Starting phenix.real_space_refine on Wed Jan 14 04:41:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fvj_29489/01_2026/8fvj_29489.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fvj_29489/01_2026/8fvj_29489.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8fvj_29489/01_2026/8fvj_29489.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fvj_29489/01_2026/8fvj_29489.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8fvj_29489/01_2026/8fvj_29489.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fvj_29489/01_2026/8fvj_29489.map" } resolution = 3.54 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 2 6.06 5 S 74 5.16 5 C 7998 2.51 5 N 2178 2.21 5 O 2310 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s 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: 12562 Number of models: 1 Model: "" Number of chains: 12 Chain: "0" Number of atoms: 1139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1139 Classifications: {'peptide': 138} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 134} Chain breaks: 2 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "1" Number of atoms: 1344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1344 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 8, 'TRANS': 153} Chain breaks: 3 Chain: "3" Number of atoms: 687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 687 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 6, 'TRANS': 80} Chain breaks: 1 Chain: "4" Number of atoms: 691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 691 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 5, 'TRANS': 81} Chain breaks: 1 Chain: "2" Number of atoms: 2419 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2419 Classifications: {'peptide': 294} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 8, 'TRANS': 285} Chain breaks: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "5" Number of atoms: 1139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1139 Classifications: {'peptide': 138} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 134} Chain breaks: 2 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "6" Number of atoms: 1344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1344 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 8, 'TRANS': 153} Chain breaks: 3 Chain: "8" Number of atoms: 687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 687 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 6, 'TRANS': 80} Chain breaks: 1 Chain: "9" Number of atoms: 691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 691 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 5, 'TRANS': 81} Chain breaks: 1 Chain: "7" Number of atoms: 2419 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2419 Classifications: {'peptide': 294} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 8, 'TRANS': 285} Chain breaks: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "1" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "6" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2059 SG CYS 1 114 21.625 89.343 24.693 1.00 45.00 S ATOM 2206 SG CYS 1 133 19.079 87.318 27.525 1.00 43.58 S ATOM 8339 SG CYS 6 114 98.520 58.577 25.713 1.00 44.80 S ATOM 8486 SG CYS 6 133 100.248 61.597 27.483 1.00 43.28 S Time building chain proxies: 2.68, per 1000 atoms: 0.21 Number of scatterers: 12562 At special positions: 0 Unit cell: (119.85, 149.94, 82.62, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 2 29.99 S 74 16.00 O 2310 8.00 N 2178 7.00 C 7998 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=0, symmetry=0 Time building additional restraints: 0.92 Conformation dependent library (CDL) restraints added in 522.2 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 1 201 " pdb="ZN ZN 1 201 " - pdb=" NE2 HIS 1 139 " pdb="ZN ZN 1 201 " - pdb=" NE2 HIS 1 108 " pdb="ZN ZN 1 201 " - pdb=" SG CYS 1 114 " pdb="ZN ZN 1 201 " - pdb=" SG CYS 1 133 " pdb=" ZN 6 201 " pdb="ZN ZN 6 201 " - pdb=" NE2 HIS 6 139 " pdb="ZN ZN 6 201 " - pdb=" NE2 HIS 6 108 " pdb="ZN ZN 6 201 " - pdb=" SG CYS 6 114 " pdb="ZN ZN 6 201 " - pdb=" SG CYS 6 133 " Number of angles added : 4 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2952 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 12 sheets defined 56.4% alpha, 9.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain '0' and resid 7 through 15 removed outlier: 3.742A pdb=" N PHE 0 12 " --> pdb=" O GLN 0 8 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N GLU 0 13 " --> pdb=" O ARG 0 9 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASN 0 14 " --> pdb=" O SER 0 10 " (cutoff:3.500A) Processing helix chain '0' and resid 15 through 22 removed outlier: 3.560A pdb=" N ARG 0 19 " --> pdb=" O GLU 0 15 " (cutoff:3.500A) Processing helix chain '0' and resid 36 through 49 Processing helix chain '0' and resid 128 through 135 Processing helix chain '0' and resid 136 through 149 removed outlier: 3.547A pdb=" N GLN 0 140 " --> pdb=" O ASP 0 136 " (cutoff:3.500A) Processing helix chain '1' and resid 14 through 31 Processing helix chain '1' and resid 99 through 109 Processing helix chain '1' and resid 116 through 119 Processing helix chain '1' and resid 120 through 125 Processing helix chain '1' and resid 135 through 139 Processing helix chain '1' and resid 145 through 155 Processing helix chain '1' and resid 167 through 172 removed outlier: 3.826A pdb=" N THR 1 171 " --> pdb=" O VAL 1 167 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLU 1 172 " --> pdb=" O ARG 1 168 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 167 through 172' Processing helix chain '3' and resid 23 through 30 removed outlier: 3.910A pdb=" N ILE 3 30 " --> pdb=" O GLU 3 26 " (cutoff:3.500A) Processing helix chain '3' and resid 32 through 36 removed outlier: 4.213A pdb=" N LEU 3 35 " --> pdb=" O GLU 3 32 " (cutoff:3.500A) Processing helix chain '3' and resid 56 through 61 removed outlier: 3.867A pdb=" N CYS 3 60 " --> pdb=" O THR 3 56 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY 3 61 " --> pdb=" O LEU 3 57 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 56 through 61' Processing helix chain '4' and resid 32 through 37 Processing helix chain '4' and resid 39 through 47 Processing helix chain '4' and resid 66 through 83 removed outlier: 5.090A pdb=" N LYS 4 72 " --> pdb=" O HIS 4 68 " (cutoff:3.500A) Processing helix chain '4' and resid 99 through 110 Processing helix chain '2' and resid 14 through 31 removed outlier: 3.601A pdb=" N LYS 2 18 " --> pdb=" O GLN 2 14 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N ASP 2 20 " --> pdb=" O GLU 2 16 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N PHE 2 21 " --> pdb=" O ASP 2 17 " (cutoff:3.500A) Proline residue: 2 24 - end of helix Processing helix chain '2' and resid 36 through 54 Processing helix chain '2' and resid 56 through 83 removed outlier: 4.291A pdb=" N HIS 2 83 " --> pdb=" O ARG 2 79 " (cutoff:3.500A) Processing helix chain '2' and resid 85 through 107 Processing helix chain '2' and resid 111 through 118 Processing helix chain '2' and resid 134 through 169 removed outlier: 5.141A pdb=" N SER 2 149 " --> pdb=" O GLU 2 145 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N ASN 2 150 " --> pdb=" O SER 2 146 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ASN 2 153 " --> pdb=" O SER 2 149 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N ARG 2 154 " --> pdb=" O ASN 2 150 " (cutoff:3.500A) Processing helix chain '2' and resid 173 through 187 removed outlier: 4.213A pdb=" N VAL 2 177 " --> pdb=" O ASP 2 173 " (cutoff:3.500A) Processing helix chain '2' and resid 195 through 225 removed outlier: 3.766A pdb=" N GLU 2 203 " --> pdb=" O ARG 2 199 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N LYS 2 204 " --> pdb=" O ASP 2 200 " (cutoff:3.500A) Proline residue: 2 219 - end of helix Processing helix chain '2' and resid 227 through 248 Processing helix chain '2' and resid 257 through 270 Processing helix chain '2' and resid 273 through 288 removed outlier: 4.015A pdb=" N GLN 2 282 " --> pdb=" O LEU 2 278 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N GLY 2 283 " --> pdb=" O ALA 2 279 " (cutoff:3.500A) Processing helix chain '2' and resid 289 through 300 Processing helix chain '2' and resid 306 through 319 removed outlier: 4.452A pdb=" N MET 2 310 " --> pdb=" O GLY 2 306 " (cutoff:3.500A) Processing helix chain '5' and resid 8 through 15 removed outlier: 3.737A pdb=" N PHE 5 12 " --> pdb=" O GLN 5 8 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N GLU 5 13 " --> pdb=" O ARG 5 9 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASN 5 14 " --> pdb=" O SER 5 10 " (cutoff:3.500A) Processing helix chain '5' and resid 15 through 22 removed outlier: 3.562A pdb=" N ARG 5 19 " --> pdb=" O GLU 5 15 " (cutoff:3.500A) Processing helix chain '5' and resid 36 through 49 Processing helix chain '5' and resid 128 through 135 Processing helix chain '5' and resid 136 through 149 removed outlier: 3.549A pdb=" N GLN 5 140 " --> pdb=" O ASP 5 136 " (cutoff:3.500A) Processing helix chain '6' and resid 14 through 31 Processing helix chain '6' and resid 99 through 109 Processing helix chain '6' and resid 116 through 119 Processing helix chain '6' and resid 120 through 125 Processing helix chain '6' and resid 135 through 139 Processing helix chain '6' and resid 145 through 155 Processing helix chain '6' and resid 167 through 172 removed outlier: 3.816A pdb=" N THR 6 171 " --> pdb=" O VAL 6 167 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLU 6 172 " --> pdb=" O ARG 6 168 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 167 through 172' Processing helix chain '8' and resid 23 through 30 removed outlier: 3.922A pdb=" N ILE 8 30 " --> pdb=" O GLU 8 26 " (cutoff:3.500A) Processing helix chain '8' and resid 32 through 36 removed outlier: 4.220A pdb=" N LEU 8 35 " --> pdb=" O GLU 8 32 " (cutoff:3.500A) Processing helix chain '8' and resid 56 through 61 removed outlier: 3.876A pdb=" N CYS 8 60 " --> pdb=" O THR 8 56 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY 8 61 " --> pdb=" O LEU 8 57 " (cutoff:3.500A) No H-bonds generated for 'chain '8' and resid 56 through 61' Processing helix chain '9' and resid 32 through 37 removed outlier: 3.508A pdb=" N ALA 9 36 " --> pdb=" O LYS 9 32 " (cutoff:3.500A) Processing helix chain '9' and resid 39 through 47 Processing helix chain '9' and resid 66 through 83 removed outlier: 5.112A pdb=" N LYS 9 72 " --> pdb=" O HIS 9 68 " (cutoff:3.500A) Processing helix chain '9' and resid 99 through 110 Processing helix chain '7' and resid 14 through 31 removed outlier: 3.602A pdb=" N LYS 7 18 " --> pdb=" O GLN 7 14 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N ASP 7 20 " --> pdb=" O GLU 7 16 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N PHE 7 21 " --> pdb=" O ASP 7 17 " (cutoff:3.500A) Proline residue: 7 24 - end of helix Processing helix chain '7' and resid 36 through 54 Processing helix chain '7' and resid 56 through 83 removed outlier: 4.286A pdb=" N HIS 7 83 " --> pdb=" O ARG 7 79 " (cutoff:3.500A) Processing helix chain '7' and resid 85 through 107 Processing helix chain '7' and resid 111 through 118 Processing helix chain '7' and resid 134 through 169 removed outlier: 5.127A pdb=" N SER 7 149 " --> pdb=" O GLU 7 145 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N ASN 7 150 " --> pdb=" O SER 7 146 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ASN 7 153 " --> pdb=" O SER 7 149 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N ARG 7 154 " --> pdb=" O ASN 7 150 " (cutoff:3.500A) Processing helix chain '7' and resid 173 through 187 removed outlier: 4.219A pdb=" N VAL 7 177 " --> pdb=" O ASP 7 173 " (cutoff:3.500A) Processing helix chain '7' and resid 195 through 201 Processing helix chain '7' and resid 201 through 225 Proline residue: 7 219 - end of helix Processing helix chain '7' and resid 227 through 248 Processing helix chain '7' and resid 257 through 270 Processing helix chain '7' and resid 273 through 286 removed outlier: 4.044A pdb=" N GLN 7 282 " --> pdb=" O LEU 7 278 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N GLY 7 283 " --> pdb=" O ALA 7 279 " (cutoff:3.500A) Processing helix chain '7' and resid 289 through 300 Processing helix chain '7' and resid 306 through 319 removed outlier: 4.330A pdb=" N MET 7 310 " --> pdb=" O GLY 7 306 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain '0' and resid 25 through 27 Processing sheet with id=AA2, first strand: chain '0' and resid 55 through 57 removed outlier: 3.541A pdb=" N ILE 0 55 " --> pdb=" O PHE 0 68 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLN 1 83 " --> pdb=" O VAL 1 13 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY 1 84 " --> pdb=" O TYR 1 69 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N LEU 1 64 " --> pdb=" O HIS 1 56 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N HIS 1 56 " --> pdb=" O LEU 1 64 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ILE 1 66 " --> pdb=" O GLU 1 54 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLU 1 54 " --> pdb=" O ILE 1 66 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N THR 1 68 " --> pdb=" O SER 1 52 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '1' and resid 6 through 7 removed outlier: 3.977A pdb=" N GLN 1 83 " --> pdb=" O VAL 1 13 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain '0' and resid 98 through 103 Processing sheet with id=AA5, first strand: chain '3' and resid 43 through 44 removed outlier: 3.749A pdb=" N ARG 3 43 " --> pdb=" O ALA 3 78 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ALA 3 78 " --> pdb=" O ARG 3 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain '4' and resid 21 through 22 Processing sheet with id=AA7, first strand: chain '5' and resid 25 through 27 Processing sheet with id=AA8, first strand: chain '5' and resid 55 through 57 removed outlier: 3.612A pdb=" N ILE 5 55 " --> pdb=" O PHE 5 68 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLN 6 83 " --> pdb=" O VAL 6 13 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY 6 84 " --> pdb=" O TYR 6 69 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N LEU 6 64 " --> pdb=" O HIS 6 56 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N HIS 6 56 " --> pdb=" O LEU 6 64 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ILE 6 66 " --> pdb=" O GLU 6 54 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N GLU 6 54 " --> pdb=" O ILE 6 66 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N THR 6 68 " --> pdb=" O SER 6 52 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain '6' and resid 6 through 7 removed outlier: 3.951A pdb=" N GLN 6 83 " --> pdb=" O VAL 6 13 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain '5' and resid 98 through 103 Processing sheet with id=AB2, first strand: chain '8' and resid 9 through 10 removed outlier: 8.187A pdb=" N LEU 8 77 " --> pdb=" O HIS 8 10 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ALA 8 78 " --> pdb=" O ARG 8 43 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ARG 8 43 " --> pdb=" O ALA 8 78 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain '9' and resid 21 through 22 629 hydrogen bonds defined for protein. 1821 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.86 Time building geometry restraints manager: 1.27 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: 4067 1.34 - 1.46: 1850 1.46 - 1.58: 6789 1.58 - 1.69: 0 1.69 - 1.81: 114 Bond restraints: 12820 Sorted by residual: bond pdb=" CA TYR 1 111 " pdb=" C TYR 1 111 " ideal model delta sigma weight residual 1.525 1.500 0.025 1.25e-02 6.40e+03 4.06e+00 bond pdb=" CA HIS 1 139 " pdb=" C HIS 1 139 " ideal model delta sigma weight residual 1.527 1.506 0.021 1.19e-02 7.06e+03 3.03e+00 bond pdb=" CA HIS 6 139 " pdb=" C HIS 6 139 " ideal model delta sigma weight residual 1.525 1.505 0.021 1.29e-02 6.01e+03 2.54e+00 bond pdb=" N ASP 6 113 " pdb=" CA ASP 6 113 " ideal model delta sigma weight residual 1.455 1.473 -0.018 1.27e-02 6.20e+03 1.96e+00 bond pdb=" C ARG 5 35 " pdb=" N PRO 5 36 " ideal model delta sigma weight residual 1.331 1.347 -0.016 1.21e-02 6.83e+03 1.73e+00 ... (remaining 12815 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.51: 16700 1.51 - 3.02: 417 3.02 - 4.52: 107 4.52 - 6.03: 41 6.03 - 7.54: 9 Bond angle restraints: 17274 Sorted by residual: angle pdb=" C LEU 2 261 " pdb=" N MET 2 262 " pdb=" CA MET 2 262 " ideal model delta sigma weight residual 121.14 114.30 6.84 1.75e+00 3.27e-01 1.53e+01 angle pdb=" C LEU 7 261 " pdb=" N MET 7 262 " pdb=" CA MET 7 262 " ideal model delta sigma weight residual 121.14 114.35 6.79 1.75e+00 3.27e-01 1.51e+01 angle pdb=" CA MET 2 262 " pdb=" CB MET 2 262 " pdb=" CG MET 2 262 " ideal model delta sigma weight residual 114.10 120.53 -6.43 2.00e+00 2.50e-01 1.03e+01 angle pdb=" N ASP 1 113 " pdb=" CA ASP 1 113 " pdb=" C ASP 1 113 " ideal model delta sigma weight residual 110.52 115.20 -4.68 1.48e+00 4.57e-01 9.99e+00 angle pdb=" CA MET 7 262 " pdb=" CB MET 7 262 " pdb=" CG MET 7 262 " ideal model delta sigma weight residual 114.10 120.21 -6.11 2.00e+00 2.50e-01 9.32e+00 ... (remaining 17269 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 6403 17.94 - 35.87: 985 35.87 - 53.81: 315 53.81 - 71.74: 54 71.74 - 89.68: 27 Dihedral angle restraints: 7784 sinusoidal: 3272 harmonic: 4512 Sorted by residual: dihedral pdb=" CA HIS 6 110 " pdb=" C HIS 6 110 " pdb=" N TYR 6 111 " pdb=" CA TYR 6 111 " ideal model delta harmonic sigma weight residual -180.00 -156.23 -23.77 0 5.00e+00 4.00e-02 2.26e+01 dihedral pdb=" CA ASP 7 200 " pdb=" C ASP 7 200 " pdb=" N ASN 7 201 " pdb=" CA ASN 7 201 " ideal model delta harmonic sigma weight residual 180.00 160.08 19.92 0 5.00e+00 4.00e-02 1.59e+01 dihedral pdb=" CA ARG 1 4 " pdb=" C ARG 1 4 " pdb=" N TRP 1 5 " pdb=" CA TRP 1 5 " ideal model delta harmonic sigma weight residual -180.00 -160.26 -19.74 0 5.00e+00 4.00e-02 1.56e+01 ... (remaining 7781 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1383 0.044 - 0.088: 383 0.088 - 0.132: 103 0.132 - 0.176: 6 0.176 - 0.220: 1 Chirality restraints: 1876 Sorted by residual: chirality pdb=" CA PHE 1 112 " pdb=" N PHE 1 112 " pdb=" C PHE 1 112 " pdb=" CB PHE 1 112 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CA GLU 2 308 " pdb=" N GLU 2 308 " pdb=" C GLU 2 308 " pdb=" CB GLU 2 308 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.38e-01 chirality pdb=" CA GLU 7 308 " pdb=" N GLU 7 308 " pdb=" C GLU 7 308 " pdb=" CB GLU 7 308 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.89e-01 ... (remaining 1873 not shown) Planarity restraints: 2212 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS 1 110 " -0.016 2.00e-02 2.50e+03 3.16e-02 9.96e+00 pdb=" C HIS 1 110 " 0.055 2.00e-02 2.50e+03 pdb=" O HIS 1 110 " -0.020 2.00e-02 2.50e+03 pdb=" N TYR 1 111 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP 2 97 " 0.020 2.00e-02 2.50e+03 1.72e-02 7.40e+00 pdb=" CG TRP 2 97 " -0.046 2.00e-02 2.50e+03 pdb=" CD1 TRP 2 97 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP 2 97 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP 2 97 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP 2 97 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP 2 97 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP 2 97 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP 2 97 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP 2 97 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP 7 97 " 0.020 2.00e-02 2.50e+03 1.68e-02 7.10e+00 pdb=" CG TRP 7 97 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 TRP 7 97 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP 7 97 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP 7 97 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP 7 97 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP 7 97 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP 7 97 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP 7 97 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP 7 97 " 0.003 2.00e-02 2.50e+03 ... (remaining 2209 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 546 2.71 - 3.26: 13224 3.26 - 3.81: 21184 3.81 - 4.35: 25207 4.35 - 4.90: 42299 Nonbonded interactions: 102460 Sorted by model distance: nonbonded pdb=" OG SER 6 53 " pdb=" OG1 THR 6 68 " model vdw 2.164 3.040 nonbonded pdb=" OG SER 1 53 " pdb=" OG1 THR 1 68 " model vdw 2.182 3.040 nonbonded pdb=" NH2 ARG 3 8 " pdb=" O GLU 3 91 " model vdw 2.194 3.120 nonbonded pdb=" O ASP 5 155 " pdb=" OG SER 6 116 " model vdw 2.238 3.040 nonbonded pdb=" NE2 GLN 5 8 " pdb=" OE1 GLN 5 140 " model vdw 2.251 3.120 ... (remaining 102455 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: 0.01 Found NCS groups: ncs_group { reference = chain '0' selection = chain '5' } ncs_group { reference = chain '1' selection = chain '6' } ncs_group { reference = chain '2' selection = chain '7' } ncs_group { reference = chain '3' selection = chain '8' } ncs_group { reference = chain '4' selection = chain '9' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 29.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.440 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.130 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 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:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6840 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 : 0.004 0.173 12828 Z= 0.165 Angle : 0.671 17.781 17278 Z= 0.349 Chirality : 0.043 0.220 1876 Planarity : 0.005 0.055 2212 Dihedral : 19.520 89.678 4832 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 15.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 0.73 % Allowed : 34.74 % Favored : 64.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.21 (0.21), residues: 1484 helix: 0.65 (0.19), residues: 764 sheet: -2.70 (0.39), residues: 134 loop : -2.31 (0.23), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG 6 90 TYR 0.027 0.002 TYR 1 148 PHE 0.011 0.001 PHE 8 4 TRP 0.046 0.002 TRP 2 97 HIS 0.007 0.001 HIS 6 43 Details of bonding type rmsd covalent geometry : bond 0.00343 (12820) covalent geometry : angle 0.65550 (17274) hydrogen bonds : bond 0.15989 ( 619) hydrogen bonds : angle 5.95713 ( 1821) metal coordination : bond 0.08725 ( 8) metal coordination : angle 9.34523 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 199 time to evaluate : 0.557 Fit side-chains revert: symmetry clash REVERT: 0 122 MET cc_start: 0.5734 (tpp) cc_final: 0.5501 (tpp) REVERT: 1 5 TRP cc_start: 0.6873 (m100) cc_final: 0.6072 (m100) REVERT: 3 46 LYS cc_start: 0.6532 (tptt) cc_final: 0.6030 (tptt) REVERT: 2 300 MET cc_start: 0.4410 (mtt) cc_final: 0.3990 (mtt) REVERT: 8 46 LYS cc_start: 0.6536 (tptt) cc_final: 0.6052 (tptt) outliers start: 10 outliers final: 3 residues processed: 205 average time/residue: 0.1270 time to fit residues: 36.4495 Evaluate side-chains 181 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 178 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 16 MET Chi-restraints excluded: chain 1 residue 44 TYR Chi-restraints excluded: chain 6 residue 16 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 98 optimal weight: 0.5980 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 3 ASN ** 1 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 186 ASN ** 6 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 186 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4585 r_free = 0.4585 target = 0.183215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.136297 restraints weight = 23378.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.138256 restraints weight = 17596.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.139460 restraints weight = 14306.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.140212 restraints weight = 12104.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.141726 restraints weight = 10989.776| |-----------------------------------------------------------------------------| r_work (final): 0.4074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.1489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.089 12828 Z= 0.270 Angle : 0.745 8.789 17278 Z= 0.390 Chirality : 0.048 0.165 1876 Planarity : 0.006 0.065 2212 Dihedral : 4.938 37.530 1668 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 14.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.82 % Favored : 92.18 % Rotamer: Outliers : 7.81 % Allowed : 28.98 % Favored : 63.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.35 (0.21), residues: 1484 helix: 0.45 (0.19), residues: 768 sheet: -2.55 (0.39), residues: 122 loop : -2.35 (0.22), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG 9 82 TYR 0.025 0.002 TYR 9 79 PHE 0.046 0.002 PHE 2 213 TRP 0.029 0.003 TRP 7 97 HIS 0.014 0.002 HIS 1 139 Details of bonding type rmsd covalent geometry : bond 0.00650 (12820) covalent geometry : angle 0.73991 (17274) hydrogen bonds : bond 0.05078 ( 619) hydrogen bonds : angle 5.16088 ( 1821) metal coordination : bond 0.04426 ( 8) metal coordination : angle 5.57775 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 188 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 0 12 PHE cc_start: 0.7713 (OUTLIER) cc_final: 0.7278 (m-80) REVERT: 3 9 ARG cc_start: 0.5598 (OUTLIER) cc_final: 0.5367 (tpt90) REVERT: 3 46 LYS cc_start: 0.6540 (tptt) cc_final: 0.6076 (tptt) REVERT: 4 72 LYS cc_start: 0.7834 (OUTLIER) cc_final: 0.7568 (mttm) REVERT: 4 95 ILE cc_start: 0.7268 (OUTLIER) cc_final: 0.6565 (pt) REVERT: 2 139 MET cc_start: 0.7144 (mmm) cc_final: 0.6837 (mtm) REVERT: 2 150 ASN cc_start: 0.6444 (OUTLIER) cc_final: 0.6211 (p0) REVERT: 5 12 PHE cc_start: 0.7687 (OUTLIER) cc_final: 0.7229 (m-80) REVERT: 8 46 LYS cc_start: 0.6503 (tptt) cc_final: 0.6058 (tptt) REVERT: 9 72 LYS cc_start: 0.7854 (OUTLIER) cc_final: 0.7546 (mttm) REVERT: 9 95 ILE cc_start: 0.7175 (OUTLIER) cc_final: 0.6431 (pt) REVERT: 7 139 MET cc_start: 0.7114 (mmm) cc_final: 0.6819 (mtm) REVERT: 7 150 ASN cc_start: 0.6483 (OUTLIER) cc_final: 0.6206 (p0) REVERT: 7 184 TYR cc_start: 0.7151 (OUTLIER) cc_final: 0.6774 (m-80) REVERT: 7 248 TYR cc_start: 0.8314 (OUTLIER) cc_final: 0.7587 (m-10) outliers start: 107 outliers final: 55 residues processed: 276 average time/residue: 0.1042 time to fit residues: 42.3188 Evaluate side-chains 239 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 173 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 12 PHE Chi-restraints excluded: chain 0 residue 21 LEU Chi-restraints excluded: chain 0 residue 55 ILE Chi-restraints excluded: chain 0 residue 58 VAL Chi-restraints excluded: chain 0 residue 62 THR Chi-restraints excluded: chain 0 residue 103 LEU Chi-restraints excluded: chain 0 residue 106 VAL Chi-restraints excluded: chain 0 residue 138 LEU Chi-restraints excluded: chain 1 residue 8 MET Chi-restraints excluded: chain 1 residue 20 THR Chi-restraints excluded: chain 1 residue 44 TYR Chi-restraints excluded: chain 1 residue 64 LEU Chi-restraints excluded: chain 1 residue 87 ILE Chi-restraints excluded: chain 1 residue 96 THR Chi-restraints excluded: chain 1 residue 98 VAL Chi-restraints excluded: chain 1 residue 145 SER Chi-restraints excluded: chain 1 residue 169 LYS Chi-restraints excluded: chain 3 residue 7 ILE Chi-restraints excluded: chain 3 residue 9 ARG Chi-restraints excluded: chain 3 residue 11 LYS Chi-restraints excluded: chain 3 residue 25 PHE Chi-restraints excluded: chain 3 residue 63 THR Chi-restraints excluded: chain 3 residue 91 GLU Chi-restraints excluded: chain 4 residue 72 LYS Chi-restraints excluded: chain 4 residue 73 VAL Chi-restraints excluded: chain 4 residue 78 THR Chi-restraints excluded: chain 4 residue 95 ILE Chi-restraints excluded: chain 2 residue 50 VAL Chi-restraints excluded: chain 2 residue 67 GLU Chi-restraints excluded: chain 2 residue 150 ASN Chi-restraints excluded: chain 2 residue 212 ARG Chi-restraints excluded: chain 2 residue 310 MET Chi-restraints excluded: chain 5 residue 12 PHE Chi-restraints excluded: chain 5 residue 21 LEU Chi-restraints excluded: chain 5 residue 46 ASN Chi-restraints excluded: chain 5 residue 55 ILE Chi-restraints excluded: chain 5 residue 58 VAL Chi-restraints excluded: chain 5 residue 62 THR Chi-restraints excluded: chain 5 residue 103 LEU Chi-restraints excluded: chain 5 residue 106 VAL Chi-restraints excluded: chain 5 residue 138 LEU Chi-restraints excluded: chain 6 residue 7 VAL Chi-restraints excluded: chain 6 residue 20 THR Chi-restraints excluded: chain 6 residue 44 TYR Chi-restraints excluded: chain 6 residue 64 LEU Chi-restraints excluded: chain 6 residue 87 ILE Chi-restraints excluded: chain 6 residue 96 THR Chi-restraints excluded: chain 6 residue 98 VAL Chi-restraints excluded: chain 6 residue 120 ILE Chi-restraints excluded: chain 6 residue 145 SER Chi-restraints excluded: chain 6 residue 169 LYS Chi-restraints excluded: chain 6 residue 173 ASP Chi-restraints excluded: chain 8 residue 7 ILE Chi-restraints excluded: chain 8 residue 25 PHE Chi-restraints excluded: chain 8 residue 63 THR Chi-restraints excluded: chain 9 residue 45 MET Chi-restraints excluded: chain 9 residue 72 LYS Chi-restraints excluded: chain 9 residue 73 VAL Chi-restraints excluded: chain 9 residue 78 THR Chi-restraints excluded: chain 9 residue 95 ILE Chi-restraints excluded: chain 7 residue 50 VAL Chi-restraints excluded: chain 7 residue 150 ASN Chi-restraints excluded: chain 7 residue 184 TYR Chi-restraints excluded: chain 7 residue 198 TYR Chi-restraints excluded: chain 7 residue 248 TYR Chi-restraints excluded: chain 7 residue 301 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 140 optimal weight: 10.0000 chunk 35 optimal weight: 0.0010 chunk 142 optimal weight: 0.9990 chunk 68 optimal weight: 0.9980 chunk 112 optimal weight: 4.9990 chunk 58 optimal weight: 9.9990 chunk 47 optimal weight: 3.9990 chunk 100 optimal weight: 0.9980 chunk 122 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 69 optimal weight: 9.9990 overall best weight: 1.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4607 r_free = 0.4607 target = 0.191760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.139691 restraints weight = 24094.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.142309 restraints weight = 17891.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.143393 restraints weight = 14464.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.143658 restraints weight = 11637.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.143781 restraints weight = 12040.987| |-----------------------------------------------------------------------------| r_work (final): 0.4085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 12828 Z= 0.178 Angle : 0.642 7.040 17278 Z= 0.335 Chirality : 0.044 0.151 1876 Planarity : 0.005 0.063 2212 Dihedral : 4.635 35.963 1662 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 7.01 % Allowed : 29.85 % Favored : 63.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.21), residues: 1484 helix: 0.50 (0.19), residues: 782 sheet: -2.54 (0.39), residues: 122 loop : -2.33 (0.23), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG 9 82 TYR 0.016 0.002 TYR 2 214 PHE 0.049 0.002 PHE 2 213 TRP 0.023 0.002 TRP 7 97 HIS 0.007 0.001 HIS 6 139 Details of bonding type rmsd covalent geometry : bond 0.00422 (12820) covalent geometry : angle 0.63745 (17274) hydrogen bonds : bond 0.04450 ( 619) hydrogen bonds : angle 4.94687 ( 1821) metal coordination : bond 0.02707 ( 8) metal coordination : angle 4.87361 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 195 time to evaluate : 0.651 Fit side-chains revert: symmetry clash REVERT: 0 12 PHE cc_start: 0.7695 (OUTLIER) cc_final: 0.7344 (m-80) REVERT: 0 66 LEU cc_start: 0.8249 (mm) cc_final: 0.7656 (mm) REVERT: 1 70 TRP cc_start: 0.7287 (OUTLIER) cc_final: 0.6870 (m100) REVERT: 3 46 LYS cc_start: 0.6509 (tptt) cc_final: 0.6046 (tptt) REVERT: 3 62 PHE cc_start: 0.4787 (OUTLIER) cc_final: 0.4573 (t80) REVERT: 4 72 LYS cc_start: 0.7802 (OUTLIER) cc_final: 0.7547 (mttm) REVERT: 2 150 ASN cc_start: 0.6431 (OUTLIER) cc_final: 0.6181 (p0) REVERT: 5 12 PHE cc_start: 0.7650 (OUTLIER) cc_final: 0.7290 (m-80) REVERT: 5 66 LEU cc_start: 0.8312 (mm) cc_final: 0.7676 (mm) REVERT: 6 70 TRP cc_start: 0.7143 (OUTLIER) cc_final: 0.6753 (m100) REVERT: 8 46 LYS cc_start: 0.6447 (tptt) cc_final: 0.5996 (tptt) REVERT: 8 62 PHE cc_start: 0.4779 (OUTLIER) cc_final: 0.4578 (t80) REVERT: 7 150 ASN cc_start: 0.6479 (OUTLIER) cc_final: 0.6234 (p0) REVERT: 7 184 TYR cc_start: 0.7136 (OUTLIER) cc_final: 0.6742 (m-10) REVERT: 7 248 TYR cc_start: 0.8299 (OUTLIER) cc_final: 0.7611 (m-10) outliers start: 96 outliers final: 47 residues processed: 271 average time/residue: 0.1037 time to fit residues: 41.5812 Evaluate side-chains 232 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 174 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 12 PHE Chi-restraints excluded: chain 0 residue 55 ILE Chi-restraints excluded: chain 0 residue 103 LEU Chi-restraints excluded: chain 0 residue 106 VAL Chi-restraints excluded: chain 0 residue 138 LEU Chi-restraints excluded: chain 1 residue 8 MET Chi-restraints excluded: chain 1 residue 20 THR Chi-restraints excluded: chain 1 residue 44 TYR Chi-restraints excluded: chain 1 residue 70 TRP Chi-restraints excluded: chain 1 residue 87 ILE Chi-restraints excluded: chain 1 residue 98 VAL Chi-restraints excluded: chain 1 residue 120 ILE Chi-restraints excluded: chain 1 residue 145 SER Chi-restraints excluded: chain 1 residue 169 LYS Chi-restraints excluded: chain 3 residue 7 ILE Chi-restraints excluded: chain 3 residue 25 PHE Chi-restraints excluded: chain 3 residue 35 LEU Chi-restraints excluded: chain 3 residue 43 ARG Chi-restraints excluded: chain 3 residue 62 PHE Chi-restraints excluded: chain 3 residue 63 THR Chi-restraints excluded: chain 3 residue 91 GLU Chi-restraints excluded: chain 4 residue 27 HIS Chi-restraints excluded: chain 4 residue 72 LYS Chi-restraints excluded: chain 2 residue 67 GLU Chi-restraints excluded: chain 2 residue 90 LEU Chi-restraints excluded: chain 2 residue 150 ASN Chi-restraints excluded: chain 2 residue 198 TYR Chi-restraints excluded: chain 2 residue 310 MET Chi-restraints excluded: chain 5 residue 12 PHE Chi-restraints excluded: chain 5 residue 21 LEU Chi-restraints excluded: chain 5 residue 46 ASN Chi-restraints excluded: chain 5 residue 103 LEU Chi-restraints excluded: chain 5 residue 106 VAL Chi-restraints excluded: chain 5 residue 138 LEU Chi-restraints excluded: chain 6 residue 7 VAL Chi-restraints excluded: chain 6 residue 20 THR Chi-restraints excluded: chain 6 residue 44 TYR Chi-restraints excluded: chain 6 residue 70 TRP Chi-restraints excluded: chain 6 residue 87 ILE Chi-restraints excluded: chain 6 residue 98 VAL Chi-restraints excluded: chain 6 residue 129 VAL Chi-restraints excluded: chain 6 residue 145 SER Chi-restraints excluded: chain 6 residue 169 LYS Chi-restraints excluded: chain 6 residue 173 ASP Chi-restraints excluded: chain 8 residue 7 ILE Chi-restraints excluded: chain 8 residue 25 PHE Chi-restraints excluded: chain 8 residue 35 LEU Chi-restraints excluded: chain 8 residue 43 ARG Chi-restraints excluded: chain 8 residue 62 PHE Chi-restraints excluded: chain 8 residue 63 THR Chi-restraints excluded: chain 9 residue 27 HIS Chi-restraints excluded: chain 7 residue 150 ASN Chi-restraints excluded: chain 7 residue 184 TYR Chi-restraints excluded: chain 7 residue 198 TYR Chi-restraints excluded: chain 7 residue 210 THR Chi-restraints excluded: chain 7 residue 248 TYR Chi-restraints excluded: chain 7 residue 301 ASP Chi-restraints excluded: chain 7 residue 310 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 58 optimal weight: 9.9990 chunk 97 optimal weight: 0.9980 chunk 117 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 18 optimal weight: 0.2980 chunk 46 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 chunk 43 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 35 optimal weight: 6.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 103 GLN ** 6 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 103 GLN ** 7 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4606 r_free = 0.4606 target = 0.185516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.137910 restraints weight = 23244.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.140703 restraints weight = 17326.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.141576 restraints weight = 14332.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.142283 restraints weight = 11639.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.142653 restraints weight = 11154.453| |-----------------------------------------------------------------------------| r_work (final): 0.4099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12828 Z= 0.159 Angle : 0.627 6.770 17278 Z= 0.328 Chirality : 0.043 0.166 1876 Planarity : 0.005 0.100 2212 Dihedral : 4.595 35.381 1662 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 6.57 % Allowed : 30.36 % Favored : 63.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.12 (0.21), residues: 1484 helix: 0.60 (0.19), residues: 782 sheet: -2.47 (0.39), residues: 122 loop : -2.25 (0.23), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG 3 68 TYR 0.014 0.002 TYR 2 221 PHE 0.032 0.002 PHE 2 213 TRP 0.025 0.002 TRP 7 97 HIS 0.006 0.001 HIS 6 139 Details of bonding type rmsd covalent geometry : bond 0.00373 (12820) covalent geometry : angle 0.62267 (17274) hydrogen bonds : bond 0.04220 ( 619) hydrogen bonds : angle 4.87154 ( 1821) metal coordination : bond 0.02252 ( 8) metal coordination : angle 4.81124 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 192 time to evaluate : 0.521 Fit side-chains REVERT: 0 12 PHE cc_start: 0.7591 (OUTLIER) cc_final: 0.7075 (m-80) REVERT: 1 70 TRP cc_start: 0.7221 (OUTLIER) cc_final: 0.6858 (m100) REVERT: 3 46 LYS cc_start: 0.6512 (tptt) cc_final: 0.6070 (tptt) REVERT: 3 64 SER cc_start: 0.8427 (p) cc_final: 0.8186 (m) REVERT: 2 150 ASN cc_start: 0.6400 (OUTLIER) cc_final: 0.6167 (p0) REVERT: 2 160 MET cc_start: 0.7548 (mmm) cc_final: 0.6809 (mmm) REVERT: 2 212 ARG cc_start: 0.8744 (OUTLIER) cc_final: 0.8463 (ptt90) REVERT: 2 300 MET cc_start: 0.4423 (mtt) cc_final: 0.4092 (mtt) REVERT: 5 12 PHE cc_start: 0.7565 (OUTLIER) cc_final: 0.7046 (m-80) REVERT: 6 5 TRP cc_start: 0.6896 (m100) cc_final: 0.6204 (m100) REVERT: 6 70 TRP cc_start: 0.7079 (OUTLIER) cc_final: 0.6684 (m100) REVERT: 8 46 LYS cc_start: 0.6444 (tptt) cc_final: 0.6002 (tptt) REVERT: 9 72 LYS cc_start: 0.7832 (OUTLIER) cc_final: 0.7493 (mttm) REVERT: 7 150 ASN cc_start: 0.6450 (OUTLIER) cc_final: 0.6187 (p0) REVERT: 7 160 MET cc_start: 0.7729 (mmm) cc_final: 0.6890 (mmm) REVERT: 7 184 TYR cc_start: 0.7173 (OUTLIER) cc_final: 0.6751 (m-80) REVERT: 7 248 TYR cc_start: 0.8283 (OUTLIER) cc_final: 0.7590 (m-10) outliers start: 90 outliers final: 58 residues processed: 263 average time/residue: 0.1006 time to fit residues: 39.7618 Evaluate side-chains 248 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 180 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 12 PHE Chi-restraints excluded: chain 0 residue 55 ILE Chi-restraints excluded: chain 0 residue 58 VAL Chi-restraints excluded: chain 0 residue 103 LEU Chi-restraints excluded: chain 0 residue 106 VAL Chi-restraints excluded: chain 0 residue 109 ILE Chi-restraints excluded: chain 0 residue 138 LEU Chi-restraints excluded: chain 1 residue 8 MET Chi-restraints excluded: chain 1 residue 44 TYR Chi-restraints excluded: chain 1 residue 70 TRP Chi-restraints excluded: chain 1 residue 87 ILE Chi-restraints excluded: chain 1 residue 96 THR Chi-restraints excluded: chain 1 residue 98 VAL Chi-restraints excluded: chain 1 residue 129 VAL Chi-restraints excluded: chain 1 residue 145 SER Chi-restraints excluded: chain 1 residue 169 LYS Chi-restraints excluded: chain 3 residue 5 LEU Chi-restraints excluded: chain 3 residue 7 ILE Chi-restraints excluded: chain 3 residue 11 LYS Chi-restraints excluded: chain 3 residue 35 LEU Chi-restraints excluded: chain 3 residue 43 ARG Chi-restraints excluded: chain 3 residue 63 THR Chi-restraints excluded: chain 3 residue 91 GLU Chi-restraints excluded: chain 4 residue 27 HIS Chi-restraints excluded: chain 4 residue 73 VAL Chi-restraints excluded: chain 2 residue 25 ILE Chi-restraints excluded: chain 2 residue 67 GLU Chi-restraints excluded: chain 2 residue 90 LEU Chi-restraints excluded: chain 2 residue 150 ASN Chi-restraints excluded: chain 2 residue 198 TYR Chi-restraints excluded: chain 2 residue 212 ARG Chi-restraints excluded: chain 2 residue 310 MET Chi-restraints excluded: chain 5 residue 12 PHE Chi-restraints excluded: chain 5 residue 21 LEU Chi-restraints excluded: chain 5 residue 46 ASN Chi-restraints excluded: chain 5 residue 53 SER Chi-restraints excluded: chain 5 residue 55 ILE Chi-restraints excluded: chain 5 residue 58 VAL Chi-restraints excluded: chain 5 residue 103 LEU Chi-restraints excluded: chain 5 residue 106 VAL Chi-restraints excluded: chain 5 residue 138 LEU Chi-restraints excluded: chain 6 residue 7 VAL Chi-restraints excluded: chain 6 residue 20 THR Chi-restraints excluded: chain 6 residue 43 HIS Chi-restraints excluded: chain 6 residue 44 TYR Chi-restraints excluded: chain 6 residue 70 TRP Chi-restraints excluded: chain 6 residue 87 ILE Chi-restraints excluded: chain 6 residue 96 THR Chi-restraints excluded: chain 6 residue 98 VAL Chi-restraints excluded: chain 6 residue 120 ILE Chi-restraints excluded: chain 6 residue 129 VAL Chi-restraints excluded: chain 6 residue 145 SER Chi-restraints excluded: chain 6 residue 169 LYS Chi-restraints excluded: chain 6 residue 173 ASP Chi-restraints excluded: chain 8 residue 7 ILE Chi-restraints excluded: chain 8 residue 35 LEU Chi-restraints excluded: chain 8 residue 43 ARG Chi-restraints excluded: chain 8 residue 57 LEU Chi-restraints excluded: chain 8 residue 63 THR Chi-restraints excluded: chain 9 residue 27 HIS Chi-restraints excluded: chain 9 residue 72 LYS Chi-restraints excluded: chain 9 residue 73 VAL Chi-restraints excluded: chain 7 residue 25 ILE Chi-restraints excluded: chain 7 residue 150 ASN Chi-restraints excluded: chain 7 residue 184 TYR Chi-restraints excluded: chain 7 residue 198 TYR Chi-restraints excluded: chain 7 residue 248 TYR Chi-restraints excluded: chain 7 residue 301 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 5 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 67 optimal weight: 7.9990 chunk 53 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 129 optimal weight: 5.9990 chunk 41 optimal weight: 0.9990 chunk 105 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 chunk 130 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 196 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4624 r_free = 0.4624 target = 0.191584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 90)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.144756 restraints weight = 24367.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.146665 restraints weight = 18457.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.147331 restraints weight = 15388.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.147787 restraints weight = 13192.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.147958 restraints weight = 12685.999| |-----------------------------------------------------------------------------| r_work (final): 0.4109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12828 Z= 0.151 Angle : 0.610 7.082 17278 Z= 0.318 Chirality : 0.043 0.183 1876 Planarity : 0.005 0.060 2212 Dihedral : 4.475 34.309 1662 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 6.35 % Allowed : 30.58 % Favored : 63.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.21), residues: 1484 helix: 0.61 (0.19), residues: 782 sheet: -2.44 (0.39), residues: 122 loop : -2.18 (0.23), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG 9 82 TYR 0.015 0.001 TYR 2 221 PHE 0.023 0.001 PHE 2 213 TRP 0.028 0.002 TRP 7 97 HIS 0.006 0.001 HIS 6 139 Details of bonding type rmsd covalent geometry : bond 0.00352 (12820) covalent geometry : angle 0.60576 (17274) hydrogen bonds : bond 0.04036 ( 619) hydrogen bonds : angle 4.79398 ( 1821) metal coordination : bond 0.02068 ( 8) metal coordination : angle 4.89444 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 191 time to evaluate : 0.573 Fit side-chains revert: symmetry clash REVERT: 0 12 PHE cc_start: 0.7555 (OUTLIER) cc_final: 0.7082 (m-80) REVERT: 1 70 TRP cc_start: 0.7189 (OUTLIER) cc_final: 0.6776 (m100) REVERT: 3 46 LYS cc_start: 0.6542 (tptt) cc_final: 0.6103 (tptt) REVERT: 2 150 ASN cc_start: 0.6315 (OUTLIER) cc_final: 0.6082 (p0) REVERT: 2 160 MET cc_start: 0.7532 (mmm) cc_final: 0.6760 (mmm) REVERT: 2 300 MET cc_start: 0.4312 (mtt) cc_final: 0.3848 (mtt) REVERT: 5 12 PHE cc_start: 0.7534 (OUTLIER) cc_final: 0.7069 (m-80) REVERT: 6 5 TRP cc_start: 0.6867 (m100) cc_final: 0.6204 (m100) REVERT: 6 70 TRP cc_start: 0.7101 (OUTLIER) cc_final: 0.6695 (m100) REVERT: 8 4 PHE cc_start: 0.4968 (m-80) cc_final: 0.4738 (m-80) REVERT: 8 46 LYS cc_start: 0.6441 (tptt) cc_final: 0.6037 (tptt) REVERT: 9 72 LYS cc_start: 0.7824 (OUTLIER) cc_final: 0.7528 (mttm) REVERT: 7 150 ASN cc_start: 0.6380 (OUTLIER) cc_final: 0.6122 (p0) REVERT: 7 160 MET cc_start: 0.7683 (mmm) cc_final: 0.6820 (mmm) REVERT: 7 184 TYR cc_start: 0.7116 (OUTLIER) cc_final: 0.6676 (m-80) REVERT: 7 237 LYS cc_start: 0.7995 (tttt) cc_final: 0.7755 (tptm) REVERT: 7 248 TYR cc_start: 0.8284 (OUTLIER) cc_final: 0.7622 (m-10) outliers start: 87 outliers final: 65 residues processed: 264 average time/residue: 0.1080 time to fit residues: 42.1085 Evaluate side-chains 258 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 184 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 12 PHE Chi-restraints excluded: chain 0 residue 55 ILE Chi-restraints excluded: chain 0 residue 58 VAL Chi-restraints excluded: chain 0 residue 62 THR Chi-restraints excluded: chain 0 residue 103 LEU Chi-restraints excluded: chain 0 residue 106 VAL Chi-restraints excluded: chain 0 residue 109 ILE Chi-restraints excluded: chain 0 residue 138 LEU Chi-restraints excluded: chain 1 residue 8 MET Chi-restraints excluded: chain 1 residue 20 THR Chi-restraints excluded: chain 1 residue 44 TYR Chi-restraints excluded: chain 1 residue 64 LEU Chi-restraints excluded: chain 1 residue 70 TRP Chi-restraints excluded: chain 1 residue 87 ILE Chi-restraints excluded: chain 1 residue 96 THR Chi-restraints excluded: chain 1 residue 98 VAL Chi-restraints excluded: chain 1 residue 120 ILE Chi-restraints excluded: chain 1 residue 129 VAL Chi-restraints excluded: chain 1 residue 145 SER Chi-restraints excluded: chain 1 residue 169 LYS Chi-restraints excluded: chain 3 residue 5 LEU Chi-restraints excluded: chain 3 residue 7 ILE Chi-restraints excluded: chain 3 residue 11 LYS Chi-restraints excluded: chain 3 residue 35 LEU Chi-restraints excluded: chain 3 residue 63 THR Chi-restraints excluded: chain 3 residue 91 GLU Chi-restraints excluded: chain 4 residue 27 HIS Chi-restraints excluded: chain 4 residue 41 THR Chi-restraints excluded: chain 4 residue 73 VAL Chi-restraints excluded: chain 2 residue 25 ILE Chi-restraints excluded: chain 2 residue 67 GLU Chi-restraints excluded: chain 2 residue 89 LEU Chi-restraints excluded: chain 2 residue 90 LEU Chi-restraints excluded: chain 2 residue 150 ASN Chi-restraints excluded: chain 2 residue 198 TYR Chi-restraints excluded: chain 2 residue 212 ARG Chi-restraints excluded: chain 2 residue 310 MET Chi-restraints excluded: chain 5 residue 12 PHE Chi-restraints excluded: chain 5 residue 46 ASN Chi-restraints excluded: chain 5 residue 53 SER Chi-restraints excluded: chain 5 residue 55 ILE Chi-restraints excluded: chain 5 residue 58 VAL Chi-restraints excluded: chain 5 residue 62 THR Chi-restraints excluded: chain 5 residue 103 LEU Chi-restraints excluded: chain 5 residue 106 VAL Chi-restraints excluded: chain 5 residue 109 ILE Chi-restraints excluded: chain 5 residue 138 LEU Chi-restraints excluded: chain 6 residue 7 VAL Chi-restraints excluded: chain 6 residue 20 THR Chi-restraints excluded: chain 6 residue 43 HIS Chi-restraints excluded: chain 6 residue 44 TYR Chi-restraints excluded: chain 6 residue 70 TRP Chi-restraints excluded: chain 6 residue 87 ILE Chi-restraints excluded: chain 6 residue 96 THR Chi-restraints excluded: chain 6 residue 98 VAL Chi-restraints excluded: chain 6 residue 120 ILE Chi-restraints excluded: chain 6 residue 129 VAL Chi-restraints excluded: chain 6 residue 145 SER Chi-restraints excluded: chain 6 residue 169 LYS Chi-restraints excluded: chain 6 residue 173 ASP Chi-restraints excluded: chain 8 residue 7 ILE Chi-restraints excluded: chain 8 residue 24 VAL Chi-restraints excluded: chain 8 residue 35 LEU Chi-restraints excluded: chain 8 residue 43 ARG Chi-restraints excluded: chain 8 residue 57 LEU Chi-restraints excluded: chain 8 residue 63 THR Chi-restraints excluded: chain 9 residue 27 HIS Chi-restraints excluded: chain 9 residue 72 LYS Chi-restraints excluded: chain 7 residue 25 ILE Chi-restraints excluded: chain 7 residue 150 ASN Chi-restraints excluded: chain 7 residue 184 TYR Chi-restraints excluded: chain 7 residue 198 TYR Chi-restraints excluded: chain 7 residue 248 TYR Chi-restraints excluded: chain 7 residue 301 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 57 optimal weight: 5.9990 chunk 112 optimal weight: 4.9990 chunk 146 optimal weight: 0.7980 chunk 38 optimal weight: 5.9990 chunk 121 optimal weight: 0.9990 chunk 102 optimal weight: 0.9990 chunk 19 optimal weight: 0.5980 chunk 34 optimal weight: 9.9990 chunk 133 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 chunk 99 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4629 r_free = 0.4629 target = 0.191992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.145143 restraints weight = 24116.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.147805 restraints weight = 18703.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.148206 restraints weight = 14278.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.148333 restraints weight = 13045.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.148564 restraints weight = 13383.074| |-----------------------------------------------------------------------------| r_work (final): 0.4117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7230 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12828 Z= 0.142 Angle : 0.613 8.355 17278 Z= 0.316 Chirality : 0.043 0.173 1876 Planarity : 0.004 0.060 2212 Dihedral : 4.409 33.645 1662 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 6.20 % Allowed : 31.31 % Favored : 62.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.21), residues: 1484 helix: 0.61 (0.19), residues: 782 sheet: -2.32 (0.39), residues: 122 loop : -2.15 (0.23), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG 6 90 TYR 0.014 0.001 TYR 9 83 PHE 0.011 0.001 PHE 2 41 TRP 0.029 0.002 TRP 7 97 HIS 0.005 0.001 HIS 6 48 Details of bonding type rmsd covalent geometry : bond 0.00332 (12820) covalent geometry : angle 0.60951 (17274) hydrogen bonds : bond 0.03928 ( 619) hydrogen bonds : angle 4.75783 ( 1821) metal coordination : bond 0.01859 ( 8) metal coordination : angle 4.61561 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 198 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 12 PHE cc_start: 0.7541 (OUTLIER) cc_final: 0.7057 (m-80) REVERT: 0 131 ARG cc_start: 0.7561 (OUTLIER) cc_final: 0.6643 (mtm180) REVERT: 1 70 TRP cc_start: 0.7190 (OUTLIER) cc_final: 0.6809 (m100) REVERT: 3 46 LYS cc_start: 0.6498 (tptt) cc_final: 0.6031 (tptt) REVERT: 3 62 PHE cc_start: 0.4632 (OUTLIER) cc_final: 0.4398 (t80) REVERT: 2 150 ASN cc_start: 0.6227 (OUTLIER) cc_final: 0.6003 (p0) REVERT: 2 160 MET cc_start: 0.7632 (mmm) cc_final: 0.6847 (mmm) REVERT: 2 212 ARG cc_start: 0.8753 (OUTLIER) cc_final: 0.8394 (ptt90) REVERT: 2 300 MET cc_start: 0.4312 (mtt) cc_final: 0.3980 (mtt) REVERT: 5 12 PHE cc_start: 0.7498 (OUTLIER) cc_final: 0.7084 (m-80) REVERT: 5 24 GLU cc_start: 0.6304 (tp30) cc_final: 0.6043 (tp30) REVERT: 5 122 MET cc_start: 0.6578 (tpp) cc_final: 0.6288 (tpp) REVERT: 6 5 TRP cc_start: 0.6802 (m100) cc_final: 0.6115 (m100) REVERT: 8 46 LYS cc_start: 0.6403 (tptt) cc_final: 0.6006 (tptt) REVERT: 9 72 LYS cc_start: 0.7817 (OUTLIER) cc_final: 0.7526 (mttm) REVERT: 7 150 ASN cc_start: 0.6364 (OUTLIER) cc_final: 0.6113 (p0) REVERT: 7 160 MET cc_start: 0.7711 (mmm) cc_final: 0.6857 (mmm) REVERT: 7 184 TYR cc_start: 0.7123 (OUTLIER) cc_final: 0.6684 (m-80) REVERT: 7 237 LYS cc_start: 0.8018 (tttt) cc_final: 0.7776 (tptm) REVERT: 7 248 TYR cc_start: 0.8265 (OUTLIER) cc_final: 0.7607 (m-10) REVERT: 7 311 LEU cc_start: 0.1259 (mt) cc_final: 0.0411 (pp) outliers start: 85 outliers final: 66 residues processed: 267 average time/residue: 0.1111 time to fit residues: 43.1742 Evaluate side-chains 266 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 189 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 12 PHE Chi-restraints excluded: chain 0 residue 55 ILE Chi-restraints excluded: chain 0 residue 58 VAL Chi-restraints excluded: chain 0 residue 103 LEU Chi-restraints excluded: chain 0 residue 106 VAL Chi-restraints excluded: chain 0 residue 109 ILE Chi-restraints excluded: chain 0 residue 131 ARG Chi-restraints excluded: chain 0 residue 138 LEU Chi-restraints excluded: chain 1 residue 20 THR Chi-restraints excluded: chain 1 residue 44 TYR Chi-restraints excluded: chain 1 residue 70 TRP Chi-restraints excluded: chain 1 residue 87 ILE Chi-restraints excluded: chain 1 residue 98 VAL Chi-restraints excluded: chain 1 residue 120 ILE Chi-restraints excluded: chain 1 residue 129 VAL Chi-restraints excluded: chain 1 residue 169 LYS Chi-restraints excluded: chain 3 residue 5 LEU Chi-restraints excluded: chain 3 residue 7 ILE Chi-restraints excluded: chain 3 residue 11 LYS Chi-restraints excluded: chain 3 residue 24 VAL Chi-restraints excluded: chain 3 residue 35 LEU Chi-restraints excluded: chain 3 residue 43 ARG Chi-restraints excluded: chain 3 residue 62 PHE Chi-restraints excluded: chain 3 residue 63 THR Chi-restraints excluded: chain 3 residue 75 VAL Chi-restraints excluded: chain 3 residue 91 GLU Chi-restraints excluded: chain 4 residue 27 HIS Chi-restraints excluded: chain 4 residue 41 THR Chi-restraints excluded: chain 4 residue 67 SER Chi-restraints excluded: chain 4 residue 82 ARG Chi-restraints excluded: chain 2 residue 25 ILE Chi-restraints excluded: chain 2 residue 45 SER Chi-restraints excluded: chain 2 residue 67 GLU Chi-restraints excluded: chain 2 residue 89 LEU Chi-restraints excluded: chain 2 residue 90 LEU Chi-restraints excluded: chain 2 residue 150 ASN Chi-restraints excluded: chain 2 residue 198 TYR Chi-restraints excluded: chain 2 residue 212 ARG Chi-restraints excluded: chain 2 residue 310 MET Chi-restraints excluded: chain 5 residue 12 PHE Chi-restraints excluded: chain 5 residue 46 ASN Chi-restraints excluded: chain 5 residue 53 SER Chi-restraints excluded: chain 5 residue 55 ILE Chi-restraints excluded: chain 5 residue 58 VAL Chi-restraints excluded: chain 5 residue 62 THR Chi-restraints excluded: chain 5 residue 103 LEU Chi-restraints excluded: chain 5 residue 106 VAL Chi-restraints excluded: chain 5 residue 109 ILE Chi-restraints excluded: chain 5 residue 138 LEU Chi-restraints excluded: chain 6 residue 7 VAL Chi-restraints excluded: chain 6 residue 43 HIS Chi-restraints excluded: chain 6 residue 44 TYR Chi-restraints excluded: chain 6 residue 64 LEU Chi-restraints excluded: chain 6 residue 87 ILE Chi-restraints excluded: chain 6 residue 98 VAL Chi-restraints excluded: chain 6 residue 120 ILE Chi-restraints excluded: chain 6 residue 169 LYS Chi-restraints excluded: chain 6 residue 173 ASP Chi-restraints excluded: chain 8 residue 7 ILE Chi-restraints excluded: chain 8 residue 24 VAL Chi-restraints excluded: chain 8 residue 35 LEU Chi-restraints excluded: chain 8 residue 43 ARG Chi-restraints excluded: chain 8 residue 57 LEU Chi-restraints excluded: chain 8 residue 63 THR Chi-restraints excluded: chain 8 residue 75 VAL Chi-restraints excluded: chain 9 residue 27 HIS Chi-restraints excluded: chain 9 residue 41 THR Chi-restraints excluded: chain 9 residue 72 LYS Chi-restraints excluded: chain 9 residue 73 VAL Chi-restraints excluded: chain 7 residue 25 ILE Chi-restraints excluded: chain 7 residue 36 THR Chi-restraints excluded: chain 7 residue 45 SER Chi-restraints excluded: chain 7 residue 150 ASN Chi-restraints excluded: chain 7 residue 184 TYR Chi-restraints excluded: chain 7 residue 198 TYR Chi-restraints excluded: chain 7 residue 248 TYR Chi-restraints excluded: chain 7 residue 301 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 87 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 132 optimal weight: 10.0000 chunk 139 optimal weight: 6.9990 chunk 94 optimal weight: 1.9990 chunk 136 optimal weight: 0.9990 chunk 19 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 chunk 47 optimal weight: 3.9990 chunk 5 optimal weight: 0.0270 overall best weight: 0.7042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4636 r_free = 0.4636 target = 0.192600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.146448 restraints weight = 24130.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.148464 restraints weight = 17609.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.149684 restraints weight = 14274.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.150843 restraints weight = 12432.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.151243 restraints weight = 11234.308| |-----------------------------------------------------------------------------| r_work (final): 0.4159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7146 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12828 Z= 0.135 Angle : 0.600 7.072 17278 Z= 0.311 Chirality : 0.042 0.170 1876 Planarity : 0.004 0.060 2212 Dihedral : 4.355 31.872 1662 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 6.93 % Allowed : 30.95 % Favored : 62.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.96 (0.21), residues: 1484 helix: 0.64 (0.19), residues: 782 sheet: -2.17 (0.41), residues: 122 loop : -2.08 (0.23), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG 9 82 TYR 0.016 0.001 TYR 9 83 PHE 0.018 0.001 PHE 2 41 TRP 0.031 0.002 TRP 7 97 HIS 0.005 0.001 HIS 6 48 Details of bonding type rmsd covalent geometry : bond 0.00313 (12820) covalent geometry : angle 0.59703 (17274) hydrogen bonds : bond 0.03834 ( 619) hydrogen bonds : angle 4.68945 ( 1821) metal coordination : bond 0.01583 ( 8) metal coordination : angle 4.23955 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 198 time to evaluate : 0.587 Fit side-chains revert: symmetry clash REVERT: 0 12 PHE cc_start: 0.7495 (OUTLIER) cc_final: 0.7078 (m-80) REVERT: 0 131 ARG cc_start: 0.7540 (OUTLIER) cc_final: 0.6653 (mtm180) REVERT: 1 70 TRP cc_start: 0.7144 (OUTLIER) cc_final: 0.6761 (m100) REVERT: 3 4 PHE cc_start: 0.4732 (m-80) cc_final: 0.4482 (m-80) REVERT: 3 46 LYS cc_start: 0.6470 (tptt) cc_final: 0.6037 (tptt) REVERT: 3 62 PHE cc_start: 0.4835 (OUTLIER) cc_final: 0.4612 (t80) REVERT: 2 150 ASN cc_start: 0.6129 (OUTLIER) cc_final: 0.5915 (p0) REVERT: 2 160 MET cc_start: 0.7695 (mmm) cc_final: 0.7111 (mmm) REVERT: 2 212 ARG cc_start: 0.8741 (OUTLIER) cc_final: 0.8483 (ptp-170) REVERT: 2 221 TYR cc_start: 0.7046 (t80) cc_final: 0.6844 (t80) REVERT: 2 231 MET cc_start: 0.8447 (mmt) cc_final: 0.8194 (mmp) REVERT: 2 300 MET cc_start: 0.4304 (mtt) cc_final: 0.4021 (mtt) REVERT: 2 311 LEU cc_start: 0.1338 (OUTLIER) cc_final: 0.0472 (pp) REVERT: 5 12 PHE cc_start: 0.7422 (OUTLIER) cc_final: 0.7020 (m-80) REVERT: 5 131 ARG cc_start: 0.7578 (OUTLIER) cc_final: 0.6652 (mtm180) REVERT: 6 5 TRP cc_start: 0.6763 (m100) cc_final: 0.6107 (m100) REVERT: 6 70 TRP cc_start: 0.7060 (OUTLIER) cc_final: 0.6656 (m100) REVERT: 8 46 LYS cc_start: 0.6314 (tptt) cc_final: 0.5952 (tptt) REVERT: 9 72 LYS cc_start: 0.7754 (OUTLIER) cc_final: 0.7526 (ttmm) REVERT: 7 150 ASN cc_start: 0.6275 (OUTLIER) cc_final: 0.6029 (p0) REVERT: 7 160 MET cc_start: 0.7691 (mmm) cc_final: 0.7029 (mmm) REVERT: 7 184 TYR cc_start: 0.7080 (OUTLIER) cc_final: 0.6452 (m-80) REVERT: 7 221 TYR cc_start: 0.7040 (t80) cc_final: 0.6771 (t80) REVERT: 7 230 TYR cc_start: 0.9035 (t80) cc_final: 0.8682 (t80) REVERT: 7 237 LYS cc_start: 0.8001 (tttt) cc_final: 0.7759 (tptm) REVERT: 7 248 TYR cc_start: 0.8266 (OUTLIER) cc_final: 0.7627 (m-10) REVERT: 7 311 LEU cc_start: 0.0926 (mt) cc_final: 0.0443 (pp) outliers start: 95 outliers final: 64 residues processed: 276 average time/residue: 0.1132 time to fit residues: 44.9679 Evaluate side-chains 268 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 190 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 12 PHE Chi-restraints excluded: chain 0 residue 58 VAL Chi-restraints excluded: chain 0 residue 62 THR Chi-restraints excluded: chain 0 residue 103 LEU Chi-restraints excluded: chain 0 residue 106 VAL Chi-restraints excluded: chain 0 residue 109 ILE Chi-restraints excluded: chain 0 residue 131 ARG Chi-restraints excluded: chain 0 residue 138 LEU Chi-restraints excluded: chain 1 residue 20 THR Chi-restraints excluded: chain 1 residue 64 LEU Chi-restraints excluded: chain 1 residue 70 TRP Chi-restraints excluded: chain 1 residue 87 ILE Chi-restraints excluded: chain 1 residue 96 THR Chi-restraints excluded: chain 1 residue 98 VAL Chi-restraints excluded: chain 1 residue 120 ILE Chi-restraints excluded: chain 1 residue 145 SER Chi-restraints excluded: chain 1 residue 169 LYS Chi-restraints excluded: chain 3 residue 5 LEU Chi-restraints excluded: chain 3 residue 7 ILE Chi-restraints excluded: chain 3 residue 24 VAL Chi-restraints excluded: chain 3 residue 35 LEU Chi-restraints excluded: chain 3 residue 43 ARG Chi-restraints excluded: chain 3 residue 62 PHE Chi-restraints excluded: chain 3 residue 63 THR Chi-restraints excluded: chain 3 residue 91 GLU Chi-restraints excluded: chain 4 residue 41 THR Chi-restraints excluded: chain 2 residue 25 ILE Chi-restraints excluded: chain 2 residue 36 THR Chi-restraints excluded: chain 2 residue 45 SER Chi-restraints excluded: chain 2 residue 67 GLU Chi-restraints excluded: chain 2 residue 89 LEU Chi-restraints excluded: chain 2 residue 90 LEU Chi-restraints excluded: chain 2 residue 150 ASN Chi-restraints excluded: chain 2 residue 198 TYR Chi-restraints excluded: chain 2 residue 212 ARG Chi-restraints excluded: chain 2 residue 310 MET Chi-restraints excluded: chain 2 residue 311 LEU Chi-restraints excluded: chain 5 residue 12 PHE Chi-restraints excluded: chain 5 residue 46 ASN Chi-restraints excluded: chain 5 residue 53 SER Chi-restraints excluded: chain 5 residue 55 ILE Chi-restraints excluded: chain 5 residue 58 VAL Chi-restraints excluded: chain 5 residue 103 LEU Chi-restraints excluded: chain 5 residue 106 VAL Chi-restraints excluded: chain 5 residue 109 ILE Chi-restraints excluded: chain 5 residue 131 ARG Chi-restraints excluded: chain 5 residue 138 LEU Chi-restraints excluded: chain 6 residue 7 VAL Chi-restraints excluded: chain 6 residue 20 THR Chi-restraints excluded: chain 6 residue 43 HIS Chi-restraints excluded: chain 6 residue 44 TYR Chi-restraints excluded: chain 6 residue 64 LEU Chi-restraints excluded: chain 6 residue 70 TRP Chi-restraints excluded: chain 6 residue 87 ILE Chi-restraints excluded: chain 6 residue 96 THR Chi-restraints excluded: chain 6 residue 98 VAL Chi-restraints excluded: chain 6 residue 129 VAL Chi-restraints excluded: chain 6 residue 145 SER Chi-restraints excluded: chain 6 residue 169 LYS Chi-restraints excluded: chain 6 residue 173 ASP Chi-restraints excluded: chain 8 residue 7 ILE Chi-restraints excluded: chain 8 residue 24 VAL Chi-restraints excluded: chain 8 residue 35 LEU Chi-restraints excluded: chain 8 residue 43 ARG Chi-restraints excluded: chain 8 residue 57 LEU Chi-restraints excluded: chain 8 residue 63 THR Chi-restraints excluded: chain 8 residue 75 VAL Chi-restraints excluded: chain 9 residue 27 HIS Chi-restraints excluded: chain 9 residue 41 THR Chi-restraints excluded: chain 9 residue 72 LYS Chi-restraints excluded: chain 7 residue 25 ILE Chi-restraints excluded: chain 7 residue 36 THR Chi-restraints excluded: chain 7 residue 45 SER Chi-restraints excluded: chain 7 residue 150 ASN Chi-restraints excluded: chain 7 residue 184 TYR Chi-restraints excluded: chain 7 residue 198 TYR Chi-restraints excluded: chain 7 residue 248 TYR Chi-restraints excluded: chain 7 residue 301 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 123 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 132 optimal weight: 8.9990 chunk 108 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 11 optimal weight: 0.3980 chunk 12 optimal weight: 0.7980 chunk 107 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 103 GLN 6 3 ASN ** 6 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 103 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4635 r_free = 0.4635 target = 0.192799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.145410 restraints weight = 24130.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.147927 restraints weight = 19069.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.148801 restraints weight = 14591.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.149090 restraints weight = 13001.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.149292 restraints weight = 13039.435| |-----------------------------------------------------------------------------| r_work (final): 0.4125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7223 moved from start: 0.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12828 Z= 0.140 Angle : 0.613 6.599 17278 Z= 0.318 Chirality : 0.043 0.168 1876 Planarity : 0.005 0.089 2212 Dihedral : 4.275 21.081 1660 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 6.42 % Allowed : 30.80 % Favored : 62.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.94 (0.21), residues: 1484 helix: 0.64 (0.19), residues: 784 sheet: -2.14 (0.41), residues: 122 loop : -2.04 (0.23), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG 4 82 TYR 0.014 0.001 TYR 2 221 PHE 0.019 0.001 PHE 7 41 TRP 0.044 0.002 TRP 2 97 HIS 0.005 0.001 HIS 6 48 Details of bonding type rmsd covalent geometry : bond 0.00326 (12820) covalent geometry : angle 0.60961 (17274) hydrogen bonds : bond 0.03933 ( 619) hydrogen bonds : angle 4.69430 ( 1821) metal coordination : bond 0.01685 ( 8) metal coordination : angle 4.53078 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 194 time to evaluate : 0.529 Fit side-chains revert: symmetry clash REVERT: 0 12 PHE cc_start: 0.7506 (OUTLIER) cc_final: 0.7076 (m-80) REVERT: 0 131 ARG cc_start: 0.7556 (OUTLIER) cc_final: 0.6659 (mtm180) REVERT: 1 70 TRP cc_start: 0.7166 (OUTLIER) cc_final: 0.6754 (m100) REVERT: 3 11 LYS cc_start: 0.7555 (OUTLIER) cc_final: 0.6743 (mptp) REVERT: 3 46 LYS cc_start: 0.6366 (tptt) cc_final: 0.5953 (tptt) REVERT: 3 62 PHE cc_start: 0.4627 (OUTLIER) cc_final: 0.4329 (t80) REVERT: 2 150 ASN cc_start: 0.6252 (OUTLIER) cc_final: 0.6047 (p0) REVERT: 2 160 MET cc_start: 0.7888 (mmm) cc_final: 0.7157 (mmm) REVERT: 2 212 ARG cc_start: 0.8733 (OUTLIER) cc_final: 0.8486 (ptp-170) REVERT: 2 248 TYR cc_start: 0.8211 (OUTLIER) cc_final: 0.7508 (m-10) REVERT: 2 300 MET cc_start: 0.4383 (mtt) cc_final: 0.4113 (mtt) REVERT: 2 311 LEU cc_start: 0.1190 (OUTLIER) cc_final: 0.0437 (pp) REVERT: 5 12 PHE cc_start: 0.7460 (OUTLIER) cc_final: 0.7052 (m-80) REVERT: 5 24 GLU cc_start: 0.6309 (tp30) cc_final: 0.6059 (tp30) REVERT: 5 122 MET cc_start: 0.6592 (tpp) cc_final: 0.6328 (tpp) REVERT: 5 131 ARG cc_start: 0.7609 (OUTLIER) cc_final: 0.6659 (mtm180) REVERT: 6 5 TRP cc_start: 0.6807 (m100) cc_final: 0.6174 (m100) REVERT: 6 70 TRP cc_start: 0.7063 (OUTLIER) cc_final: 0.6634 (m100) REVERT: 8 46 LYS cc_start: 0.6232 (tptt) cc_final: 0.5905 (tptt) REVERT: 7 150 ASN cc_start: 0.6394 (OUTLIER) cc_final: 0.6168 (p0) REVERT: 7 160 MET cc_start: 0.7882 (mmm) cc_final: 0.7088 (mmm) REVERT: 7 184 TYR cc_start: 0.7198 (OUTLIER) cc_final: 0.6529 (m-80) REVERT: 7 221 TYR cc_start: 0.7084 (t80) cc_final: 0.6807 (t80) REVERT: 7 230 TYR cc_start: 0.9066 (t80) cc_final: 0.8700 (t80) REVERT: 7 248 TYR cc_start: 0.8234 (OUTLIER) cc_final: 0.7617 (m-10) REVERT: 7 311 LEU cc_start: 0.1160 (mt) cc_final: 0.0731 (pp) outliers start: 88 outliers final: 63 residues processed: 265 average time/residue: 0.1047 time to fit residues: 40.5124 Evaluate side-chains 267 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 189 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 12 PHE Chi-restraints excluded: chain 0 residue 58 VAL Chi-restraints excluded: chain 0 residue 62 THR Chi-restraints excluded: chain 0 residue 103 LEU Chi-restraints excluded: chain 0 residue 106 VAL Chi-restraints excluded: chain 0 residue 109 ILE Chi-restraints excluded: chain 0 residue 131 ARG Chi-restraints excluded: chain 0 residue 138 LEU Chi-restraints excluded: chain 1 residue 20 THR Chi-restraints excluded: chain 1 residue 64 LEU Chi-restraints excluded: chain 1 residue 70 TRP Chi-restraints excluded: chain 1 residue 87 ILE Chi-restraints excluded: chain 1 residue 96 THR Chi-restraints excluded: chain 1 residue 120 ILE Chi-restraints excluded: chain 1 residue 145 SER Chi-restraints excluded: chain 1 residue 169 LYS Chi-restraints excluded: chain 3 residue 7 ILE Chi-restraints excluded: chain 3 residue 11 LYS Chi-restraints excluded: chain 3 residue 24 VAL Chi-restraints excluded: chain 3 residue 35 LEU Chi-restraints excluded: chain 3 residue 43 ARG Chi-restraints excluded: chain 3 residue 62 PHE Chi-restraints excluded: chain 3 residue 91 GLU Chi-restraints excluded: chain 4 residue 27 HIS Chi-restraints excluded: chain 2 residue 25 ILE Chi-restraints excluded: chain 2 residue 36 THR Chi-restraints excluded: chain 2 residue 45 SER Chi-restraints excluded: chain 2 residue 67 GLU Chi-restraints excluded: chain 2 residue 89 LEU Chi-restraints excluded: chain 2 residue 90 LEU Chi-restraints excluded: chain 2 residue 150 ASN Chi-restraints excluded: chain 2 residue 198 TYR Chi-restraints excluded: chain 2 residue 212 ARG Chi-restraints excluded: chain 2 residue 248 TYR Chi-restraints excluded: chain 2 residue 310 MET Chi-restraints excluded: chain 2 residue 311 LEU Chi-restraints excluded: chain 5 residue 12 PHE Chi-restraints excluded: chain 5 residue 46 ASN Chi-restraints excluded: chain 5 residue 53 SER Chi-restraints excluded: chain 5 residue 55 ILE Chi-restraints excluded: chain 5 residue 58 VAL Chi-restraints excluded: chain 5 residue 62 THR Chi-restraints excluded: chain 5 residue 103 LEU Chi-restraints excluded: chain 5 residue 106 VAL Chi-restraints excluded: chain 5 residue 109 ILE Chi-restraints excluded: chain 5 residue 131 ARG Chi-restraints excluded: chain 5 residue 138 LEU Chi-restraints excluded: chain 6 residue 3 ASN Chi-restraints excluded: chain 6 residue 7 VAL Chi-restraints excluded: chain 6 residue 20 THR Chi-restraints excluded: chain 6 residue 43 HIS Chi-restraints excluded: chain 6 residue 44 TYR Chi-restraints excluded: chain 6 residue 64 LEU Chi-restraints excluded: chain 6 residue 70 TRP Chi-restraints excluded: chain 6 residue 87 ILE Chi-restraints excluded: chain 6 residue 96 THR Chi-restraints excluded: chain 6 residue 98 VAL Chi-restraints excluded: chain 6 residue 120 ILE Chi-restraints excluded: chain 6 residue 129 VAL Chi-restraints excluded: chain 6 residue 145 SER Chi-restraints excluded: chain 6 residue 169 LYS Chi-restraints excluded: chain 6 residue 173 ASP Chi-restraints excluded: chain 8 residue 7 ILE Chi-restraints excluded: chain 8 residue 24 VAL Chi-restraints excluded: chain 8 residue 35 LEU Chi-restraints excluded: chain 8 residue 43 ARG Chi-restraints excluded: chain 8 residue 63 THR Chi-restraints excluded: chain 8 residue 75 VAL Chi-restraints excluded: chain 9 residue 27 HIS Chi-restraints excluded: chain 9 residue 41 THR Chi-restraints excluded: chain 9 residue 73 VAL Chi-restraints excluded: chain 7 residue 36 THR Chi-restraints excluded: chain 7 residue 45 SER Chi-restraints excluded: chain 7 residue 150 ASN Chi-restraints excluded: chain 7 residue 184 TYR Chi-restraints excluded: chain 7 residue 198 TYR Chi-restraints excluded: chain 7 residue 248 TYR Chi-restraints excluded: chain 7 residue 301 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 124 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 91 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 27 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 56 optimal weight: 0.6980 chunk 145 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 3 ASN ** 6 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 139 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 = 0.4638 r_free = 0.4638 target = 0.192760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.147243 restraints weight = 24088.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.148865 restraints weight = 18595.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.148626 restraints weight = 14249.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.148904 restraints weight = 14561.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.149082 restraints weight = 13435.949| |-----------------------------------------------------------------------------| r_work (final): 0.4119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7234 moved from start: 0.2393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12828 Z= 0.140 Angle : 0.620 6.700 17278 Z= 0.321 Chirality : 0.043 0.165 1876 Planarity : 0.005 0.114 2212 Dihedral : 4.284 21.081 1660 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 6.42 % Allowed : 31.17 % Favored : 62.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.94 (0.21), residues: 1484 helix: 0.66 (0.19), residues: 782 sheet: -2.15 (0.41), residues: 122 loop : -2.07 (0.23), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG 4 82 TYR 0.012 0.001 TYR 9 83 PHE 0.026 0.002 PHE 3 4 TRP 0.048 0.002 TRP 7 97 HIS 0.005 0.001 HIS 6 48 Details of bonding type rmsd covalent geometry : bond 0.00326 (12820) covalent geometry : angle 0.61617 (17274) hydrogen bonds : bond 0.03907 ( 619) hydrogen bonds : angle 4.66576 ( 1821) metal coordination : bond 0.01660 ( 8) metal coordination : angle 4.53495 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 192 time to evaluate : 0.561 Fit side-chains REVERT: 0 12 PHE cc_start: 0.7519 (OUTLIER) cc_final: 0.7088 (m-80) REVERT: 0 131 ARG cc_start: 0.7572 (OUTLIER) cc_final: 0.6656 (mtm180) REVERT: 1 70 TRP cc_start: 0.7132 (OUTLIER) cc_final: 0.6732 (m100) REVERT: 3 11 LYS cc_start: 0.7639 (OUTLIER) cc_final: 0.6848 (mptp) REVERT: 3 46 LYS cc_start: 0.6310 (tptt) cc_final: 0.5918 (tptt) REVERT: 3 62 PHE cc_start: 0.4539 (OUTLIER) cc_final: 0.4122 (t80) REVERT: 2 150 ASN cc_start: 0.6230 (OUTLIER) cc_final: 0.6026 (p0) REVERT: 2 160 MET cc_start: 0.7886 (mmm) cc_final: 0.7168 (mmm) REVERT: 2 184 TYR cc_start: 0.7169 (OUTLIER) cc_final: 0.6482 (m-80) REVERT: 2 212 ARG cc_start: 0.8730 (OUTLIER) cc_final: 0.8492 (ptp-170) REVERT: 2 248 TYR cc_start: 0.8221 (OUTLIER) cc_final: 0.7548 (m-10) REVERT: 2 300 MET cc_start: 0.4422 (mtt) cc_final: 0.4181 (mtt) REVERT: 2 311 LEU cc_start: 0.1030 (OUTLIER) cc_final: 0.0398 (pp) REVERT: 5 12 PHE cc_start: 0.7486 (OUTLIER) cc_final: 0.7074 (m-80) REVERT: 5 24 GLU cc_start: 0.6393 (tp30) cc_final: 0.6086 (tp30) REVERT: 5 122 MET cc_start: 0.6681 (tpp) cc_final: 0.6363 (tpp) REVERT: 5 131 ARG cc_start: 0.7611 (OUTLIER) cc_final: 0.6714 (mtm180) REVERT: 6 5 TRP cc_start: 0.6761 (m100) cc_final: 0.6494 (m100) REVERT: 6 70 TRP cc_start: 0.7040 (OUTLIER) cc_final: 0.6637 (m100) REVERT: 8 46 LYS cc_start: 0.6194 (tptt) cc_final: 0.5848 (tptt) REVERT: 8 62 PHE cc_start: 0.4657 (OUTLIER) cc_final: 0.4435 (t80) REVERT: 7 150 ASN cc_start: 0.6425 (OUTLIER) cc_final: 0.6214 (p0) REVERT: 7 160 MET cc_start: 0.7883 (mmm) cc_final: 0.7095 (mmm) REVERT: 7 184 TYR cc_start: 0.7235 (OUTLIER) cc_final: 0.6554 (m-80) REVERT: 7 230 TYR cc_start: 0.9064 (t80) cc_final: 0.8647 (t80) REVERT: 7 248 TYR cc_start: 0.8242 (OUTLIER) cc_final: 0.7620 (m-10) REVERT: 7 311 LEU cc_start: 0.0999 (mt) cc_final: 0.0721 (pp) outliers start: 88 outliers final: 64 residues processed: 263 average time/residue: 0.1038 time to fit residues: 40.4712 Evaluate side-chains 271 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 190 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 12 PHE Chi-restraints excluded: chain 0 residue 55 ILE Chi-restraints excluded: chain 0 residue 58 VAL Chi-restraints excluded: chain 0 residue 62 THR Chi-restraints excluded: chain 0 residue 103 LEU Chi-restraints excluded: chain 0 residue 106 VAL Chi-restraints excluded: chain 0 residue 109 ILE Chi-restraints excluded: chain 0 residue 131 ARG Chi-restraints excluded: chain 0 residue 138 LEU Chi-restraints excluded: chain 1 residue 8 MET Chi-restraints excluded: chain 1 residue 20 THR Chi-restraints excluded: chain 1 residue 64 LEU Chi-restraints excluded: chain 1 residue 70 TRP Chi-restraints excluded: chain 1 residue 87 ILE Chi-restraints excluded: chain 1 residue 96 THR Chi-restraints excluded: chain 1 residue 98 VAL Chi-restraints excluded: chain 1 residue 120 ILE Chi-restraints excluded: chain 1 residue 145 SER Chi-restraints excluded: chain 1 residue 169 LYS Chi-restraints excluded: chain 3 residue 7 ILE Chi-restraints excluded: chain 3 residue 11 LYS Chi-restraints excluded: chain 3 residue 24 VAL Chi-restraints excluded: chain 3 residue 35 LEU Chi-restraints excluded: chain 3 residue 43 ARG Chi-restraints excluded: chain 3 residue 62 PHE Chi-restraints excluded: chain 3 residue 91 GLU Chi-restraints excluded: chain 4 residue 73 VAL Chi-restraints excluded: chain 2 residue 25 ILE Chi-restraints excluded: chain 2 residue 36 THR Chi-restraints excluded: chain 2 residue 45 SER Chi-restraints excluded: chain 2 residue 67 GLU Chi-restraints excluded: chain 2 residue 90 LEU Chi-restraints excluded: chain 2 residue 150 ASN Chi-restraints excluded: chain 2 residue 184 TYR Chi-restraints excluded: chain 2 residue 198 TYR Chi-restraints excluded: chain 2 residue 212 ARG Chi-restraints excluded: chain 2 residue 248 TYR Chi-restraints excluded: chain 2 residue 310 MET Chi-restraints excluded: chain 2 residue 311 LEU Chi-restraints excluded: chain 5 residue 12 PHE Chi-restraints excluded: chain 5 residue 46 ASN Chi-restraints excluded: chain 5 residue 53 SER Chi-restraints excluded: chain 5 residue 55 ILE Chi-restraints excluded: chain 5 residue 58 VAL Chi-restraints excluded: chain 5 residue 62 THR Chi-restraints excluded: chain 5 residue 103 LEU Chi-restraints excluded: chain 5 residue 106 VAL Chi-restraints excluded: chain 5 residue 109 ILE Chi-restraints excluded: chain 5 residue 131 ARG Chi-restraints excluded: chain 5 residue 138 LEU Chi-restraints excluded: chain 6 residue 7 VAL Chi-restraints excluded: chain 6 residue 20 THR Chi-restraints excluded: chain 6 residue 43 HIS Chi-restraints excluded: chain 6 residue 44 TYR Chi-restraints excluded: chain 6 residue 64 LEU Chi-restraints excluded: chain 6 residue 70 TRP Chi-restraints excluded: chain 6 residue 87 ILE Chi-restraints excluded: chain 6 residue 96 THR Chi-restraints excluded: chain 6 residue 98 VAL Chi-restraints excluded: chain 6 residue 120 ILE Chi-restraints excluded: chain 6 residue 129 VAL Chi-restraints excluded: chain 6 residue 145 SER Chi-restraints excluded: chain 6 residue 169 LYS Chi-restraints excluded: chain 6 residue 173 ASP Chi-restraints excluded: chain 8 residue 7 ILE Chi-restraints excluded: chain 8 residue 24 VAL Chi-restraints excluded: chain 8 residue 35 LEU Chi-restraints excluded: chain 8 residue 43 ARG Chi-restraints excluded: chain 8 residue 57 LEU Chi-restraints excluded: chain 8 residue 62 PHE Chi-restraints excluded: chain 8 residue 63 THR Chi-restraints excluded: chain 8 residue 75 VAL Chi-restraints excluded: chain 9 residue 27 HIS Chi-restraints excluded: chain 7 residue 25 ILE Chi-restraints excluded: chain 7 residue 36 THR Chi-restraints excluded: chain 7 residue 45 SER Chi-restraints excluded: chain 7 residue 150 ASN Chi-restraints excluded: chain 7 residue 184 TYR Chi-restraints excluded: chain 7 residue 198 TYR Chi-restraints excluded: chain 7 residue 248 TYR Chi-restraints excluded: chain 7 residue 301 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 84 optimal weight: 6.9990 chunk 23 optimal weight: 0.5980 chunk 134 optimal weight: 10.0000 chunk 128 optimal weight: 0.0770 chunk 33 optimal weight: 0.9980 chunk 91 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 65 optimal weight: 7.9990 chunk 86 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 overall best weight: 0.8740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4631 r_free = 0.4631 target = 0.191404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.145514 restraints weight = 24072.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.147085 restraints weight = 18983.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.147512 restraints weight = 15191.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.147604 restraints weight = 13861.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.147756 restraints weight = 14774.440| |-----------------------------------------------------------------------------| r_work (final): 0.4108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.2455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12828 Z= 0.150 Angle : 0.629 7.226 17278 Z= 0.326 Chirality : 0.043 0.164 1876 Planarity : 0.005 0.082 2212 Dihedral : 4.324 20.999 1660 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 6.28 % Allowed : 31.46 % Favored : 62.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.96 (0.21), residues: 1484 helix: 0.62 (0.19), residues: 784 sheet: -2.14 (0.41), residues: 122 loop : -2.07 (0.23), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG 1 90 TYR 0.012 0.001 TYR 7 221 PHE 0.024 0.002 PHE 2 41 TRP 0.047 0.002 TRP 7 97 HIS 0.005 0.001 HIS 6 139 Details of bonding type rmsd covalent geometry : bond 0.00352 (12820) covalent geometry : angle 0.62435 (17274) hydrogen bonds : bond 0.03965 ( 619) hydrogen bonds : angle 4.67732 ( 1821) metal coordination : bond 0.01863 ( 8) metal coordination : angle 5.06964 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 190 time to evaluate : 0.539 Fit side-chains REVERT: 0 12 PHE cc_start: 0.7550 (OUTLIER) cc_final: 0.7113 (m-80) REVERT: 0 66 LEU cc_start: 0.8222 (mm) cc_final: 0.7636 (mm) REVERT: 0 131 ARG cc_start: 0.7590 (OUTLIER) cc_final: 0.6666 (mtm180) REVERT: 1 70 TRP cc_start: 0.7116 (OUTLIER) cc_final: 0.6766 (m100) REVERT: 3 11 LYS cc_start: 0.7568 (OUTLIER) cc_final: 0.6814 (mptp) REVERT: 3 46 LYS cc_start: 0.6357 (tptt) cc_final: 0.5928 (tptt) REVERT: 3 62 PHE cc_start: 0.4619 (OUTLIER) cc_final: 0.4115 (t80) REVERT: 2 150 ASN cc_start: 0.6171 (OUTLIER) cc_final: 0.5940 (p0) REVERT: 2 160 MET cc_start: 0.7796 (mmm) cc_final: 0.7089 (mmm) REVERT: 2 184 TYR cc_start: 0.7035 (OUTLIER) cc_final: 0.6389 (m-80) REVERT: 2 212 ARG cc_start: 0.8712 (OUTLIER) cc_final: 0.8476 (ptp-170) REVERT: 2 248 TYR cc_start: 0.8241 (OUTLIER) cc_final: 0.7511 (m-10) REVERT: 2 300 MET cc_start: 0.4353 (mtt) cc_final: 0.4142 (mtt) REVERT: 2 311 LEU cc_start: 0.1057 (OUTLIER) cc_final: 0.0510 (pp) REVERT: 5 12 PHE cc_start: 0.7503 (OUTLIER) cc_final: 0.7077 (m-80) REVERT: 5 24 GLU cc_start: 0.6360 (tp30) cc_final: 0.6052 (tp30) REVERT: 5 66 LEU cc_start: 0.8301 (mm) cc_final: 0.7677 (mm) REVERT: 5 122 MET cc_start: 0.6671 (tpp) cc_final: 0.6374 (tpp) REVERT: 5 131 ARG cc_start: 0.7632 (OUTLIER) cc_final: 0.6660 (mtm180) REVERT: 6 5 TRP cc_start: 0.6724 (m100) cc_final: 0.6437 (m100) REVERT: 6 70 TRP cc_start: 0.7048 (OUTLIER) cc_final: 0.6651 (m100) REVERT: 8 46 LYS cc_start: 0.6224 (tptt) cc_final: 0.5871 (tptt) REVERT: 8 62 PHE cc_start: 0.4723 (OUTLIER) cc_final: 0.4500 (t80) REVERT: 9 17 MET cc_start: 0.6938 (ppp) cc_final: 0.6539 (ptm) REVERT: 7 150 ASN cc_start: 0.6384 (OUTLIER) cc_final: 0.6162 (p0) REVERT: 7 160 MET cc_start: 0.7825 (mmm) cc_final: 0.7067 (mmm) REVERT: 7 184 TYR cc_start: 0.7134 (OUTLIER) cc_final: 0.6485 (m-80) REVERT: 7 230 TYR cc_start: 0.9004 (t80) cc_final: 0.8748 (t80) REVERT: 7 248 TYR cc_start: 0.8256 (OUTLIER) cc_final: 0.7626 (m-10) outliers start: 86 outliers final: 67 residues processed: 258 average time/residue: 0.1043 time to fit residues: 39.9588 Evaluate side-chains 273 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 189 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 12 PHE Chi-restraints excluded: chain 0 residue 55 ILE Chi-restraints excluded: chain 0 residue 58 VAL Chi-restraints excluded: chain 0 residue 62 THR Chi-restraints excluded: chain 0 residue 103 LEU Chi-restraints excluded: chain 0 residue 106 VAL Chi-restraints excluded: chain 0 residue 109 ILE Chi-restraints excluded: chain 0 residue 131 ARG Chi-restraints excluded: chain 0 residue 138 LEU Chi-restraints excluded: chain 1 residue 8 MET Chi-restraints excluded: chain 1 residue 20 THR Chi-restraints excluded: chain 1 residue 64 LEU Chi-restraints excluded: chain 1 residue 70 TRP Chi-restraints excluded: chain 1 residue 87 ILE Chi-restraints excluded: chain 1 residue 96 THR Chi-restraints excluded: chain 1 residue 98 VAL Chi-restraints excluded: chain 1 residue 120 ILE Chi-restraints excluded: chain 1 residue 129 VAL Chi-restraints excluded: chain 1 residue 145 SER Chi-restraints excluded: chain 1 residue 169 LYS Chi-restraints excluded: chain 3 residue 7 ILE Chi-restraints excluded: chain 3 residue 11 LYS Chi-restraints excluded: chain 3 residue 24 VAL Chi-restraints excluded: chain 3 residue 35 LEU Chi-restraints excluded: chain 3 residue 43 ARG Chi-restraints excluded: chain 3 residue 62 PHE Chi-restraints excluded: chain 3 residue 91 GLU Chi-restraints excluded: chain 4 residue 27 HIS Chi-restraints excluded: chain 4 residue 45 MET Chi-restraints excluded: chain 2 residue 25 ILE Chi-restraints excluded: chain 2 residue 36 THR Chi-restraints excluded: chain 2 residue 45 SER Chi-restraints excluded: chain 2 residue 67 GLU Chi-restraints excluded: chain 2 residue 90 LEU Chi-restraints excluded: chain 2 residue 150 ASN Chi-restraints excluded: chain 2 residue 184 TYR Chi-restraints excluded: chain 2 residue 198 TYR Chi-restraints excluded: chain 2 residue 212 ARG Chi-restraints excluded: chain 2 residue 248 TYR Chi-restraints excluded: chain 2 residue 310 MET Chi-restraints excluded: chain 2 residue 311 LEU Chi-restraints excluded: chain 5 residue 12 PHE Chi-restraints excluded: chain 5 residue 46 ASN Chi-restraints excluded: chain 5 residue 53 SER Chi-restraints excluded: chain 5 residue 55 ILE Chi-restraints excluded: chain 5 residue 58 VAL Chi-restraints excluded: chain 5 residue 62 THR Chi-restraints excluded: chain 5 residue 103 LEU Chi-restraints excluded: chain 5 residue 106 VAL Chi-restraints excluded: chain 5 residue 109 ILE Chi-restraints excluded: chain 5 residue 131 ARG Chi-restraints excluded: chain 5 residue 138 LEU Chi-restraints excluded: chain 6 residue 7 VAL Chi-restraints excluded: chain 6 residue 20 THR Chi-restraints excluded: chain 6 residue 43 HIS Chi-restraints excluded: chain 6 residue 44 TYR Chi-restraints excluded: chain 6 residue 64 LEU Chi-restraints excluded: chain 6 residue 70 TRP Chi-restraints excluded: chain 6 residue 87 ILE Chi-restraints excluded: chain 6 residue 96 THR Chi-restraints excluded: chain 6 residue 98 VAL Chi-restraints excluded: chain 6 residue 120 ILE Chi-restraints excluded: chain 6 residue 129 VAL Chi-restraints excluded: chain 6 residue 145 SER Chi-restraints excluded: chain 6 residue 169 LYS Chi-restraints excluded: chain 6 residue 173 ASP Chi-restraints excluded: chain 8 residue 7 ILE Chi-restraints excluded: chain 8 residue 24 VAL Chi-restraints excluded: chain 8 residue 35 LEU Chi-restraints excluded: chain 8 residue 43 ARG Chi-restraints excluded: chain 8 residue 57 LEU Chi-restraints excluded: chain 8 residue 62 PHE Chi-restraints excluded: chain 8 residue 63 THR Chi-restraints excluded: chain 8 residue 75 VAL Chi-restraints excluded: chain 9 residue 27 HIS Chi-restraints excluded: chain 9 residue 45 MET Chi-restraints excluded: chain 7 residue 25 ILE Chi-restraints excluded: chain 7 residue 36 THR Chi-restraints excluded: chain 7 residue 45 SER Chi-restraints excluded: chain 7 residue 150 ASN Chi-restraints excluded: chain 7 residue 184 TYR Chi-restraints excluded: chain 7 residue 198 TYR Chi-restraints excluded: chain 7 residue 248 TYR Chi-restraints excluded: chain 7 residue 301 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 114 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 108 optimal weight: 4.9990 chunk 98 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 chunk 126 optimal weight: 5.9990 chunk 59 optimal weight: 0.6980 chunk 89 optimal weight: 0.6980 chunk 130 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4631 r_free = 0.4631 target = 0.191485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.144759 restraints weight = 24087.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.147426 restraints weight = 18300.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.148458 restraints weight = 14300.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.149537 restraints weight = 11598.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.149501 restraints weight = 11919.886| |-----------------------------------------------------------------------------| r_work (final): 0.4133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7203 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12828 Z= 0.148 Angle : 0.639 14.498 17278 Z= 0.326 Chirality : 0.043 0.249 1876 Planarity : 0.005 0.067 2212 Dihedral : 4.325 21.148 1660 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 6.13 % Allowed : 31.53 % Favored : 62.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.98 (0.21), residues: 1484 helix: 0.60 (0.19), residues: 784 sheet: -2.09 (0.42), residues: 122 loop : -2.07 (0.23), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG 1 90 TYR 0.016 0.001 TYR 2 221 PHE 0.023 0.002 PHE 2 41 TRP 0.047 0.002 TRP 7 97 HIS 0.005 0.001 HIS 6 48 Details of bonding type rmsd covalent geometry : bond 0.00347 (12820) covalent geometry : angle 0.63476 (17274) hydrogen bonds : bond 0.03954 ( 619) hydrogen bonds : angle 4.68203 ( 1821) metal coordination : bond 0.01822 ( 8) metal coordination : angle 4.97416 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3032.79 seconds wall clock time: 53 minutes 11.99 seconds (3191.99 seconds total)