Starting phenix.real_space_refine on Mon Apr 6 22:12:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8i79_35212/04_2026/8i79_35212.cif Found real_map, /net/cci-nas-00/data/ceres_data/8i79_35212/04_2026/8i79_35212.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8i79_35212/04_2026/8i79_35212.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8i79_35212/04_2026/8i79_35212.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8i79_35212/04_2026/8i79_35212.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8i79_35212/04_2026/8i79_35212.map" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.036 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 8126 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 66 5.16 5 C 10314 2.51 5 N 2918 2.21 5 O 2995 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 43 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16293 Number of models: 1 Model: "" Number of chains: 10 Chain: "F" Number of atoms: 1634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1634 Classifications: {'peptide': 200} Link IDs: {'PTRANS': 11, 'TRANS': 188} Chain breaks: 2 Chain: "B" Number of atoms: 1683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1683 Classifications: {'peptide': 246} Incomplete info: {'truncation_to_alanine': 99} Link IDs: {'PTRANS': 2, 'TRANS': 243} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 358 Unresolved non-hydrogen angles: 445 Unresolved non-hydrogen dihedrals: 291 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLU:plan': 19, 'ARG:plan': 9, 'GLN:plan1': 4, 'ASP:plan': 4, 'ASN:plan1': 3, 'TYR:plan': 2, 'PHE:plan': 5, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 207 Chain: "A" Number of atoms: 1634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1634 Classifications: {'peptide': 200} Link IDs: {'PTRANS': 11, 'TRANS': 188} Chain breaks: 2 Chain: "C" Number of atoms: 1651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1651 Classifications: {'peptide': 240} Incomplete info: {'truncation_to_alanine': 90} Link IDs: {'PTRANS': 2, 'TRANS': 237} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 345 Unresolved non-hydrogen angles: 424 Unresolved non-hydrogen dihedrals: 286 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'ARG:plan': 10, 'GLU:plan': 18, 'GLN:plan1': 4, 'ASP:plan': 3, 'TYR:plan': 2, 'PHE:plan': 5, 'ASN:plan1': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 202 Chain: "D" Number of atoms: 1631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1631 Classifications: {'peptide': 200} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 188} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 1660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1660 Classifications: {'peptide': 242} Incomplete info: {'truncation_to_alanine': 96} Link IDs: {'PTRANS': 2, 'TRANS': 239} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 350 Unresolved non-hydrogen angles: 436 Unresolved non-hydrogen dihedrals: 284 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLU:plan': 19, 'ARG:plan': 9, 'GLN:plan1': 4, 'ASP:plan': 4, 'ASN:plan1': 3, 'TYR:plan': 2, 'PHE:plan': 5, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 207 Chain: "G" Number of atoms: 1634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1634 Classifications: {'peptide': 200} Link IDs: {'PTRANS': 11, 'TRANS': 188} Chain breaks: 2 Chain: "H" Number of atoms: 1646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1646 Classifications: {'peptide': 242} Incomplete info: {'truncation_to_alanine': 100} Link IDs: {'PTRANS': 2, 'TRANS': 239} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 366 Unresolved non-hydrogen angles: 455 Unresolved non-hydrogen dihedrals: 299 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLU:plan': 18, 'ARG:plan': 10, 'ASP:plan': 5, 'HIS:plan': 2, 'GLN:plan1': 4, 'ASN:plan1': 2, 'TYR:plan': 2, 'PHE:plan': 5} Unresolved non-hydrogen planarities: 213 Chain: "I" Number of atoms: 1634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1634 Classifications: {'peptide': 200} Link IDs: {'PTRANS': 11, 'TRANS': 188} Chain breaks: 2 Chain: "J" Number of atoms: 1486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1486 Classifications: {'peptide': 228} Incomplete info: {'truncation_to_alanine': 115} Link IDs: {'PTRANS': 2, 'TRANS': 225} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 420 Unresolved non-hydrogen angles: 520 Unresolved non-hydrogen dihedrals: 337 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'ASP:plan': 7, 'GLN:plan1': 5, 'GLU:plan': 21, 'ARG:plan': 12, 'ASN:plan1': 8, 'HIS:plan': 2, 'TYR:plan': 1, 'PHE:plan': 4} Unresolved non-hydrogen planarities: 250 Time building chain proxies: 3.71, per 1000 atoms: 0.23 Number of scatterers: 16293 At special positions: 0 Unit cell: (179.355, 179.355, 93.482, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 66 16.00 O 2995 8.00 N 2918 7.00 C 10314 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: 1.38 Conformation dependent library (CDL) restraints added in 757.3 milliseconds 4300 Ramachandran restraints generated. 2150 Oldfield, 0 Emsley, 2150 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4178 Finding SS restraints... Secondary structure from input PDB file: 110 helices and 10 sheets defined 71.8% alpha, 7.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'F' and resid 66 through 70 Processing helix chain 'F' and resid 75 through 81 Processing helix chain 'F' and resid 103 through 113 removed outlier: 3.821A pdb=" N VAL F 107 " --> pdb=" O HIS F 103 " (cutoff:3.500A) Processing helix chain 'F' and resid 121 through 133 Processing helix chain 'F' and resid 134 through 143 Processing helix chain 'F' and resid 144 through 158 removed outlier: 4.366A pdb=" N GLU F 150 " --> pdb=" O PRO F 146 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N PHE F 156 " --> pdb=" O VAL F 152 " (cutoff:3.500A) Processing helix chain 'F' and resid 162 through 182 Processing helix chain 'F' and resid 240 through 255 Processing helix chain 'B' and resid 27 through 46 Processing helix chain 'B' and resid 53 through 67 Processing helix chain 'B' and resid 69 through 86 Processing helix chain 'B' and resid 88 through 96 Processing helix chain 'B' and resid 100 through 123 Processing helix chain 'B' and resid 123 through 129 Processing helix chain 'B' and resid 129 through 134 removed outlier: 3.548A pdb=" N ASN B 134 " --> pdb=" O TYR B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 152 Processing helix chain 'B' and resid 154 through 175 Processing helix chain 'B' and resid 179 through 194 removed outlier: 3.994A pdb=" N GLY B 194 " --> pdb=" O LEU B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 205 Processing helix chain 'B' and resid 205 through 228 removed outlier: 3.554A pdb=" N GLN B 222 " --> pdb=" O GLN B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 252 Processing helix chain 'B' and resid 256 through 270 Processing helix chain 'A' and resid 66 through 70 Processing helix chain 'A' and resid 75 through 81 Processing helix chain 'A' and resid 103 through 113 removed outlier: 3.781A pdb=" N VAL A 107 " --> pdb=" O HIS A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 120 No H-bonds generated for 'chain 'A' and resid 118 through 120' Processing helix chain 'A' and resid 121 through 133 Processing helix chain 'A' and resid 134 through 143 Processing helix chain 'A' and resid 144 through 158 removed outlier: 4.277A pdb=" N GLU A 150 " --> pdb=" O PRO A 146 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N PHE A 156 " --> pdb=" O VAL A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 182 Processing helix chain 'A' and resid 240 through 255 removed outlier: 3.641A pdb=" N LEU A 244 " --> pdb=" O ASP A 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 46 Processing helix chain 'C' and resid 53 through 67 removed outlier: 3.542A pdb=" N LEU C 57 " --> pdb=" O SER C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 86 removed outlier: 3.598A pdb=" N LEU C 73 " --> pdb=" O HIS C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 96 Processing helix chain 'C' and resid 100 through 123 Processing helix chain 'C' and resid 123 through 129 Processing helix chain 'C' and resid 129 through 134 Processing helix chain 'C' and resid 138 through 151 Processing helix chain 'C' and resid 154 through 175 Processing helix chain 'C' and resid 180 through 193 Processing helix chain 'C' and resid 198 through 205 Processing helix chain 'C' and resid 205 through 228 Processing helix chain 'C' and resid 229 through 252 Processing helix chain 'C' and resid 256 through 267 Processing helix chain 'D' and resid 66 through 70 Processing helix chain 'D' and resid 75 through 81 Processing helix chain 'D' and resid 103 through 113 removed outlier: 3.718A pdb=" N VAL D 107 " --> pdb=" O HIS D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 133 Processing helix chain 'D' and resid 134 through 143 Processing helix chain 'D' and resid 144 through 158 removed outlier: 4.008A pdb=" N GLU D 150 " --> pdb=" O PRO D 146 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N PHE D 156 " --> pdb=" O VAL D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 162 through 182 Processing helix chain 'D' and resid 240 through 255 removed outlier: 3.584A pdb=" N LEU D 244 " --> pdb=" O ASP D 240 " (cutoff:3.500A) Processing helix chain 'E' and resid 27 through 46 Processing helix chain 'E' and resid 53 through 67 removed outlier: 3.537A pdb=" N LEU E 57 " --> pdb=" O SER E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 69 through 86 removed outlier: 3.619A pdb=" N LEU E 73 " --> pdb=" O HIS E 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 96 Processing helix chain 'E' and resid 100 through 123 Processing helix chain 'E' and resid 123 through 129 removed outlier: 3.738A pdb=" N ASP E 127 " --> pdb=" O LEU E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 129 through 134 Processing helix chain 'E' and resid 138 through 152 Processing helix chain 'E' and resid 154 through 175 Processing helix chain 'E' and resid 179 through 194 removed outlier: 3.993A pdb=" N GLY E 194 " --> pdb=" O LEU E 190 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 205 Processing helix chain 'E' and resid 205 through 228 Processing helix chain 'E' and resid 229 through 252 Processing helix chain 'E' and resid 256 through 267 removed outlier: 3.513A pdb=" N ILE E 260 " --> pdb=" O THR E 256 " (cutoff:3.500A) Processing helix chain 'G' and resid 66 through 70 Processing helix chain 'G' and resid 75 through 81 Processing helix chain 'G' and resid 103 through 113 removed outlier: 3.746A pdb=" N VAL G 107 " --> pdb=" O HIS G 103 " (cutoff:3.500A) Processing helix chain 'G' and resid 121 through 133 Processing helix chain 'G' and resid 134 through 143 Processing helix chain 'G' and resid 144 through 158 removed outlier: 4.216A pdb=" N GLU G 150 " --> pdb=" O PRO G 146 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N PHE G 156 " --> pdb=" O VAL G 152 " (cutoff:3.500A) Processing helix chain 'G' and resid 162 through 182 Processing helix chain 'G' and resid 240 through 255 Processing helix chain 'H' and resid 27 through 46 Processing helix chain 'H' and resid 53 through 67 removed outlier: 3.503A pdb=" N LEU H 57 " --> pdb=" O SER H 53 " (cutoff:3.500A) Processing helix chain 'H' and resid 69 through 86 Processing helix chain 'H' and resid 88 through 95 Processing helix chain 'H' and resid 100 through 123 Processing helix chain 'H' and resid 123 through 129 removed outlier: 3.755A pdb=" N ASP H 127 " --> pdb=" O LEU H 123 " (cutoff:3.500A) Processing helix chain 'H' and resid 129 through 134 Processing helix chain 'H' and resid 138 through 152 Processing helix chain 'H' and resid 154 through 175 Processing helix chain 'H' and resid 179 through 194 removed outlier: 3.965A pdb=" N GLY H 194 " --> pdb=" O LEU H 190 " (cutoff:3.500A) Processing helix chain 'H' and resid 198 through 205 removed outlier: 3.598A pdb=" N ASP H 204 " --> pdb=" O VAL H 200 " (cutoff:3.500A) Processing helix chain 'H' and resid 205 through 224 Processing helix chain 'H' and resid 230 through 252 Processing helix chain 'H' and resid 256 through 270 Processing helix chain 'I' and resid 66 through 70 Processing helix chain 'I' and resid 75 through 81 Processing helix chain 'I' and resid 103 through 113 removed outlier: 3.770A pdb=" N VAL I 107 " --> pdb=" O HIS I 103 " (cutoff:3.500A) Processing helix chain 'I' and resid 121 through 133 Processing helix chain 'I' and resid 134 through 143 Processing helix chain 'I' and resid 144 through 158 removed outlier: 4.146A pdb=" N GLU I 150 " --> pdb=" O PRO I 146 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N PHE I 156 " --> pdb=" O VAL I 152 " (cutoff:3.500A) Processing helix chain 'I' and resid 162 through 182 Processing helix chain 'I' and resid 240 through 255 removed outlier: 3.524A pdb=" N LEU I 244 " --> pdb=" O ASP I 240 " (cutoff:3.500A) Processing helix chain 'J' and resid 27 through 46 Processing helix chain 'J' and resid 53 through 67 Processing helix chain 'J' and resid 69 through 97 removed outlier: 3.643A pdb=" N LEU J 73 " --> pdb=" O HIS J 69 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASN J 95 " --> pdb=" O GLU J 91 " (cutoff:3.500A) Processing helix chain 'J' and resid 100 through 123 Processing helix chain 'J' and resid 123 through 129 removed outlier: 3.660A pdb=" N ASP J 127 " --> pdb=" O LEU J 123 " (cutoff:3.500A) Processing helix chain 'J' and resid 129 through 134 Processing helix chain 'J' and resid 138 through 152 Processing helix chain 'J' and resid 154 through 175 Processing helix chain 'J' and resid 179 through 194 removed outlier: 3.869A pdb=" N GLY J 194 " --> pdb=" O LEU J 190 " (cutoff:3.500A) Processing helix chain 'J' and resid 198 through 205 Processing helix chain 'J' and resid 205 through 220 Processing helix chain 'J' and resid 235 through 252 Processing helix chain 'J' and resid 256 through 268 Processing sheet with id=AA1, first strand: chain 'F' and resid 60 through 65 Processing sheet with id=AA2, first strand: chain 'F' and resid 230 through 232 removed outlier: 9.659A pdb=" N VAL F 230 " --> pdb=" O LYS F 187 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LYS F 189 " --> pdb=" O VAL F 230 " (cutoff:3.500A) removed outlier: 8.232A pdb=" N PHE F 232 " --> pdb=" O LYS F 189 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N CYS F 191 " --> pdb=" O PHE F 232 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N THR F 258 " --> pdb=" O THR F 287 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 60 through 65 Processing sheet with id=AA4, first strand: chain 'A' and resid 230 through 232 removed outlier: 9.702A pdb=" N VAL A 230 " --> pdb=" O LYS A 187 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LYS A 189 " --> pdb=" O VAL A 230 " (cutoff:3.500A) removed outlier: 8.292A pdb=" N PHE A 232 " --> pdb=" O LYS A 189 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N CYS A 191 " --> pdb=" O PHE A 232 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N THR A 258 " --> pdb=" O THR A 287 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 60 through 65 Processing sheet with id=AA6, first strand: chain 'D' and resid 230 through 232 removed outlier: 9.702A pdb=" N VAL D 230 " --> pdb=" O LYS D 187 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N LYS D 189 " --> pdb=" O VAL D 230 " (cutoff:3.500A) removed outlier: 8.296A pdb=" N PHE D 232 " --> pdb=" O LYS D 189 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N CYS D 191 " --> pdb=" O PHE D 232 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N THR D 258 " --> pdb=" O THR D 287 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 60 through 65 Processing sheet with id=AA8, first strand: chain 'G' and resid 230 through 232 removed outlier: 9.720A pdb=" N VAL G 230 " --> pdb=" O LYS G 187 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LYS G 189 " --> pdb=" O VAL G 230 " (cutoff:3.500A) removed outlier: 8.277A pdb=" N PHE G 232 " --> pdb=" O LYS G 189 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N CYS G 191 " --> pdb=" O PHE G 232 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N THR G 258 " --> pdb=" O THR G 287 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 60 through 65 Processing sheet with id=AB1, first strand: chain 'I' and resid 230 through 232 removed outlier: 9.724A pdb=" N VAL I 230 " --> pdb=" O LYS I 187 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N LYS I 189 " --> pdb=" O VAL I 230 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N PHE I 232 " --> pdb=" O LYS I 189 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N CYS I 191 " --> pdb=" O PHE I 232 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N THR I 258 " --> pdb=" O THR I 287 " (cutoff:3.500A) 1204 hydrogen bonds defined for protein. 3582 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: 2.69 Time building geometry restraints manager: 1.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 5589 1.34 - 1.46: 2811 1.46 - 1.58: 8081 1.58 - 1.69: 0 1.69 - 1.81: 111 Bond restraints: 16592 Sorted by residual: bond pdb=" N PRO G 118 " pdb=" CA PRO G 118 " ideal model delta sigma weight residual 1.468 1.477 -0.009 7.90e-03 1.60e+04 1.41e+00 bond pdb=" CB GLN C 132 " pdb=" CG GLN C 132 " ideal model delta sigma weight residual 1.520 1.555 -0.035 3.00e-02 1.11e+03 1.40e+00 bond pdb=" CA VAL E 151 " pdb=" CB VAL E 151 " ideal model delta sigma weight residual 1.536 1.549 -0.013 1.24e-02 6.50e+03 1.16e+00 bond pdb=" CD GLU D 172 " pdb=" OE1 GLU D 172 " ideal model delta sigma weight residual 1.249 1.230 0.019 1.90e-02 2.77e+03 1.03e+00 bond pdb=" C ILE H 269 " pdb=" O ILE H 269 " ideal model delta sigma weight residual 1.231 1.242 -0.010 1.02e-02 9.61e+03 1.02e+00 ... (remaining 16587 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.31: 21689 1.31 - 2.62: 718 2.62 - 3.94: 127 3.94 - 5.25: 28 5.25 - 6.56: 7 Bond angle restraints: 22569 Sorted by residual: angle pdb=" C ARG C 128 " pdb=" N VAL C 129 " pdb=" CA VAL C 129 " ideal model delta sigma weight residual 123.16 118.38 4.78 1.06e+00 8.90e-01 2.03e+01 angle pdb=" C ARG J 128 " pdb=" N VAL J 129 " pdb=" CA VAL J 129 " ideal model delta sigma weight residual 123.16 118.50 4.66 1.06e+00 8.90e-01 1.93e+01 angle pdb=" N VAL J 152 " pdb=" CA VAL J 152 " pdb=" C VAL J 152 " ideal model delta sigma weight residual 111.90 108.79 3.11 8.10e-01 1.52e+00 1.48e+01 angle pdb=" C ARG E 128 " pdb=" N VAL E 129 " pdb=" CA VAL E 129 " ideal model delta sigma weight residual 123.16 119.09 4.07 1.06e+00 8.90e-01 1.47e+01 angle pdb=" N VAL B 152 " pdb=" CA VAL B 152 " pdb=" C VAL B 152 " ideal model delta sigma weight residual 112.12 109.02 3.10 8.40e-01 1.42e+00 1.36e+01 ... (remaining 22564 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.45: 9156 17.45 - 34.90: 565 34.90 - 52.35: 106 52.35 - 69.81: 9 69.81 - 87.26: 12 Dihedral angle restraints: 9848 sinusoidal: 3406 harmonic: 6442 Sorted by residual: dihedral pdb=" CA MET F 144 " pdb=" C MET F 144 " pdb=" N GLN F 145 " pdb=" CA GLN F 145 " ideal model delta harmonic sigma weight residual 180.00 -156.50 -23.50 0 5.00e+00 4.00e-02 2.21e+01 dihedral pdb=" CA MET D 144 " pdb=" C MET D 144 " pdb=" N GLN D 145 " pdb=" CA GLN D 145 " ideal model delta harmonic sigma weight residual -180.00 -157.53 -22.47 0 5.00e+00 4.00e-02 2.02e+01 dihedral pdb=" CA VAL B 129 " pdb=" C VAL B 129 " pdb=" N TYR B 130 " pdb=" CA TYR B 130 " ideal model delta harmonic sigma weight residual -180.00 -161.18 -18.82 0 5.00e+00 4.00e-02 1.42e+01 ... (remaining 9845 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1964 0.042 - 0.085: 502 0.085 - 0.127: 95 0.127 - 0.169: 14 0.169 - 0.212: 3 Chirality restraints: 2578 Sorted by residual: chirality pdb=" CA GLU D 172 " pdb=" N GLU D 172 " pdb=" C GLU D 172 " pdb=" CB GLU D 172 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CB VAL E 151 " pdb=" CA VAL E 151 " pdb=" CG1 VAL E 151 " pdb=" CG2 VAL E 151 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CA GLU A 172 " pdb=" N GLU A 172 " pdb=" C GLU A 172 " pdb=" CB GLU A 172 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.77e-01 ... (remaining 2575 not shown) Planarity restraints: 2960 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP H 34 " -0.034 2.00e-02 2.50e+03 2.52e-02 1.58e+01 pdb=" CG TRP H 34 " 0.069 2.00e-02 2.50e+03 pdb=" CD1 TRP H 34 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP H 34 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP H 34 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP H 34 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP H 34 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 34 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 34 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP H 34 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 34 " -0.029 2.00e-02 2.50e+03 2.27e-02 1.29e+01 pdb=" CG TRP E 34 " 0.059 2.00e-02 2.50e+03 pdb=" CD1 TRP E 34 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP E 34 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP E 34 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP E 34 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP E 34 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 34 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 34 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP E 34 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU E 85 " 0.012 2.00e-02 2.50e+03 2.52e-02 6.35e+00 pdb=" C LEU E 85 " -0.044 2.00e-02 2.50e+03 pdb=" O LEU E 85 " 0.016 2.00e-02 2.50e+03 pdb=" N ILE E 86 " 0.015 2.00e-02 2.50e+03 ... (remaining 2957 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1199 2.74 - 3.28: 16629 3.28 - 3.82: 28259 3.82 - 4.36: 30687 4.36 - 4.90: 55575 Nonbonded interactions: 132349 Sorted by model distance: nonbonded pdb=" OH TYR C 74 " pdb=" NH2 ARG C 78 " model vdw 2.195 3.120 nonbonded pdb=" NH2 ARG C 128 " pdb=" O ASP G 74 " model vdw 2.200 3.120 nonbonded pdb=" OH TYR J 74 " pdb=" NH2 ARG J 78 " model vdw 2.203 3.120 nonbonded pdb=" O PRO G 136 " pdb=" NE2 GLN G 140 " model vdw 2.207 3.120 nonbonded pdb=" ND2 ASN I 56 " pdb=" OD2 ASP I 90 " model vdw 2.208 3.120 ... (remaining 132344 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 45 and (name N or name CA or name C or name O or name CB \ )) or resid 46 through 289)) selection = chain 'D' selection = (chain 'F' and ((resid 45 and (name N or name CA or name C or name O or name CB \ )) or resid 46 through 289)) selection = (chain 'G' and ((resid 45 and (name N or name CA or name C or name O or name CB \ )) or resid 46 through 289)) selection = (chain 'I' and ((resid 45 and (name N or name CA or name C or name O or name CB \ )) or resid 46 through 289)) } ncs_group { reference = (chain 'B' and ((resid 26 and (name N or name CA or name C or name O or name CB \ )) or resid 27 or (resid 28 and (name N or name CA or name C or name O or name C \ B )) or resid 29 through 37 or (resid 38 and (name N or name CA or name C or nam \ e O or name CB )) or resid 39 through 41 or (resid 42 through 43 and (name N or \ name CA or name C or name O or name CB )) or resid 44 or (resid 45 through 49 an \ d (name N or name CA or name C or name O or name CB )) or resid 52 through 71 or \ (resid 72 and (name N or name CA or name C or name O or name CB )) or resid 73 \ through 78 or (resid 79 and (name N or name CA or name C or name O or name CB )) \ or resid 80 through 86 or (resid 87 through 99 and (name N or name CA or name C \ or name O or name CB )) or resid 100 through 117 or (resid 118 and (name N or n \ ame CA or name C or name O or name CB )) or resid 119 through 156 or (resid 157 \ through 174 and (name N or name CA or name C or name O or name CB )) or resid 17 \ 5 through 176 or resid 179 through 220 or resid 234 through 267)) selection = (chain 'C' and ((resid 26 and (name N or name CA or name C or name O or name CB \ )) or resid 27 through 41 or (resid 42 through 43 and (name N or name CA or name \ C or name O or name CB )) or resid 44 or (resid 45 through 49 and (name N or na \ me CA or name C or name O or name CB )) or resid 52 through 78 or (resid 79 and \ (name N or name CA or name C or name O or name CB )) or resid 80 through 86 or ( \ resid 87 through 99 and (name N or name CA or name C or name O or name CB )) or \ resid 100 through 117 or (resid 118 and (name N or name CA or name C or name O o \ r name CB )) or resid 119 through 157 or (resid 158 through 174 and (name N or n \ ame CA or name C or name O or name CB )) or (resid 175 through 193 and (name N o \ r name CA or name C or name O or name CB )) or (resid 194 through 220 and (name \ N or name CA or name C or name O or name CB )) or resid 234 through 267)) selection = (chain 'E' and ((resid 26 and (name N or name CA or name C or name O or name CB \ )) or resid 27 or (resid 28 and (name N or name CA or name C or name O or name C \ B )) or resid 29 through 37 or (resid 38 and (name N or name CA or name C or nam \ e O or name CB )) or resid 39 through 41 or (resid 42 through 43 and (name N or \ name CA or name C or name O or name CB )) or resid 44 or (resid 45 through 49 an \ d (name N or name CA or name C or name O or name CB )) or resid 52 through 71 or \ (resid 72 and (name N or name CA or name C or name O or name CB )) or resid 73 \ through 78 or (resid 79 and (name N or name CA or name C or name O or name CB )) \ or resid 80 through 86 or (resid 87 through 99 and (name N or name CA or name C \ or name O or name CB )) or resid 100 through 117 or (resid 118 and (name N or n \ ame CA or name C or name O or name CB )) or resid 119 through 156 or (resid 157 \ through 174 and (name N or name CA or name C or name O or name CB )) or resid 17 \ 5 through 176 or resid 179 through 220 or resid 234 through 267)) selection = (chain 'H' and ((resid 26 and (name N or name CA or name C or name O or name CB \ )) or resid 27 or (resid 28 and (name N or name CA or name C or name O or name C \ B )) or resid 29 through 37 or (resid 38 and (name N or name CA or name C or nam \ e O or name CB )) or resid 39 through 41 or (resid 42 through 43 and (name N or \ name CA or name C or name O or name CB )) or resid 44 or (resid 45 through 49 an \ d (name N or name CA or name C or name O or name CB )) or resid 52 through 71 or \ (resid 72 and (name N or name CA or name C or name O or name CB )) or resid 73 \ through 78 or (resid 79 and (name N or name CA or name C or name O or name CB )) \ or resid 80 through 86 or (resid 87 through 99 and (name N or name CA or name C \ or name O or name CB )) or resid 100 through 117 or (resid 118 and (name N or n \ ame CA or name C or name O or name CB )) or resid 119 through 156 or (resid 157 \ through 174 and (name N or name CA or name C or name O or name CB )) or resid 17 \ 5 through 176 or resid 179 through 220 or resid 234 through 267)) selection = (chain 'J' and (resid 26 through 156 or (resid 157 through 174 and (name N or na \ me CA or name C or name O or name CB )) or resid 175 through 176 or resid 179 th \ rough 267)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 15.230 Find NCS groups from input model: 0.340 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:6.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 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 : 0.003 0.035 16592 Z= 0.149 Angle : 0.569 6.562 22569 Z= 0.335 Chirality : 0.039 0.212 2578 Planarity : 0.004 0.060 2960 Dihedral : 12.356 87.257 5670 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 0.00 % Allowed : 0.07 % Favored : 99.93 % 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: 1.30 (0.18), residues: 2150 helix: 1.84 (0.14), residues: 1449 sheet: 0.45 (0.37), residues: 165 loop : -1.78 (0.22), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 148 TYR 0.017 0.002 TYR B 74 PHE 0.017 0.001 PHE D 185 TRP 0.069 0.002 TRP H 34 HIS 0.004 0.001 HIS C 160 Details of bonding type rmsd covalent geometry : bond 0.00323 (16592) covalent geometry : angle 0.56866 (22569) hydrogen bonds : bond 0.13572 ( 1204) hydrogen bonds : angle 5.89605 ( 3582) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4300 Ramachandran restraints generated. 2150 Oldfield, 0 Emsley, 2150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4300 Ramachandran restraints generated. 2150 Oldfield, 0 Emsley, 2150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 397 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 113 GLN cc_start: 0.8767 (mt0) cc_final: 0.8538 (mp10) REVERT: B 145 ILE cc_start: 0.8562 (mt) cc_final: 0.8356 (pp) REVERT: C 204 ASP cc_start: 0.7001 (m-30) cc_final: 0.6632 (m-30) REVERT: E 45 GLN cc_start: 0.8513 (mt0) cc_final: 0.7954 (pp30) REVERT: E 104 THR cc_start: 0.9454 (t) cc_final: 0.9245 (p) REVERT: E 113 GLN cc_start: 0.8781 (mt0) cc_final: 0.8511 (mp10) REVERT: E 150 GLN cc_start: 0.8170 (mm-40) cc_final: 0.7935 (mp10) REVERT: H 113 GLN cc_start: 0.8711 (mt0) cc_final: 0.8496 (mt0) REVERT: H 145 ILE cc_start: 0.8571 (mt) cc_final: 0.8357 (pp) REVERT: H 150 GLN cc_start: 0.8268 (mm-40) cc_final: 0.8028 (mm110) REVERT: J 39 ASN cc_start: 0.8481 (t0) cc_final: 0.8280 (t0) REVERT: J 104 THR cc_start: 0.9235 (t) cc_final: 0.9011 (t) REVERT: J 138 ASN cc_start: 0.8336 (p0) cc_final: 0.7884 (p0) outliers start: 0 outliers final: 1 residues processed: 397 average time/residue: 0.6285 time to fit residues: 273.2610 Evaluate side-chains 246 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 245 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 119 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 216 optimal weight: 40.0000 chunk 98 optimal weight: 0.6980 chunk 194 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 20.0000 chunk 103 optimal weight: 4.9990 chunk 200 optimal weight: 10.0000 chunk 212 optimal weight: 20.0000 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 45 GLN C 107 GLN C 112 HIS C 135 ASN ** D 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 107 GLN ** I 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 31 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.069969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.047308 restraints weight = 65088.098| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 3.48 r_work: 0.2819 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.2348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 16592 Z= 0.246 Angle : 0.633 9.044 22569 Z= 0.335 Chirality : 0.041 0.156 2578 Planarity : 0.004 0.057 2960 Dihedral : 4.262 35.383 2381 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.33 % Allowed : 13.89 % Favored : 83.78 % 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: 1.41 (0.17), residues: 2150 helix: 1.88 (0.13), residues: 1479 sheet: 0.70 (0.46), residues: 115 loop : -1.66 (0.21), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 78 TYR 0.022 0.002 TYR B 154 PHE 0.017 0.002 PHE E 147 TRP 0.031 0.002 TRP E 34 HIS 0.008 0.001 HIS B 84 Details of bonding type rmsd covalent geometry : bond 0.00543 (16592) covalent geometry : angle 0.63331 (22569) hydrogen bonds : bond 0.04065 ( 1204) hydrogen bonds : angle 4.92500 ( 3582) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4300 Ramachandran restraints generated. 2150 Oldfield, 0 Emsley, 2150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4300 Ramachandran restraints generated. 2150 Oldfield, 0 Emsley, 2150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 261 time to evaluate : 0.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 285 LYS cc_start: 0.9226 (OUTLIER) cc_final: 0.9010 (ttmm) REVERT: B 38 LYS cc_start: 0.8763 (tmmt) cc_final: 0.8557 (tmmt) REVERT: B 56 GLU cc_start: 0.8790 (mt-10) cc_final: 0.8552 (pt0) REVERT: B 113 GLN cc_start: 0.9060 (mt0) cc_final: 0.8647 (mp10) REVERT: B 116 MET cc_start: 0.9388 (tpp) cc_final: 0.8596 (mmm) REVERT: A 160 MET cc_start: 0.9521 (mtm) cc_final: 0.9280 (mtt) REVERT: C 79 GLU cc_start: 0.9082 (mm-30) cc_final: 0.8848 (pp20) REVERT: C 126 MET cc_start: 0.9077 (OUTLIER) cc_final: 0.8482 (tmm) REVERT: C 145 ILE cc_start: 0.8367 (pp) cc_final: 0.8156 (pp) REVERT: C 203 GLU cc_start: 0.9223 (pp20) cc_final: 0.8867 (pp20) REVERT: C 204 ASP cc_start: 0.6897 (m-30) cc_final: 0.5908 (m-30) REVERT: E 113 GLN cc_start: 0.9070 (mt0) cc_final: 0.8659 (mt0) REVERT: H 56 GLU cc_start: 0.8551 (mt-10) cc_final: 0.8301 (mp0) REVERT: H 103 GLN cc_start: 0.9235 (tm-30) cc_final: 0.8668 (tm-30) REVERT: H 107 GLN cc_start: 0.9434 (tp40) cc_final: 0.9006 (mm-40) REVERT: H 113 GLN cc_start: 0.9051 (mt0) cc_final: 0.8687 (mt0) REVERT: H 145 ILE cc_start: 0.8307 (mt) cc_final: 0.8054 (mp) REVERT: I 285 LYS cc_start: 0.9345 (OUTLIER) cc_final: 0.9127 (tttm) REVERT: J 39 ASN cc_start: 0.9091 (t0) cc_final: 0.8862 (t0) REVERT: J 120 ARG cc_start: 0.9320 (tmm-80) cc_final: 0.9081 (ptm160) REVERT: J 150 GLN cc_start: 0.6348 (OUTLIER) cc_final: 0.5740 (tm-30) outliers start: 34 outliers final: 7 residues processed: 280 average time/residue: 0.5962 time to fit residues: 184.2088 Evaluate side-chains 228 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 217 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 285 LYS Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 126 MET Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain I residue 285 LYS Chi-restraints excluded: chain J residue 32 SER Chi-restraints excluded: chain J residue 77 LEU Chi-restraints excluded: chain J residue 127 ASP Chi-restraints excluded: chain J residue 150 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 95 optimal weight: 0.8980 chunk 105 optimal weight: 0.9990 chunk 28 optimal weight: 4.9990 chunk 170 optimal weight: 50.0000 chunk 31 optimal weight: 3.9990 chunk 148 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 119 optimal weight: 10.0000 chunk 140 optimal weight: 1.9990 chunk 152 optimal weight: 5.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 112 HIS ** G 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 135 ASN ** I 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 103 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 = 0.3670 r_free = 0.3670 target = 0.070520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.047958 restraints weight = 65803.955| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 3.52 r_work: 0.2839 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 16592 Z= 0.160 Angle : 0.563 11.588 22569 Z= 0.295 Chirality : 0.039 0.135 2578 Planarity : 0.004 0.063 2960 Dihedral : 4.079 22.024 2379 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.57 % Allowed : 16.50 % Favored : 81.93 % 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: 1.53 (0.18), residues: 2150 helix: 1.95 (0.13), residues: 1487 sheet: 0.61 (0.46), residues: 115 loop : -1.57 (0.22), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 78 TYR 0.022 0.002 TYR E 74 PHE 0.015 0.001 PHE E 147 TRP 0.015 0.001 TRP E 34 HIS 0.006 0.001 HIS B 84 Details of bonding type rmsd covalent geometry : bond 0.00357 (16592) covalent geometry : angle 0.56283 (22569) hydrogen bonds : bond 0.03628 ( 1204) hydrogen bonds : angle 4.68056 ( 3582) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4300 Ramachandran restraints generated. 2150 Oldfield, 0 Emsley, 2150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4300 Ramachandran restraints generated. 2150 Oldfield, 0 Emsley, 2150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 255 time to evaluate : 0.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 38 LYS cc_start: 0.8690 (tmmt) cc_final: 0.8075 (tmmt) REVERT: B 56 GLU cc_start: 0.8779 (mt-10) cc_final: 0.8454 (pt0) REVERT: B 113 GLN cc_start: 0.9058 (mt0) cc_final: 0.8646 (mp10) REVERT: B 116 MET cc_start: 0.9375 (tpp) cc_final: 0.8600 (mmm) REVERT: A 160 MET cc_start: 0.9558 (mtm) cc_final: 0.9267 (mtt) REVERT: C 35 ASP cc_start: 0.9410 (t0) cc_final: 0.9092 (m-30) REVERT: C 79 GLU cc_start: 0.9085 (mm-30) cc_final: 0.8880 (pp20) REVERT: C 113 GLN cc_start: 0.9051 (mm110) cc_final: 0.8752 (mm110) REVERT: C 126 MET cc_start: 0.9151 (OUTLIER) cc_final: 0.8573 (tmm) REVERT: C 200 VAL cc_start: 0.8553 (OUTLIER) cc_final: 0.8053 (p) REVERT: C 204 ASP cc_start: 0.6787 (m-30) cc_final: 0.6106 (m-30) REVERT: E 56 GLU cc_start: 0.8719 (pt0) cc_final: 0.8490 (pm20) REVERT: E 113 GLN cc_start: 0.9022 (mt0) cc_final: 0.8628 (mt0) REVERT: G 74 ASP cc_start: 0.9244 (m-30) cc_final: 0.8913 (t0) REVERT: G 285 LYS cc_start: 0.9227 (OUTLIER) cc_final: 0.8972 (ttmm) REVERT: H 56 GLU cc_start: 0.8540 (mt-10) cc_final: 0.8277 (mp0) REVERT: H 91 GLU cc_start: 0.8157 (mp0) cc_final: 0.7279 (pp20) REVERT: H 113 GLN cc_start: 0.9008 (mt0) cc_final: 0.8631 (mt0) REVERT: H 126 MET cc_start: 0.9074 (mmm) cc_final: 0.8626 (mmm) REVERT: H 149 ASP cc_start: 0.8965 (m-30) cc_final: 0.8732 (m-30) REVERT: I 285 LYS cc_start: 0.9366 (OUTLIER) cc_final: 0.9159 (tttm) REVERT: J 39 ASN cc_start: 0.9104 (t0) cc_final: 0.8877 (t0) REVERT: J 113 GLN cc_start: 0.9039 (mm110) cc_final: 0.8640 (mp-120) REVERT: J 120 ARG cc_start: 0.9344 (tmm-80) cc_final: 0.9091 (ptm160) outliers start: 23 outliers final: 6 residues processed: 267 average time/residue: 0.5539 time to fit residues: 164.2253 Evaluate side-chains 222 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 212 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 126 MET Chi-restraints excluded: chain C residue 127 ASP Chi-restraints excluded: chain C residue 147 PHE Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain G residue 285 LYS Chi-restraints excluded: chain I residue 285 LYS Chi-restraints excluded: chain J residue 127 ASP Chi-restraints excluded: chain J residue 131 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 36 optimal weight: 7.9990 chunk 89 optimal weight: 4.9990 chunk 175 optimal weight: 50.0000 chunk 93 optimal weight: 3.9990 chunk 118 optimal weight: 9.9990 chunk 216 optimal weight: 40.0000 chunk 195 optimal weight: 3.9990 chunk 126 optimal weight: 50.0000 chunk 107 optimal weight: 5.9990 chunk 81 optimal weight: 0.8980 chunk 162 optimal weight: 3.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 166 HIS D 166 HIS ** E 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 47 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 = 0.3629 r_free = 0.3629 target = 0.068517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.045701 restraints weight = 65774.091| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 3.48 r_work: 0.2774 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.2919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.108 16592 Z= 0.323 Angle : 0.660 11.893 22569 Z= 0.342 Chirality : 0.042 0.139 2578 Planarity : 0.004 0.054 2960 Dihedral : 4.211 25.868 2379 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.87 % Allowed : 17.04 % Favored : 80.08 % 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: 1.39 (0.18), residues: 2150 helix: 1.84 (0.13), residues: 1491 sheet: 0.12 (0.37), residues: 155 loop : -1.66 (0.23), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 120 TYR 0.023 0.002 TYR I 126 PHE 0.015 0.002 PHE D 81 TRP 0.010 0.002 TRP G 235 HIS 0.009 0.001 HIS B 84 Details of bonding type rmsd covalent geometry : bond 0.00724 (16592) covalent geometry : angle 0.66042 (22569) hydrogen bonds : bond 0.04004 ( 1204) hydrogen bonds : angle 4.84688 ( 3582) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4300 Ramachandran restraints generated. 2150 Oldfield, 0 Emsley, 2150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4300 Ramachandran restraints generated. 2150 Oldfield, 0 Emsley, 2150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 224 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 47 LYS cc_start: 0.9346 (mttt) cc_final: 0.9065 (mmtp) REVERT: B 56 GLU cc_start: 0.8798 (mt-10) cc_final: 0.8491 (pt0) REVERT: B 113 GLN cc_start: 0.9042 (mt0) cc_final: 0.8655 (mt0) REVERT: A 160 MET cc_start: 0.9540 (mtm) cc_final: 0.9305 (mtt) REVERT: C 55 GLU cc_start: 0.9253 (OUTLIER) cc_final: 0.8881 (tm-30) REVERT: C 79 GLU cc_start: 0.9111 (mm-30) cc_final: 0.8874 (pp20) REVERT: C 113 GLN cc_start: 0.9095 (mm110) cc_final: 0.8788 (mm110) REVERT: C 126 MET cc_start: 0.9147 (OUTLIER) cc_final: 0.8529 (tmm) REVERT: C 193 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8521 (mp) REVERT: E 56 GLU cc_start: 0.8681 (OUTLIER) cc_final: 0.8438 (pm20) REVERT: E 113 GLN cc_start: 0.9084 (mt0) cc_final: 0.8660 (mt0) REVERT: G 74 ASP cc_start: 0.9253 (m-30) cc_final: 0.8899 (t0) REVERT: G 285 LYS cc_start: 0.9322 (OUTLIER) cc_final: 0.9079 (ttmm) REVERT: H 56 GLU cc_start: 0.8612 (mt-10) cc_final: 0.8289 (mp0) REVERT: H 113 GLN cc_start: 0.9050 (mt0) cc_final: 0.8720 (mt0) REVERT: H 126 MET cc_start: 0.9152 (mmm) cc_final: 0.8763 (mmm) REVERT: J 39 ASN cc_start: 0.9179 (t0) cc_final: 0.8948 (t0) REVERT: J 120 ARG cc_start: 0.9354 (tmm-80) cc_final: 0.9084 (ptm160) outliers start: 42 outliers final: 11 residues processed: 253 average time/residue: 0.5738 time to fit residues: 160.6480 Evaluate side-chains 217 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 201 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 55 GLU Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 126 MET Chi-restraints excluded: chain C residue 127 ASP Chi-restraints excluded: chain C residue 147 PHE Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain E residue 56 GLU Chi-restraints excluded: chain E residue 127 ASP Chi-restraints excluded: chain G residue 285 LYS Chi-restraints excluded: chain H residue 44 ILE Chi-restraints excluded: chain H residue 131 VAL Chi-restraints excluded: chain J residue 127 ASP Chi-restraints excluded: chain J residue 131 VAL Chi-restraints excluded: chain J residue 141 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 149 optimal weight: 0.9980 chunk 53 optimal weight: 0.7980 chunk 89 optimal weight: 0.7980 chunk 85 optimal weight: 40.0000 chunk 90 optimal weight: 0.8980 chunk 50 optimal weight: 0.6980 chunk 177 optimal weight: 0.6980 chunk 71 optimal weight: 8.9990 chunk 6 optimal weight: 0.6980 chunk 92 optimal weight: 0.7980 chunk 29 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 103 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 = 0.3675 r_free = 0.3675 target = 0.070511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.047918 restraints weight = 64653.683| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 3.50 r_work: 0.2842 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.3023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 16592 Z= 0.127 Angle : 0.570 12.181 22569 Z= 0.294 Chirality : 0.039 0.137 2578 Planarity : 0.004 0.055 2960 Dihedral : 4.053 23.394 2379 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.37 % Allowed : 19.64 % Favored : 78.99 % 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: 1.55 (0.18), residues: 2150 helix: 1.94 (0.13), residues: 1495 sheet: 0.51 (0.45), residues: 115 loop : -1.52 (0.23), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 46 TYR 0.026 0.002 TYR I 126 PHE 0.017 0.001 PHE E 147 TRP 0.010 0.001 TRP H 34 HIS 0.005 0.001 HIS B 84 Details of bonding type rmsd covalent geometry : bond 0.00290 (16592) covalent geometry : angle 0.56957 (22569) hydrogen bonds : bond 0.03351 ( 1204) hydrogen bonds : angle 4.52822 ( 3582) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4300 Ramachandran restraints generated. 2150 Oldfield, 0 Emsley, 2150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4300 Ramachandran restraints generated. 2150 Oldfield, 0 Emsley, 2150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 248 time to evaluate : 0.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 144 MET cc_start: 0.9116 (mtm) cc_final: 0.8892 (mtp) REVERT: F 180 GLN cc_start: 0.9197 (tt0) cc_final: 0.8681 (tm-30) REVERT: B 47 LYS cc_start: 0.9294 (mttt) cc_final: 0.9033 (mmtp) REVERT: B 56 GLU cc_start: 0.8799 (mt-10) cc_final: 0.8325 (pt0) REVERT: B 79 GLU cc_start: 0.9118 (mm-30) cc_final: 0.8853 (pp20) REVERT: B 107 GLN cc_start: 0.9343 (mm-40) cc_final: 0.8935 (tp-100) REVERT: B 113 GLN cc_start: 0.9054 (mt0) cc_final: 0.8630 (mp10) REVERT: A 160 MET cc_start: 0.9560 (mtm) cc_final: 0.9248 (mtt) REVERT: A 180 GLN cc_start: 0.9174 (tt0) cc_final: 0.8756 (tm-30) REVERT: C 126 MET cc_start: 0.9069 (OUTLIER) cc_final: 0.8311 (tmm) REVERT: D 74 ASP cc_start: 0.9027 (m-30) cc_final: 0.8776 (t0) REVERT: D 262 GLN cc_start: 0.8134 (pp30) cc_final: 0.7737 (pp30) REVERT: E 113 GLN cc_start: 0.9025 (mt0) cc_final: 0.8659 (mt0) REVERT: G 74 ASP cc_start: 0.9207 (m-30) cc_final: 0.8797 (t0) REVERT: G 180 GLN cc_start: 0.9224 (tt0) cc_final: 0.8769 (tm-30) REVERT: G 285 LYS cc_start: 0.9262 (OUTLIER) cc_final: 0.8979 (ttmm) REVERT: H 56 GLU cc_start: 0.8637 (mt-10) cc_final: 0.8272 (mp0) REVERT: H 79 GLU cc_start: 0.9270 (mm-30) cc_final: 0.9001 (pp20) REVERT: H 91 GLU cc_start: 0.8238 (mp0) cc_final: 0.7363 (pp20) REVERT: H 107 GLN cc_start: 0.9427 (mm-40) cc_final: 0.8919 (tp-100) REVERT: H 113 GLN cc_start: 0.8995 (mt0) cc_final: 0.8607 (mt0) REVERT: H 126 MET cc_start: 0.9064 (mmm) cc_final: 0.8627 (mmm) REVERT: J 39 ASN cc_start: 0.9162 (t0) cc_final: 0.8925 (t0) REVERT: J 120 ARG cc_start: 0.9343 (tmm-80) cc_final: 0.9078 (ptm160) outliers start: 20 outliers final: 5 residues processed: 260 average time/residue: 0.5635 time to fit residues: 162.8439 Evaluate side-chains 219 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 212 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain C residue 126 MET Chi-restraints excluded: chain C residue 147 PHE Chi-restraints excluded: chain G residue 285 LYS Chi-restraints excluded: chain H residue 131 VAL Chi-restraints excluded: chain J residue 127 ASP Chi-restraints excluded: chain J residue 131 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 196 optimal weight: 3.9990 chunk 217 optimal weight: 20.0000 chunk 90 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 156 optimal weight: 7.9990 chunk 212 optimal weight: 30.0000 chunk 85 optimal weight: 50.0000 chunk 93 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 126 optimal weight: 40.0000 chunk 49 optimal weight: 4.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 31 ASN C 113 GLN ** E 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 166 HIS ** H 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 113 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.068511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.045648 restraints weight = 65966.789| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 3.49 r_work: 0.2782 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.3220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.097 16592 Z= 0.293 Angle : 0.669 12.582 22569 Z= 0.342 Chirality : 0.041 0.145 2578 Planarity : 0.004 0.053 2960 Dihedral : 4.162 26.498 2379 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.98 % Allowed : 20.05 % Favored : 77.96 % 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: 1.45 (0.18), residues: 2150 helix: 1.91 (0.13), residues: 1489 sheet: 0.01 (0.36), residues: 155 loop : -1.66 (0.24), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 120 TYR 0.030 0.002 TYR I 126 PHE 0.018 0.002 PHE E 147 TRP 0.011 0.002 TRP G 235 HIS 0.008 0.001 HIS B 84 Details of bonding type rmsd covalent geometry : bond 0.00661 (16592) covalent geometry : angle 0.66870 (22569) hydrogen bonds : bond 0.03770 ( 1204) hydrogen bonds : angle 4.71328 ( 3582) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4300 Ramachandran restraints generated. 2150 Oldfield, 0 Emsley, 2150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4300 Ramachandran restraints generated. 2150 Oldfield, 0 Emsley, 2150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 221 time to evaluate : 0.546 Fit side-chains revert: symmetry clash REVERT: F 180 GLN cc_start: 0.9202 (tt0) cc_final: 0.8744 (tm-30) REVERT: B 47 LYS cc_start: 0.9352 (mmtt) cc_final: 0.9109 (mmmt) REVERT: B 56 GLU cc_start: 0.8755 (mt-10) cc_final: 0.8324 (pt0) REVERT: B 107 GLN cc_start: 0.9394 (mm-40) cc_final: 0.8986 (tp-100) REVERT: B 113 GLN cc_start: 0.9033 (mt0) cc_final: 0.8637 (mt0) REVERT: A 262 GLN cc_start: 0.8293 (OUTLIER) cc_final: 0.7866 (pp30) REVERT: C 79 GLU cc_start: 0.8835 (pp20) cc_final: 0.8578 (pp20) REVERT: C 83 GLU cc_start: 0.9072 (tm-30) cc_final: 0.8768 (pp20) REVERT: C 126 MET cc_start: 0.9090 (OUTLIER) cc_final: 0.8336 (tmm) REVERT: C 187 CYS cc_start: 0.8830 (t) cc_final: 0.8318 (p) REVERT: D 74 ASP cc_start: 0.9140 (m-30) cc_final: 0.8714 (t0) REVERT: D 180 GLN cc_start: 0.9136 (tt0) cc_final: 0.8841 (tm-30) REVERT: D 262 GLN cc_start: 0.8339 (pp30) cc_final: 0.7990 (pp30) REVERT: E 113 GLN cc_start: 0.9064 (mt0) cc_final: 0.8718 (mt0) REVERT: E 116 MET cc_start: 0.9482 (tpp) cc_final: 0.8885 (mmm) REVERT: G 74 ASP cc_start: 0.9255 (m-30) cc_final: 0.8759 (t0) REVERT: G 180 GLN cc_start: 0.9232 (tt0) cc_final: 0.8784 (tm-30) REVERT: G 285 LYS cc_start: 0.9343 (OUTLIER) cc_final: 0.9124 (ttmm) REVERT: H 47 LYS cc_start: 0.9346 (mmtt) cc_final: 0.9054 (mmtp) REVERT: H 56 GLU cc_start: 0.8654 (mt-10) cc_final: 0.8336 (mp0) REVERT: H 91 GLU cc_start: 0.8246 (mp0) cc_final: 0.7454 (pp20) REVERT: H 107 GLN cc_start: 0.9468 (mm-40) cc_final: 0.9013 (tp-100) REVERT: H 113 GLN cc_start: 0.9008 (mt0) cc_final: 0.8588 (mt0) REVERT: H 126 MET cc_start: 0.9139 (mmm) cc_final: 0.8808 (mmm) REVERT: J 39 ASN cc_start: 0.9146 (t0) cc_final: 0.8917 (t0) REVERT: J 103 GLN cc_start: 0.8989 (pp30) cc_final: 0.8607 (pp30) REVERT: J 113 GLN cc_start: 0.9039 (mm110) cc_final: 0.8695 (mm110) REVERT: J 120 ARG cc_start: 0.9354 (tmm-80) cc_final: 0.9089 (ptm160) outliers start: 29 outliers final: 12 residues processed: 241 average time/residue: 0.5734 time to fit residues: 152.8380 Evaluate side-chains 221 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 206 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain A residue 262 GLN Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 126 MET Chi-restraints excluded: chain C residue 127 ASP Chi-restraints excluded: chain C residue 154 TYR Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 79 GLU Chi-restraints excluded: chain E residue 127 ASP Chi-restraints excluded: chain G residue 170 ILE Chi-restraints excluded: chain G residue 285 LYS Chi-restraints excluded: chain H residue 131 VAL Chi-restraints excluded: chain J residue 127 ASP Chi-restraints excluded: chain J residue 131 VAL Chi-restraints excluded: chain J residue 141 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 11 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 17 optimal weight: 0.6980 chunk 211 optimal weight: 20.0000 chunk 121 optimal weight: 0.3980 chunk 207 optimal weight: 6.9990 chunk 140 optimal weight: 0.6980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 103 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 = 0.3658 r_free = 0.3658 target = 0.069662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.046837 restraints weight = 64751.878| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 3.49 r_work: 0.2819 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.3280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 16592 Z= 0.162 Angle : 0.620 13.324 22569 Z= 0.315 Chirality : 0.039 0.144 2578 Planarity : 0.004 0.054 2960 Dihedral : 4.100 25.073 2379 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.23 % Allowed : 21.22 % Favored : 77.55 % 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: 1.49 (0.18), residues: 2150 helix: 1.92 (0.13), residues: 1489 sheet: 0.38 (0.45), residues: 115 loop : -1.55 (0.23), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 120 TYR 0.032 0.002 TYR I 126 PHE 0.022 0.001 PHE E 147 TRP 0.011 0.001 TRP H 34 HIS 0.007 0.001 HIS B 84 Details of bonding type rmsd covalent geometry : bond 0.00370 (16592) covalent geometry : angle 0.62037 (22569) hydrogen bonds : bond 0.03409 ( 1204) hydrogen bonds : angle 4.54942 ( 3582) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4300 Ramachandran restraints generated. 2150 Oldfield, 0 Emsley, 2150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4300 Ramachandran restraints generated. 2150 Oldfield, 0 Emsley, 2150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 229 time to evaluate : 0.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 144 MET cc_start: 0.9137 (mtm) cc_final: 0.8916 (mtp) REVERT: F 180 GLN cc_start: 0.9199 (tt0) cc_final: 0.8722 (tm-30) REVERT: B 47 LYS cc_start: 0.9307 (mmtt) cc_final: 0.9060 (mmmt) REVERT: B 56 GLU cc_start: 0.8764 (mt-10) cc_final: 0.8303 (pt0) REVERT: B 79 GLU cc_start: 0.9155 (mm-30) cc_final: 0.8842 (pp20) REVERT: B 107 GLN cc_start: 0.9386 (mm-40) cc_final: 0.8954 (tp-100) REVERT: B 113 GLN cc_start: 0.9073 (mt0) cc_final: 0.8707 (mt0) REVERT: C 103 GLN cc_start: 0.9254 (tm-30) cc_final: 0.8738 (tm-30) REVERT: C 107 GLN cc_start: 0.9512 (mm-40) cc_final: 0.9080 (mm-40) REVERT: C 116 MET cc_start: 0.9420 (tpp) cc_final: 0.9140 (tpp) REVERT: C 126 MET cc_start: 0.9094 (OUTLIER) cc_final: 0.8314 (tmm) REVERT: C 187 CYS cc_start: 0.8798 (t) cc_final: 0.8245 (p) REVERT: D 74 ASP cc_start: 0.9069 (m-30) cc_final: 0.8721 (t0) REVERT: D 180 GLN cc_start: 0.9126 (tt0) cc_final: 0.8839 (tm-30) REVERT: D 262 GLN cc_start: 0.8273 (pp30) cc_final: 0.7881 (pp30) REVERT: E 113 GLN cc_start: 0.9016 (mt0) cc_final: 0.8640 (mt0) REVERT: E 116 MET cc_start: 0.9466 (tpp) cc_final: 0.8823 (mmm) REVERT: G 74 ASP cc_start: 0.9221 (m-30) cc_final: 0.8804 (t0) REVERT: G 180 GLN cc_start: 0.9232 (tt0) cc_final: 0.8784 (tm-30) REVERT: G 285 LYS cc_start: 0.9320 (OUTLIER) cc_final: 0.8961 (ttmm) REVERT: H 47 LYS cc_start: 0.9300 (mmtt) cc_final: 0.9000 (mmtp) REVERT: H 56 GLU cc_start: 0.8675 (mt-10) cc_final: 0.8334 (mp0) REVERT: H 79 GLU cc_start: 0.9250 (mm-30) cc_final: 0.8965 (pp20) REVERT: H 91 GLU cc_start: 0.8221 (mp0) cc_final: 0.7408 (pp20) REVERT: H 107 GLN cc_start: 0.9484 (mm-40) cc_final: 0.9011 (tp-100) REVERT: H 113 GLN cc_start: 0.8988 (mt0) cc_final: 0.8564 (mt0) REVERT: H 126 MET cc_start: 0.9078 (mmm) cc_final: 0.8694 (mmm) REVERT: J 39 ASN cc_start: 0.9136 (t0) cc_final: 0.8893 (t0) REVERT: J 103 GLN cc_start: 0.8929 (pp30) cc_final: 0.8635 (pp30) REVERT: J 113 GLN cc_start: 0.9077 (mm110) cc_final: 0.8747 (mm110) REVERT: J 120 ARG cc_start: 0.9341 (tmm-80) cc_final: 0.9067 (ptm160) outliers start: 18 outliers final: 9 residues processed: 242 average time/residue: 0.5931 time to fit residues: 158.5081 Evaluate side-chains 222 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 211 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 126 MET Chi-restraints excluded: chain C residue 127 ASP Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 127 ASP Chi-restraints excluded: chain G residue 285 LYS Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 131 VAL Chi-restraints excluded: chain J residue 127 ASP Chi-restraints excluded: chain J residue 131 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 119 optimal weight: 9.9990 chunk 162 optimal weight: 10.0000 chunk 147 optimal weight: 0.6980 chunk 144 optimal weight: 0.7980 chunk 4 optimal weight: 5.9990 chunk 183 optimal weight: 1.9990 chunk 98 optimal weight: 0.5980 chunk 58 optimal weight: 4.9990 chunk 88 optimal weight: 0.5980 chunk 36 optimal weight: 10.0000 chunk 83 optimal weight: 50.0000 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 103 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 = 0.3701 r_free = 0.3701 target = 0.070988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.047903 restraints weight = 66242.801| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 3.61 r_work: 0.2854 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.3415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16592 Z= 0.137 Angle : 0.632 14.077 22569 Z= 0.320 Chirality : 0.039 0.149 2578 Planarity : 0.004 0.055 2960 Dihedral : 4.017 23.389 2379 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.30 % Allowed : 21.63 % Favored : 77.07 % 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: 1.60 (0.18), residues: 2150 helix: 1.98 (0.13), residues: 1491 sheet: 0.45 (0.45), residues: 115 loop : -1.48 (0.23), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG H 128 TYR 0.035 0.002 TYR I 126 PHE 0.018 0.001 PHE E 147 TRP 0.011 0.001 TRP B 34 HIS 0.006 0.001 HIS B 84 Details of bonding type rmsd covalent geometry : bond 0.00313 (16592) covalent geometry : angle 0.63186 (22569) hydrogen bonds : bond 0.03264 ( 1204) hydrogen bonds : angle 4.43307 ( 3582) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4300 Ramachandran restraints generated. 2150 Oldfield, 0 Emsley, 2150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4300 Ramachandran restraints generated. 2150 Oldfield, 0 Emsley, 2150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 240 time to evaluate : 0.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 180 GLN cc_start: 0.9220 (tt0) cc_final: 0.8729 (tm-30) REVERT: B 47 LYS cc_start: 0.9345 (mmtt) cc_final: 0.9088 (mmtp) REVERT: B 56 GLU cc_start: 0.8845 (mt-10) cc_final: 0.8359 (pt0) REVERT: B 79 GLU cc_start: 0.9180 (mm-30) cc_final: 0.8867 (pp20) REVERT: B 91 GLU cc_start: 0.7928 (mp0) cc_final: 0.7147 (pp20) REVERT: B 107 GLN cc_start: 0.9383 (mm-40) cc_final: 0.8972 (tp-100) REVERT: B 113 GLN cc_start: 0.9031 (mt0) cc_final: 0.8656 (mt0) REVERT: A 262 GLN cc_start: 0.8186 (OUTLIER) cc_final: 0.7798 (pp30) REVERT: C 116 MET cc_start: 0.9348 (tpp) cc_final: 0.8985 (tpp) REVERT: C 126 MET cc_start: 0.9068 (OUTLIER) cc_final: 0.8204 (tmm) REVERT: D 74 ASP cc_start: 0.9122 (m-30) cc_final: 0.8781 (t0) REVERT: D 180 GLN cc_start: 0.9090 (tt0) cc_final: 0.8801 (tm-30) REVERT: D 262 GLN cc_start: 0.8187 (pp30) cc_final: 0.7750 (pp30) REVERT: E 79 GLU cc_start: 0.8702 (pp20) cc_final: 0.8482 (OUTLIER) REVERT: E 83 GLU cc_start: 0.9212 (tm-30) cc_final: 0.8969 (pp20) REVERT: E 90 ARG cc_start: 0.7279 (OUTLIER) cc_final: 0.6433 (ttm-80) REVERT: E 91 GLU cc_start: 0.7714 (mp0) cc_final: 0.6790 (pp20) REVERT: E 113 GLN cc_start: 0.9001 (mt0) cc_final: 0.8600 (mt0) REVERT: E 116 MET cc_start: 0.9389 (tpp) cc_final: 0.8754 (mmm) REVERT: G 74 ASP cc_start: 0.9303 (m-30) cc_final: 0.8794 (t0) REVERT: G 180 GLN cc_start: 0.9222 (tt0) cc_final: 0.8776 (tm-30) REVERT: G 285 LYS cc_start: 0.9169 (OUTLIER) cc_final: 0.8824 (ttmm) REVERT: H 47 LYS cc_start: 0.9319 (mmtt) cc_final: 0.9081 (mmtp) REVERT: H 56 GLU cc_start: 0.8735 (mt-10) cc_final: 0.8383 (mp0) REVERT: H 79 GLU cc_start: 0.9318 (mm-30) cc_final: 0.9087 (pp20) REVERT: H 91 GLU cc_start: 0.8251 (mp0) cc_final: 0.7429 (pp20) REVERT: H 107 GLN cc_start: 0.9481 (mm-40) cc_final: 0.8980 (tp-100) REVERT: H 113 GLN cc_start: 0.8922 (mt0) cc_final: 0.8505 (mt0) REVERT: H 126 MET cc_start: 0.9064 (mmm) cc_final: 0.8623 (mmm) REVERT: I 130 GLN cc_start: 0.9377 (mt0) cc_final: 0.9025 (mt0) REVERT: J 39 ASN cc_start: 0.9099 (t0) cc_final: 0.8857 (t0) REVERT: J 103 GLN cc_start: 0.8973 (pp30) cc_final: 0.8703 (pp30) REVERT: J 113 GLN cc_start: 0.9039 (mm110) cc_final: 0.8771 (mm110) REVERT: J 120 ARG cc_start: 0.9286 (tmm-80) cc_final: 0.9074 (ttp80) outliers start: 19 outliers final: 9 residues processed: 253 average time/residue: 0.5960 time to fit residues: 166.7375 Evaluate side-chains 227 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 215 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain A residue 262 GLN Chi-restraints excluded: chain C residue 126 MET Chi-restraints excluded: chain C residue 127 ASP Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 90 ARG Chi-restraints excluded: chain E residue 127 ASP Chi-restraints excluded: chain G residue 285 LYS Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 131 VAL Chi-restraints excluded: chain J residue 127 ASP Chi-restraints excluded: chain J residue 131 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 208 optimal weight: 10.0000 chunk 154 optimal weight: 8.9990 chunk 63 optimal weight: 4.9990 chunk 76 optimal weight: 10.0000 chunk 56 optimal weight: 1.9990 chunk 143 optimal weight: 3.9990 chunk 125 optimal weight: 7.9990 chunk 149 optimal weight: 4.9990 chunk 47 optimal weight: 0.0980 chunk 11 optimal weight: 2.9990 chunk 112 optimal weight: 0.8980 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 103 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 = 0.3681 r_free = 0.3681 target = 0.070171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.046676 restraints weight = 66540.113| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 3.61 r_work: 0.2814 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.3506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 16592 Z= 0.203 Angle : 0.656 14.567 22569 Z= 0.334 Chirality : 0.040 0.137 2578 Planarity : 0.004 0.054 2960 Dihedral : 4.099 24.813 2379 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.44 % Allowed : 22.04 % Favored : 76.52 % 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: 1.56 (0.18), residues: 2150 helix: 1.96 (0.13), residues: 1489 sheet: 0.49 (0.46), residues: 115 loop : -1.50 (0.23), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG H 128 TYR 0.034 0.002 TYR I 126 PHE 0.017 0.001 PHE E 147 TRP 0.011 0.002 TRP B 34 HIS 0.007 0.001 HIS B 84 Details of bonding type rmsd covalent geometry : bond 0.00466 (16592) covalent geometry : angle 0.65631 (22569) hydrogen bonds : bond 0.03424 ( 1204) hydrogen bonds : angle 4.51121 ( 3582) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4300 Ramachandran restraints generated. 2150 Oldfield, 0 Emsley, 2150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4300 Ramachandran restraints generated. 2150 Oldfield, 0 Emsley, 2150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 220 time to evaluate : 0.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 180 GLN cc_start: 0.9213 (tt0) cc_final: 0.8733 (tm-30) REVERT: B 47 LYS cc_start: 0.9391 (mmtt) cc_final: 0.9165 (mmtp) REVERT: B 56 GLU cc_start: 0.8828 (mt-10) cc_final: 0.8363 (pm20) REVERT: B 91 GLU cc_start: 0.7905 (mp0) cc_final: 0.7054 (pp20) REVERT: B 107 GLN cc_start: 0.9401 (mm-40) cc_final: 0.8993 (tp-100) REVERT: B 113 GLN cc_start: 0.8984 (mt0) cc_final: 0.8583 (mt0) REVERT: A 144 MET cc_start: 0.8936 (mtp) cc_final: 0.8709 (mtm) REVERT: A 262 GLN cc_start: 0.8183 (OUTLIER) cc_final: 0.7648 (pp30) REVERT: C 83 GLU cc_start: 0.8988 (tm-30) cc_final: 0.8771 (pp20) REVERT: C 113 GLN cc_start: 0.9042 (mm110) cc_final: 0.8770 (mm110) REVERT: C 116 MET cc_start: 0.9375 (tpp) cc_final: 0.8885 (tpp) REVERT: C 126 MET cc_start: 0.9052 (OUTLIER) cc_final: 0.8175 (tmm) REVERT: C 148 ARG cc_start: 0.8668 (ttp80) cc_final: 0.8465 (tmm-80) REVERT: D 74 ASP cc_start: 0.9223 (m-30) cc_final: 0.8773 (t0) REVERT: D 180 GLN cc_start: 0.9095 (tt0) cc_final: 0.8791 (tm-30) REVERT: D 262 GLN cc_start: 0.8256 (pp30) cc_final: 0.7820 (pp30) REVERT: E 113 GLN cc_start: 0.8965 (mt0) cc_final: 0.8601 (mt0) REVERT: G 180 GLN cc_start: 0.9220 (tt0) cc_final: 0.8851 (tm-30) REVERT: G 285 LYS cc_start: 0.9233 (OUTLIER) cc_final: 0.8845 (ttmm) REVERT: H 47 LYS cc_start: 0.9304 (mmtt) cc_final: 0.9020 (mmtp) REVERT: H 56 GLU cc_start: 0.8731 (mt-10) cc_final: 0.8381 (mp0) REVERT: H 79 GLU cc_start: 0.9333 (mm-30) cc_final: 0.9112 (pp20) REVERT: H 91 GLU cc_start: 0.8256 (mp0) cc_final: 0.7439 (pp20) REVERT: H 107 GLN cc_start: 0.9485 (mm-40) cc_final: 0.8975 (tp-100) REVERT: H 113 GLN cc_start: 0.8934 (mt0) cc_final: 0.8521 (mt0) REVERT: H 126 MET cc_start: 0.9075 (mmm) cc_final: 0.8787 (mmm) REVERT: I 74 ASP cc_start: 0.9292 (m-30) cc_final: 0.8902 (t0) REVERT: I 130 GLN cc_start: 0.9420 (mt0) cc_final: 0.9157 (mt0) REVERT: J 39 ASN cc_start: 0.9132 (t0) cc_final: 0.8900 (t0) REVERT: J 56 GLU cc_start: 0.9179 (tt0) cc_final: 0.8823 (mm-30) REVERT: J 103 GLN cc_start: 0.8968 (pp30) cc_final: 0.8667 (pp30) REVERT: J 113 GLN cc_start: 0.9028 (mm110) cc_final: 0.8714 (mm110) REVERT: J 120 ARG cc_start: 0.9323 (tmm-80) cc_final: 0.9033 (ptm160) outliers start: 21 outliers final: 13 residues processed: 234 average time/residue: 0.6163 time to fit residues: 158.9230 Evaluate side-chains 230 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 214 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 124 MET Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain A residue 262 GLN Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 126 MET Chi-restraints excluded: chain C residue 127 ASP Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 79 GLU Chi-restraints excluded: chain E residue 127 ASP Chi-restraints excluded: chain G residue 285 LYS Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 44 ILE Chi-restraints excluded: chain H residue 131 VAL Chi-restraints excluded: chain J residue 127 ASP Chi-restraints excluded: chain J residue 131 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 36 optimal weight: 20.0000 chunk 17 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 109 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 98 optimal weight: 0.7980 chunk 201 optimal weight: 5.9990 chunk 169 optimal weight: 30.0000 chunk 85 optimal weight: 50.0000 chunk 156 optimal weight: 1.9990 chunk 190 optimal weight: 0.8980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 103 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 = 0.3697 r_free = 0.3697 target = 0.070924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.047425 restraints weight = 66149.645| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 3.64 r_work: 0.2838 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.3551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 16592 Z= 0.152 Angle : 0.664 14.650 22569 Z= 0.337 Chirality : 0.039 0.153 2578 Planarity : 0.004 0.054 2960 Dihedral : 4.064 24.066 2379 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.23 % Allowed : 22.66 % Favored : 76.11 % 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: 1.56 (0.18), residues: 2150 helix: 1.93 (0.13), residues: 1495 sheet: 0.47 (0.45), residues: 115 loop : -1.46 (0.23), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG H 128 TYR 0.034 0.002 TYR I 126 PHE 0.017 0.001 PHE H 147 TRP 0.011 0.001 TRP B 34 HIS 0.005 0.001 HIS B 84 Details of bonding type rmsd covalent geometry : bond 0.00355 (16592) covalent geometry : angle 0.66421 (22569) hydrogen bonds : bond 0.03307 ( 1204) hydrogen bonds : angle 4.45922 ( 3582) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4300 Ramachandran restraints generated. 2150 Oldfield, 0 Emsley, 2150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4300 Ramachandran restraints generated. 2150 Oldfield, 0 Emsley, 2150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 225 time to evaluate : 0.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 180 GLN cc_start: 0.9205 (tt0) cc_final: 0.8726 (tm-30) REVERT: B 47 LYS cc_start: 0.9383 (mmtt) cc_final: 0.9149 (mmtp) REVERT: B 56 GLU cc_start: 0.8832 (mt-10) cc_final: 0.8384 (pt0) REVERT: B 91 GLU cc_start: 0.7885 (mp0) cc_final: 0.7035 (pp20) REVERT: B 107 GLN cc_start: 0.9395 (mm-40) cc_final: 0.9004 (tp-100) REVERT: B 113 GLN cc_start: 0.8996 (mt0) cc_final: 0.8594 (mt0) REVERT: A 144 MET cc_start: 0.8907 (mtp) cc_final: 0.8676 (mtm) REVERT: A 262 GLN cc_start: 0.8187 (OUTLIER) cc_final: 0.7794 (pp30) REVERT: C 83 GLU cc_start: 0.8995 (tm-30) cc_final: 0.8742 (pp20) REVERT: C 103 GLN cc_start: 0.9227 (tm-30) cc_final: 0.8754 (tm-30) REVERT: C 107 GLN cc_start: 0.9490 (mm-40) cc_final: 0.9088 (mm110) REVERT: C 113 GLN cc_start: 0.9073 (mm110) cc_final: 0.8775 (mm110) REVERT: C 116 MET cc_start: 0.9352 (tpp) cc_final: 0.8979 (tpp) REVERT: C 120 ARG cc_start: 0.9283 (ttp80) cc_final: 0.9017 (ttt-90) REVERT: C 126 MET cc_start: 0.9026 (OUTLIER) cc_final: 0.8140 (tmm) REVERT: D 74 ASP cc_start: 0.9155 (m-30) cc_final: 0.8726 (t0) REVERT: D 180 GLN cc_start: 0.9105 (tt0) cc_final: 0.8795 (tm-30) REVERT: D 262 GLN cc_start: 0.8220 (pp30) cc_final: 0.7840 (pp30) REVERT: E 79 GLU cc_start: 0.8700 (pp20) cc_final: 0.8454 (OUTLIER) REVERT: E 83 GLU cc_start: 0.9213 (tm-30) cc_final: 0.8964 (pp20) REVERT: E 91 GLU cc_start: 0.7754 (mp0) cc_final: 0.6735 (pp20) REVERT: E 113 GLN cc_start: 0.8995 (mt0) cc_final: 0.8601 (mt0) REVERT: E 116 MET cc_start: 0.9366 (mmm) cc_final: 0.8603 (mmm) REVERT: G 144 MET cc_start: 0.8865 (mtm) cc_final: 0.8544 (mtp) REVERT: G 180 GLN cc_start: 0.9232 (tt0) cc_final: 0.8805 (tm-30) REVERT: G 285 LYS cc_start: 0.9216 (OUTLIER) cc_final: 0.8867 (ttmm) REVERT: H 47 LYS cc_start: 0.9301 (mmtt) cc_final: 0.9060 (mmtp) REVERT: H 56 GLU cc_start: 0.8745 (mt-10) cc_final: 0.8379 (mp0) REVERT: H 79 GLU cc_start: 0.9316 (mm-30) cc_final: 0.9073 (pp20) REVERT: H 91 GLU cc_start: 0.8296 (mp0) cc_final: 0.7532 (pp20) REVERT: H 107 GLN cc_start: 0.9480 (mm-40) cc_final: 0.8972 (tp-100) REVERT: H 113 GLN cc_start: 0.8936 (mt0) cc_final: 0.8518 (mt0) REVERT: H 126 MET cc_start: 0.9051 (mmm) cc_final: 0.8799 (mmm) REVERT: I 130 GLN cc_start: 0.9404 (mt0) cc_final: 0.9052 (mt0) REVERT: J 39 ASN cc_start: 0.9117 (t0) cc_final: 0.8894 (t0) REVERT: J 56 GLU cc_start: 0.9180 (tt0) cc_final: 0.8807 (mm-30) REVERT: J 83 GLU cc_start: 0.9355 (tm-30) cc_final: 0.8953 (pp20) REVERT: J 103 GLN cc_start: 0.8952 (pp30) cc_final: 0.8665 (pp30) REVERT: J 113 GLN cc_start: 0.9021 (mm110) cc_final: 0.8726 (mm110) REVERT: J 120 ARG cc_start: 0.9304 (tmm-80) cc_final: 0.9048 (ptm160) outliers start: 18 outliers final: 11 residues processed: 237 average time/residue: 0.6124 time to fit residues: 159.8893 Evaluate side-chains 226 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 213 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain A residue 262 GLN Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 126 MET Chi-restraints excluded: chain C residue 127 ASP Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 127 ASP Chi-restraints excluded: chain G residue 285 LYS Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 131 VAL Chi-restraints excluded: chain J residue 127 ASP Chi-restraints excluded: chain J residue 131 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 6 optimal weight: 0.5980 chunk 36 optimal weight: 20.0000 chunk 108 optimal weight: 0.9990 chunk 176 optimal weight: 0.0870 chunk 131 optimal weight: 40.0000 chunk 155 optimal weight: 2.9990 chunk 69 optimal weight: 8.9990 chunk 39 optimal weight: 50.0000 chunk 185 optimal weight: 1.9990 chunk 211 optimal weight: 5.9990 chunk 189 optimal weight: 1.9990 overall best weight: 1.1364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 69 HIS ** H 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 103 GLN ** 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 = 0.3699 r_free = 0.3699 target = 0.070927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.047814 restraints weight = 65750.358| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 3.61 r_work: 0.2848 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.3668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 16592 Z= 0.151 Angle : 0.663 14.746 22569 Z= 0.335 Chirality : 0.040 0.211 2578 Planarity : 0.004 0.054 2960 Dihedral : 4.056 24.680 2379 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.03 % Allowed : 22.79 % Favored : 76.18 % 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: 1.55 (0.18), residues: 2150 helix: 1.92 (0.14), residues: 1489 sheet: 0.40 (0.45), residues: 115 loop : -1.41 (0.24), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG H 128 TYR 0.034 0.002 TYR I 126 PHE 0.014 0.001 PHE E 147 TRP 0.008 0.001 TRP H 34 HIS 0.005 0.001 HIS B 84 Details of bonding type rmsd covalent geometry : bond 0.00354 (16592) covalent geometry : angle 0.66272 (22569) hydrogen bonds : bond 0.03263 ( 1204) hydrogen bonds : angle 4.43489 ( 3582) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5961.84 seconds wall clock time: 101 minutes 49.31 seconds (6109.31 seconds total)