------| r_work (start): 0.3754 rms_B_bonded: 3.89 r_work: 0.3573 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.7463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.104 19453 Z= 0.190 Angle : 0.931 42.225 26333 Z= 0.448 Chirality : 0.046 0.474 2901 Planarity : 0.014 0.427 3238 Dihedral : 16.623 143.482 3129 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 15.14 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.93 % Favored : 95.98 % Rotamer: Outliers : 3.65 % Allowed : 24.51 % Favored : 71.84 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % 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: 0.39 (0.18), residues: 2265 helix: 1.07 (0.15), residues: 1241 sheet: -1.86 (0.45), residues: 133 loop : -0.45 (0.22), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.048 0.001 ARG B 63 TYR 0.058 0.003 TYR A 115 PHE 0.019 0.001 PHE A 154 TRP 0.015 0.001 TRP C 45 HIS 0.008 0.001 HIS S 152 Details of bonding type rmsd covalent geometry : bond 0.00395 (19396) covalent geometry : angle 0.84216 (26306) hydrogen bonds : bond 0.03636 ( 917) hydrogen bonds : angle 4.05923 ( 2666) metal coordination : bond 0.01871 ( 24) metal coordination : angle 12.42178 ( 27) Misc. bond : bond 0.01275 ( 33) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 205 time to evaluate : 0.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 GLU cc_start: 0.7878 (tp30) cc_final: 0.7624 (tt0) REVERT: A 209 GLU cc_start: 0.4556 (mm-30) cc_final: 0.4143 (mm-30) REVERT: A 212 GLU cc_start: 0.4741 (tt0) cc_final: 0.4141 (mp0) REVERT: B 111 GLU cc_start: 0.8491 (tm-30) cc_final: 0.8193 (mt-10) REVERT: B 199 LEU cc_start: 0.6363 (mp) cc_final: 0.5871 (tt) REVERT: C 73 TYR cc_start: 0.8844 (t80) cc_final: 0.8608 (t80) REVERT: C 210 MET cc_start: 0.8806 (OUTLIER) cc_final: 0.8111 (tpt) REVERT: D 114 LYS cc_start: 0.8309 (mmtt) cc_final: 0.7867 (ptmt) REVERT: E 128 ARG cc_start: 0.8543 (mmm-85) cc_final: 0.7792 (mmm-85) REVERT: E 229 MET cc_start: 0.7283 (mmt) cc_final: 0.6152 (ttt) REVERT: E 262 LYS cc_start: 0.3994 (tptm) cc_final: 0.3630 (tmtt) REVERT: F 229 MET cc_start: 0.7442 (mmt) cc_final: 0.7083 (ttt) REVERT: F 246 GLU cc_start: 0.7470 (mm-30) cc_final: 0.7160 (mt-10) REVERT: G 205 LYS cc_start: 0.8908 (ttmt) cc_final: 0.8294 (tptp) REVERT: R 156 MET cc_start: 0.4090 (tmm) cc_final: 0.3851 (ppp) REVERT: T 142 MET cc_start: 0.3826 (ptt) cc_final: 0.3390 (mmp) REVERT: T 156 MET cc_start: 0.4414 (tpt) cc_final: 0.3512 (tmm) outliers start: 69 outliers final: 65 residues processed: 255 average time/residue: 0.1610 time to fit residues: 60.4374 Evaluate side-chains 258 residues out of total 1973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 192 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 128 ARG Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain B residue 29 LYS Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 63 ARG Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain D residue 43 HIS Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 88 THR Chi-restraints excluded: chain E residue 127 ASP Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain F residue 21 LEU Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 43 HIS Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 63 ARG Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 125 PHE Chi-restraints excluded: chain F residue 153 THR Chi-restraints excluded: chain F residue 241 ILE Chi-restraints excluded: chain F residue 268 LEU Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 43 HIS Chi-restraints excluded: chain G residue 88 THR Chi-restraints excluded: chain G residue 97 HIS Chi-restraints excluded: chain G residue 113 LEU Chi-restraints excluded: chain G residue 125 PHE Chi-restraints excluded: chain G residue 164 LEU Chi-restraints excluded: chain G residue 248 LEU Chi-restraints excluded: chain R residue 42 THR Chi-restraints excluded: chain S residue 29 PHE Chi-restraints excluded: chain T residue 148 ASP Chi-restraints excluded: chain T residue 151 CYS Chi-restraints excluded: chain T residue 155 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 58 optimal weight: 0.0060 chunk 119 optimal weight: 0.9980 chunk 216 optimal weight: 10.0000 chunk 146 optimal weight: 0.7980 chunk 180 optimal weight: 6.9990 chunk 51 optimal weight: 2.9990 chunk 166 optimal weight: 0.9990 chunk 77 optimal weight: 0.7980 chunk 117 optimal weight: 0.8980 chunk 36 optimal weight: 7.9990 chunk 45 optimal weight: 1.9990 overall best weight: 0.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 GLN ** B 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.176217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.127938 restraints weight = 38359.335| |-----------------------------------------------------------------------------| r_work (start): 0.3780 rms_B_bonded: 3.74 r_work: 0.3588 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.7576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.099 19453 Z= 0.186 Angle : 0.876 28.894 26333 Z= 0.427 Chirality : 0.045 0.472 2901 Planarity : 0.013 0.373 3238 Dihedral : 16.589 144.039 3129 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 14.87 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.15 % Favored : 95.76 % Rotamer: Outliers : 3.60 % Allowed : 24.67 % Favored : 71.73 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: 0.42 (0.18), residues: 2265 helix: 1.02 (0.15), residues: 1276 sheet: -1.77 (0.46), residues: 133 loop : -0.37 (0.22), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.059 0.001 ARG E 116 TYR 0.058 0.002 TYR A 115 PHE 0.014 0.001 PHE A 154 TRP 0.018 0.002 TRP D 211 HIS 0.011 0.001 HIS R 152 Details of bonding type rmsd covalent geometry : bond 0.00386 (19396) covalent geometry : angle 0.79140 (26306) hydrogen bonds : bond 0.03520 ( 917) hydrogen bonds : angle 4.04389 ( 2666) metal coordination : bond 0.01877 ( 24) metal coordination : angle 11.75854 ( 27) Misc. bond : bond 0.01282 ( 33) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6163.88 seconds wall clock time: 106 minutes 4.60 seconds (6364.60 seconds total)