Starting phenix.real_space_refine on Thu May 22 10:37:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8i79_35212/05_2025/8i79_35212.cif Found real_map, /net/cci-nas-00/data/ceres_data/8i79_35212/05_2025/8i79_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8i79_35212/05_2025/8i79_35212.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8i79_35212/05_2025/8i79_35212.map" model { file = "/net/cci-nas-00/data/ceres_data/8i79_35212/05_2025/8i79_35212.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8i79_35212/05_2025/8i79_35212.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 3, 'ASP:plan': 4, 'PHE:plan': 5, 'GLU:plan': 19, 'ARG:plan': 9} 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: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 3, 'PHE:plan': 5, 'GLU:plan': 18, 'ARG:plan': 10} 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: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 3, 'ASP:plan': 4, 'PHE:plan': 5, 'GLU:plan': 19, 'ARG:plan': 9} 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: {'GLN:plan1': 4, 'ASP:plan': 5, 'TYR:plan': 2, 'ASN:plan1': 2, 'HIS:plan': 2, 'PHE:plan': 5, 'GLU:plan': 18, 'ARG:plan': 10} 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: {'GLN:plan1': 5, 'ASP:plan': 7, 'TYR:plan': 1, 'ASN:plan1': 8, 'HIS:plan': 2, 'PHE:plan': 4, 'GLU:plan': 21, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 250 Time building chain proxies: 9.78, per 1000 atoms: 0.60 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: 4.11 Conformation dependent library (CDL) restraints added in 2.2 seconds 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: 1.50 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: 4.72 Time building geometry restraints manager: 4.74 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: 1.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.130 Construct map_model_manager: 0.010 Extract box with map and model: 0.620 Check model and map are aligned: 0.120 Set scattering table: 0.130 Process input model: 35.980 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.070 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:11.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.690 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.18), 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 TRP 0.069 0.002 TRP H 34 HIS 0.004 0.001 HIS C 160 PHE 0.017 0.001 PHE D 185 TYR 0.017 0.002 TYR B 74 ARG 0.008 0.001 ARG C 148 Details of bonding type rmsd hydrogen bonds : bond 0.13572 ( 1204) hydrogen bonds : angle 5.89605 ( 3582) covalent geometry : bond 0.00323 (16592) covalent geometry : angle 0.56866 (22569) *********************** 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 : 1.821 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: 1.3317 time to fit residues: 581.4247 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 : 1.903 ------------------------------------------------------------------------------- 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 184 optimal weight: 2.9990 chunk 165 optimal weight: 8.9990 chunk 91 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 111 optimal weight: 4.9990 chunk 88 optimal weight: 3.9990 chunk 170 optimal weight: 7.9990 chunk 66 optimal weight: 3.9990 chunk 103 optimal weight: 4.9990 chunk 127 optimal weight: 50.0000 chunk 197 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.069052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.046386 restraints weight = 66139.665| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 3.48 r_work: 0.2791 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.102 16592 Z= 0.327 Angle : 0.681 9.167 22569 Z= 0.359 Chirality : 0.043 0.143 2578 Planarity : 0.004 0.057 2960 Dihedral : 4.307 33.379 2381 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.17), residues: 2150 helix: 1.86 (0.13), residues: 1477 sheet: 0.70 (0.46), residues: 115 loop : -1.71 (0.21), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP E 34 HIS 0.009 0.001 HIS B 84 PHE 0.017 0.002 PHE D 81 TYR 0.022 0.002 TYR B 154 ARG 0.010 0.001 ARG B 78 Details of bonding type rmsd hydrogen bonds : bond 0.04349 ( 1204) hydrogen bonds : angle 5.03695 ( 3582) covalent geometry : bond 0.00733 (16592) covalent geometry : angle 0.68120 (22569) *********************** 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 282 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 248 time to evaluate : 1.865 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 38 LYS cc_start: 0.8704 (tmmt) cc_final: 0.8487 (tmmt) REVERT: B 56 GLU cc_start: 0.8806 (mt-10) cc_final: 0.8574 (pt0) REVERT: B 113 GLN cc_start: 0.9064 (mt0) cc_final: 0.8657 (mp10) REVERT: C 79 GLU cc_start: 0.9078 (mm-30) cc_final: 0.8827 (pp20) REVERT: C 126 MET cc_start: 0.9096 (OUTLIER) cc_final: 0.8578 (tmm) REVERT: C 204 ASP cc_start: 0.6936 (m-30) cc_final: 0.6409 (m-30) REVERT: E 56 GLU cc_start: 0.8653 (pt0) cc_final: 0.8322 (pm20) REVERT: E 113 GLN cc_start: 0.9057 (mt0) cc_final: 0.8644 (mt0) REVERT: H 56 GLU cc_start: 0.8546 (mt-10) cc_final: 0.8290 (mp0) REVERT: H 107 GLN cc_start: 0.9439 (tp40) cc_final: 0.9071 (mm110) REVERT: H 113 GLN cc_start: 0.9065 (mt0) cc_final: 0.8706 (mt0) REVERT: I 285 LYS cc_start: 0.9371 (OUTLIER) cc_final: 0.9137 (tttm) REVERT: J 39 ASN cc_start: 0.9116 (t0) cc_final: 0.8897 (t0) REVERT: J 113 GLN cc_start: 0.8829 (mt0) cc_final: 0.8418 (mp10) REVERT: J 120 ARG cc_start: 0.9329 (tmm-80) cc_final: 0.9083 (ptm160) outliers start: 34 outliers final: 9 residues processed: 268 average time/residue: 1.2527 time to fit residues: 371.6246 Evaluate side-chains 220 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 209 time to evaluate : 1.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 SER 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 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 124 MET Chi-restraints excluded: chain J residue 127 ASP Chi-restraints excluded: chain J residue 154 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 51 optimal weight: 6.9990 chunk 36 optimal weight: 20.0000 chunk 119 optimal weight: 3.9990 chunk 57 optimal weight: 0.7980 chunk 195 optimal weight: 1.9990 chunk 149 optimal weight: 0.7980 chunk 43 optimal weight: 50.0000 chunk 28 optimal weight: 7.9990 chunk 157 optimal weight: 0.9990 chunk 50 optimal weight: 0.8980 chunk 181 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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** ** 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.070819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.048128 restraints weight = 64701.395| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 3.51 r_work: 0.2850 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.2584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16592 Z= 0.131 Angle : 0.554 11.409 22569 Z= 0.291 Chirality : 0.039 0.131 2578 Planarity : 0.004 0.057 2960 Dihedral : 4.071 21.608 2379 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.92 % Allowed : 16.08 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.18), residues: 2150 helix: 1.91 (0.13), residues: 1487 sheet: 0.58 (0.46), residues: 115 loop : -1.63 (0.22), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 34 HIS 0.005 0.001 HIS B 84 PHE 0.014 0.001 PHE E 147 TYR 0.020 0.002 TYR B 74 ARG 0.005 0.000 ARG C 120 Details of bonding type rmsd hydrogen bonds : bond 0.03577 ( 1204) hydrogen bonds : angle 4.68491 ( 3582) covalent geometry : bond 0.00290 (16592) covalent geometry : angle 0.55363 (22569) *********************** 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 287 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 259 time to evaluate : 2.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 38 LYS cc_start: 0.8687 (tmmt) cc_final: 0.8058 (tmmt) REVERT: B 56 GLU cc_start: 0.8783 (mt-10) cc_final: 0.8450 (pt0) REVERT: B 107 GLN cc_start: 0.9400 (mm-40) cc_final: 0.8948 (tp-100) REVERT: B 113 GLN cc_start: 0.9069 (mt0) cc_final: 0.8666 (mp10) REVERT: A 160 MET cc_start: 0.9558 (mtm) cc_final: 0.9259 (mtt) REVERT: A 262 GLN cc_start: 0.8118 (tm-30) cc_final: 0.7757 (pp30) REVERT: C 35 ASP cc_start: 0.9384 (t0) cc_final: 0.9091 (m-30) REVERT: C 55 GLU cc_start: 0.9177 (OUTLIER) cc_final: 0.8734 (tm-30) REVERT: C 113 GLN cc_start: 0.9068 (mm110) cc_final: 0.8794 (mm110) REVERT: C 126 MET cc_start: 0.9154 (OUTLIER) cc_final: 0.8564 (tmm) REVERT: C 200 VAL cc_start: 0.8540 (OUTLIER) cc_final: 0.8016 (p) REVERT: C 204 ASP cc_start: 0.6812 (m-30) cc_final: 0.6126 (m-30) REVERT: E 79 GLU cc_start: 0.9256 (mm-30) cc_final: 0.9055 (pp20) REVERT: E 113 GLN cc_start: 0.9023 (mt0) cc_final: 0.8627 (mt0) REVERT: G 74 ASP cc_start: 0.9226 (m-30) cc_final: 0.8901 (t0) REVERT: H 56 GLU cc_start: 0.8533 (mt-10) cc_final: 0.8245 (mp0) REVERT: H 91 GLU cc_start: 0.8146 (mp0) cc_final: 0.7052 (pp20) REVERT: H 113 GLN cc_start: 0.9023 (mt0) cc_final: 0.8662 (mt0) REVERT: H 126 MET cc_start: 0.9057 (mmm) cc_final: 0.8554 (mmm) REVERT: H 149 ASP cc_start: 0.8966 (m-30) cc_final: 0.8673 (m-30) REVERT: J 39 ASN cc_start: 0.9102 (t0) cc_final: 0.8873 (t0) REVERT: J 120 ARG cc_start: 0.9341 (tmm-80) cc_final: 0.9070 (ptm160) REVERT: J 150 GLN cc_start: 0.6283 (OUTLIER) cc_final: 0.5672 (tm-30) outliers start: 28 outliers final: 6 residues processed: 273 average time/residue: 1.1907 time to fit residues: 361.1718 Evaluate side-chains 227 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 217 time to evaluate : 1.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain C residue 55 GLU Chi-restraints excluded: chain C residue 126 MET 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 J residue 127 ASP Chi-restraints excluded: chain J residue 131 VAL Chi-restraints excluded: chain J residue 150 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 24 optimal weight: 6.9990 chunk 154 optimal weight: 8.9990 chunk 197 optimal weight: 7.9990 chunk 166 optimal weight: 30.0000 chunk 50 optimal weight: 3.9990 chunk 35 optimal weight: 7.9990 chunk 122 optimal weight: 30.0000 chunk 105 optimal weight: 3.9990 chunk 164 optimal weight: 6.9990 chunk 157 optimal weight: 0.9980 chunk 65 optimal weight: 4.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 166 HIS ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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** ** H 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 113 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.068156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.045266 restraints weight = 65850.678| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 3.48 r_work: 0.2763 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.2947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.121 16592 Z= 0.376 Angle : 0.696 11.790 22569 Z= 0.359 Chirality : 0.043 0.152 2578 Planarity : 0.005 0.102 2960 Dihedral : 4.234 26.356 2379 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.81 % Allowed : 18.00 % Favored : 79.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.18), residues: 2150 helix: 1.84 (0.13), residues: 1488 sheet: 0.03 (0.37), residues: 155 loop : -1.71 (0.23), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP G 288 HIS 0.009 0.001 HIS B 84 PHE 0.017 0.002 PHE D 81 TYR 0.028 0.002 TYR I 126 ARG 0.007 0.001 ARG B 120 Details of bonding type rmsd hydrogen bonds : bond 0.04104 ( 1204) hydrogen bonds : angle 4.92955 ( 3582) covalent geometry : bond 0.00841 (16592) covalent geometry : angle 0.69649 (22569) *********************** 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 261 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 220 time to evaluate : 1.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 47 LYS cc_start: 0.9339 (mmtt) cc_final: 0.9048 (mmmt) REVERT: B 56 GLU cc_start: 0.8773 (mt-10) cc_final: 0.8475 (pt0) REVERT: B 107 GLN cc_start: 0.9427 (mm-40) cc_final: 0.8995 (tp-100) REVERT: B 113 GLN cc_start: 0.9059 (mt0) cc_final: 0.8658 (mt0) REVERT: A 160 MET cc_start: 0.9538 (mtm) cc_final: 0.9235 (mtt) REVERT: C 55 GLU cc_start: 0.9251 (OUTLIER) cc_final: 0.8877 (tm-30) REVERT: C 113 GLN cc_start: 0.9101 (mm110) cc_final: 0.8776 (mm110) REVERT: C 126 MET cc_start: 0.9116 (mmm) cc_final: 0.8465 (tmm) REVERT: E 56 GLU cc_start: 0.8647 (OUTLIER) cc_final: 0.8405 (pm20) REVERT: E 113 GLN cc_start: 0.9087 (mt0) cc_final: 0.8660 (mt0) REVERT: G 74 ASP cc_start: 0.9262 (m-30) cc_final: 0.8896 (t0) REVERT: H 56 GLU cc_start: 0.8586 (mt-10) cc_final: 0.8274 (mp0) REVERT: H 113 GLN cc_start: 0.9057 (mt0) cc_final: 0.8715 (mt0) REVERT: H 126 MET cc_start: 0.9154 (mmm) cc_final: 0.8932 (mmm) REVERT: J 39 ASN cc_start: 0.9153 (t0) cc_final: 0.8927 (t0) REVERT: J 56 GLU cc_start: 0.9135 (mm-30) cc_final: 0.8418 (tp30) REVERT: J 113 GLN cc_start: 0.9047 (mm110) cc_final: 0.8704 (mm110) outliers start: 41 outliers final: 13 residues processed: 249 average time/residue: 1.2341 time to fit residues: 340.4629 Evaluate side-chains 214 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 199 time to evaluate : 2.040 ------------------------------------------------------------------------------- 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 127 ASP Chi-restraints excluded: chain C residue 154 TYR Chi-restraints excluded: chain E residue 56 GLU Chi-restraints excluded: chain E residue 127 ASP Chi-restraints excluded: chain H residue 44 ILE Chi-restraints excluded: chain H residue 131 VAL Chi-restraints excluded: chain H residue 150 GLN Chi-restraints excluded: chain H residue 154 TYR 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 79 optimal weight: 3.9990 chunk 168 optimal weight: 8.9990 chunk 109 optimal weight: 0.9980 chunk 113 optimal weight: 7.9990 chunk 50 optimal weight: 0.7980 chunk 153 optimal weight: 2.9990 chunk 119 optimal weight: 8.9990 chunk 196 optimal weight: 0.9980 chunk 157 optimal weight: 2.9990 chunk 40 optimal weight: 50.0000 chunk 76 optimal weight: 5.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- 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** ** E 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 166 HIS ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.069556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.046930 restraints weight = 65627.889| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 3.50 r_work: 0.2813 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.3045 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= 0.180 Angle : 0.596 11.083 22569 Z= 0.308 Chirality : 0.040 0.141 2578 Planarity : 0.004 0.065 2960 Dihedral : 4.124 24.847 2379 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.64 % Allowed : 19.64 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.18), residues: 2150 helix: 1.90 (0.13), residues: 1490 sheet: 0.38 (0.45), residues: 115 loop : -1.55 (0.23), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 34 HIS 0.006 0.001 HIS B 84 PHE 0.018 0.001 PHE H 147 TYR 0.032 0.002 TYR H 154 ARG 0.008 0.001 ARG B 46 Details of bonding type rmsd hydrogen bonds : bond 0.03548 ( 1204) hydrogen bonds : angle 4.64863 ( 3582) covalent geometry : bond 0.00407 (16592) covalent geometry : angle 0.59557 (22569) *********************** 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 259 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 235 time to evaluate : 1.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 144 MET cc_start: 0.9144 (mtm) cc_final: 0.8930 (mtp) REVERT: F 180 GLN cc_start: 0.9233 (tt0) cc_final: 0.8742 (tm-30) REVERT: B 47 LYS cc_start: 0.9332 (mmtt) cc_final: 0.9051 (mmmt) REVERT: B 56 GLU cc_start: 0.8786 (mt-10) cc_final: 0.8315 (pt0) REVERT: B 107 GLN cc_start: 0.9410 (mm-40) cc_final: 0.8956 (tp-100) REVERT: B 113 GLN cc_start: 0.9033 (mt0) cc_final: 0.8648 (mt0) REVERT: A 160 MET cc_start: 0.9561 (mtm) cc_final: 0.9336 (mtt) REVERT: A 262 GLN cc_start: 0.8257 (tm-30) cc_final: 0.7976 (pp30) REVERT: C 113 GLN cc_start: 0.9089 (mm110) cc_final: 0.8807 (mm110) REVERT: C 116 MET cc_start: 0.9454 (tpp) cc_final: 0.8800 (mmm) REVERT: C 126 MET cc_start: 0.9104 (OUTLIER) cc_final: 0.8422 (tmm) REVERT: D 74 ASP cc_start: 0.9021 (m-30) cc_final: 0.8648 (t0) REVERT: D 262 GLN cc_start: 0.8252 (pp30) cc_final: 0.7805 (pp30) REVERT: E 79 GLU cc_start: 0.9213 (mm-30) cc_final: 0.8991 (pp20) REVERT: E 90 ARG cc_start: 0.7548 (OUTLIER) cc_final: 0.7063 (ttm-80) REVERT: E 113 GLN cc_start: 0.9033 (mt0) cc_final: 0.8688 (mt0) REVERT: G 74 ASP cc_start: 0.9247 (m-30) cc_final: 0.8837 (t0) REVERT: G 180 GLN cc_start: 0.9233 (tt0) cc_final: 0.8771 (tm-30) REVERT: H 56 GLU cc_start: 0.8647 (mt-10) cc_final: 0.8282 (mp0) REVERT: H 90 ARG cc_start: 0.8342 (ttt90) cc_final: 0.7961 (tpp80) REVERT: H 91 GLU cc_start: 0.8211 (mp0) cc_final: 0.7264 (pp20) REVERT: H 107 GLN cc_start: 0.9453 (mm-40) cc_final: 0.8936 (tp-100) REVERT: H 113 GLN cc_start: 0.9028 (mt0) cc_final: 0.8711 (mt0) REVERT: H 126 MET cc_start: 0.9119 (mmm) cc_final: 0.8635 (mmm) REVERT: J 39 ASN cc_start: 0.9172 (t0) cc_final: 0.8941 (t0) REVERT: J 113 GLN cc_start: 0.9077 (mm110) cc_final: 0.8795 (mm110) REVERT: J 120 ARG cc_start: 0.9339 (tmm-80) cc_final: 0.9098 (ptm160) outliers start: 24 outliers final: 11 residues processed: 249 average time/residue: 1.1958 time to fit residues: 330.7189 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 : 1.872 ------------------------------------------------------------------------------- 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 C residue 154 TYR Chi-restraints excluded: chain E residue 90 ARG Chi-restraints excluded: chain E residue 127 ASP Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 131 VAL Chi-restraints excluded: chain H residue 150 GLN Chi-restraints excluded: chain H residue 154 TYR 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 135 optimal weight: 3.9990 chunk 83 optimal weight: 50.0000 chunk 161 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 111 optimal weight: 5.9990 chunk 95 optimal weight: 0.5980 chunk 113 optimal weight: 9.9990 chunk 46 optimal weight: 4.9990 chunk 168 optimal weight: 20.0000 chunk 5 optimal weight: 3.9990 chunk 97 optimal weight: 0.7980 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 31 ASN ** E 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 166 HIS ** H 69 HIS ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.068701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.046113 restraints weight = 65608.068| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 3.47 r_work: 0.2790 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.3199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 16592 Z= 0.250 Angle : 0.631 12.631 22569 Z= 0.325 Chirality : 0.041 0.156 2578 Planarity : 0.004 0.054 2960 Dihedral : 4.133 26.110 2379 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.44 % Allowed : 20.47 % Favored : 78.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.18), residues: 2150 helix: 1.88 (0.13), residues: 1487 sheet: 0.36 (0.45), residues: 115 loop : -1.62 (0.23), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 34 HIS 0.007 0.001 HIS B 84 PHE 0.015 0.001 PHE E 147 TYR 0.031 0.002 TYR I 126 ARG 0.006 0.000 ARG C 120 Details of bonding type rmsd hydrogen bonds : bond 0.03679 ( 1204) hydrogen bonds : angle 4.69788 ( 3582) covalent geometry : bond 0.00564 (16592) covalent geometry : angle 0.63121 (22569) *********************** 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 246 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 225 time to evaluate : 1.869 Fit side-chains REVERT: F 144 MET cc_start: 0.9121 (mtm) cc_final: 0.8900 (mtp) REVERT: F 180 GLN cc_start: 0.9210 (tt0) cc_final: 0.8761 (tm-30) REVERT: B 47 LYS cc_start: 0.9348 (mmtt) cc_final: 0.9105 (mmmt) REVERT: B 56 GLU cc_start: 0.8755 (mt-10) cc_final: 0.8297 (pt0) REVERT: B 107 GLN cc_start: 0.9422 (mm-40) cc_final: 0.8978 (tp-100) REVERT: B 113 GLN cc_start: 0.9044 (mt0) cc_final: 0.8611 (mt0) REVERT: A 144 MET cc_start: 0.9076 (mtp) cc_final: 0.8863 (mtm) REVERT: A 262 GLN cc_start: 0.8293 (tm-30) cc_final: 0.7927 (pp30) REVERT: C 83 GLU cc_start: 0.9043 (tm-30) cc_final: 0.8777 (pp20) REVERT: C 113 GLN cc_start: 0.9100 (mm110) cc_final: 0.8822 (mm110) REVERT: C 126 MET cc_start: 0.9096 (OUTLIER) cc_final: 0.8407 (tmm) REVERT: C 187 CYS cc_start: 0.8880 (t) cc_final: 0.8394 (p) REVERT: D 74 ASP cc_start: 0.9139 (m-30) cc_final: 0.8709 (t0) REVERT: D 140 GLN cc_start: 0.9353 (OUTLIER) cc_final: 0.8617 (mp10) REVERT: D 180 GLN cc_start: 0.9128 (tt0) cc_final: 0.8840 (tm-30) REVERT: D 262 GLN cc_start: 0.8304 (pp30) cc_final: 0.7941 (pp30) REVERT: E 56 GLU cc_start: 0.8689 (pt0) cc_final: 0.8457 (pm20) REVERT: E 79 GLU cc_start: 0.9232 (mm-30) cc_final: 0.9018 (pp20) REVERT: E 90 ARG cc_start: 0.7589 (OUTLIER) cc_final: 0.7065 (ttm-80) REVERT: E 113 GLN cc_start: 0.9080 (mt0) cc_final: 0.8688 (mt0) REVERT: E 116 MET cc_start: 0.9464 (tpp) cc_final: 0.8882 (mmm) REVERT: G 74 ASP cc_start: 0.9237 (m-30) cc_final: 0.8821 (t0) REVERT: G 180 GLN cc_start: 0.9249 (tt0) cc_final: 0.8802 (tm-30) REVERT: H 47 LYS cc_start: 0.9280 (mmtt) cc_final: 0.8983 (mmtp) REVERT: H 56 GLU cc_start: 0.8635 (mt-10) cc_final: 0.8262 (mp0) REVERT: H 79 GLU cc_start: 0.9200 (mm-30) cc_final: 0.8960 (pp20) REVERT: H 91 GLU cc_start: 0.8272 (mp0) cc_final: 0.7297 (pp20) REVERT: H 107 GLN cc_start: 0.9469 (mm-40) cc_final: 0.9006 (tp-100) REVERT: H 113 GLN cc_start: 0.9004 (mt0) cc_final: 0.8622 (mt0) REVERT: H 126 MET cc_start: 0.9129 (mmm) cc_final: 0.8796 (mmm) REVERT: I 180 GLN cc_start: 0.9341 (tt0) cc_final: 0.9004 (tm-30) REVERT: J 39 ASN cc_start: 0.9165 (t0) cc_final: 0.8934 (t0) REVERT: J 56 GLU cc_start: 0.9132 (tt0) cc_final: 0.8924 (mm-30) REVERT: J 103 GLN cc_start: 0.8939 (pp30) cc_final: 0.8637 (pp30) REVERT: J 113 GLN cc_start: 0.9064 (mm110) cc_final: 0.8824 (mm-40) REVERT: J 120 ARG cc_start: 0.9350 (tmm-80) cc_final: 0.9097 (ptm160) outliers start: 21 outliers final: 11 residues processed: 238 average time/residue: 1.2201 time to fit residues: 321.9652 Evaluate side-chains 224 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 210 time to evaluate : 1.959 ------------------------------------------------------------------------------- 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 C residue 154 TYR Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain D residue 140 GLN 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 113 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 73 optimal weight: 4.9990 chunk 148 optimal weight: 0.4980 chunk 170 optimal weight: 50.0000 chunk 23 optimal weight: 0.7980 chunk 22 optimal weight: 0.7980 chunk 181 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 142 optimal weight: 0.8980 chunk 163 optimal weight: 7.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 69 HIS ** 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 = 0.071059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.048009 restraints weight = 66408.891| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 3.62 r_work: 0.2853 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.3317 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= 0.126 Angle : 0.585 13.290 22569 Z= 0.301 Chirality : 0.039 0.144 2578 Planarity : 0.004 0.056 2960 Dihedral : 4.018 22.390 2379 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.37 % Allowed : 20.88 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.18), residues: 2150 helix: 1.96 (0.13), residues: 1492 sheet: 0.41 (0.44), residues: 115 loop : -1.48 (0.23), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 235 HIS 0.006 0.001 HIS B 84 PHE 0.014 0.001 PHE H 147 TYR 0.034 0.001 TYR I 126 ARG 0.007 0.000 ARG C 120 Details of bonding type rmsd hydrogen bonds : bond 0.03256 ( 1204) hydrogen bonds : angle 4.43877 ( 3582) covalent geometry : bond 0.00284 (16592) covalent geometry : angle 0.58546 (22569) *********************** 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 268 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 248 time to evaluate : 1.744 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 130 GLN cc_start: 0.9414 (mt0) cc_final: 0.9099 (mt0) REVERT: F 144 MET cc_start: 0.8981 (mtm) cc_final: 0.8757 (mtp) REVERT: F 180 GLN cc_start: 0.9233 (tt0) cc_final: 0.8729 (tm-30) REVERT: B 47 LYS cc_start: 0.9352 (mmtt) cc_final: 0.9107 (mmtp) REVERT: B 56 GLU cc_start: 0.8809 (mt-10) cc_final: 0.8337 (pt0) REVERT: B 79 GLU cc_start: 0.9154 (mm-30) cc_final: 0.8862 (pp20) REVERT: B 107 GLN cc_start: 0.9400 (mm-40) cc_final: 0.8967 (tp-100) REVERT: B 113 GLN cc_start: 0.8976 (mt0) cc_final: 0.8682 (mt0) REVERT: A 262 GLN cc_start: 0.8166 (tm-30) cc_final: 0.7749 (pp30) REVERT: C 113 GLN cc_start: 0.9004 (mm110) cc_final: 0.8786 (mm110) REVERT: C 116 MET cc_start: 0.9373 (tpp) cc_final: 0.9051 (tpp) REVERT: C 126 MET cc_start: 0.9038 (OUTLIER) cc_final: 0.8107 (tmm) REVERT: C 148 ARG cc_start: 0.8685 (ttp80) cc_final: 0.8444 (tmm-80) REVERT: D 74 ASP cc_start: 0.9129 (m-30) cc_final: 0.8763 (t0) REVERT: D 180 GLN cc_start: 0.9070 (tt0) cc_final: 0.8758 (tm-30) REVERT: D 262 GLN cc_start: 0.8196 (pp30) cc_final: 0.7709 (pp30) REVERT: E 90 ARG cc_start: 0.7469 (OUTLIER) cc_final: 0.6916 (ttp-110) REVERT: E 91 GLU cc_start: 0.7759 (mp0) cc_final: 0.6935 (pp20) REVERT: E 113 GLN cc_start: 0.8967 (mt0) cc_final: 0.8597 (mt0) REVERT: E 116 MET cc_start: 0.9369 (tpp) cc_final: 0.8715 (mmm) REVERT: G 74 ASP cc_start: 0.9242 (m-30) cc_final: 0.8757 (t0) REVERT: G 180 GLN cc_start: 0.9220 (tt0) cc_final: 0.8781 (tm-30) REVERT: H 47 LYS cc_start: 0.9347 (mmtt) cc_final: 0.9050 (mmtp) REVERT: H 56 GLU cc_start: 0.8716 (mt-10) cc_final: 0.8374 (mp0) REVERT: H 79 GLU cc_start: 0.9237 (mm-30) cc_final: 0.9023 (pp20) REVERT: H 91 GLU cc_start: 0.8280 (mp0) cc_final: 0.7370 (pp20) REVERT: H 107 GLN cc_start: 0.9470 (mm-40) cc_final: 0.9009 (tp-100) REVERT: H 113 GLN cc_start: 0.8924 (mt0) cc_final: 0.8487 (mt0) REVERT: H 126 MET cc_start: 0.9080 (mmm) cc_final: 0.8735 (mmm) REVERT: I 130 GLN cc_start: 0.9366 (mt0) cc_final: 0.9025 (mt0) REVERT: J 39 ASN cc_start: 0.9112 (t0) cc_final: 0.8875 (t0) REVERT: J 56 GLU cc_start: 0.9232 (tt0) cc_final: 0.8858 (mm-30) REVERT: J 103 GLN cc_start: 0.8940 (pp30) cc_final: 0.8618 (pp30) REVERT: J 113 GLN cc_start: 0.9063 (mm110) cc_final: 0.8745 (mm110) REVERT: J 120 ARG cc_start: 0.9320 (tmm-80) cc_final: 0.9045 (ptm160) outliers start: 20 outliers final: 7 residues processed: 263 average time/residue: 1.2375 time to fit residues: 360.3209 Evaluate side-chains 226 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 217 time to evaluate : 1.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain C residue 126 MET 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 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 65 optimal weight: 1.9990 chunk 164 optimal weight: 10.0000 chunk 22 optimal weight: 6.9990 chunk 48 optimal weight: 0.0030 chunk 78 optimal weight: 30.0000 chunk 167 optimal weight: 20.0000 chunk 53 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 83 optimal weight: 50.0000 overall best weight: 2.1998 ------------------------------------------------------------------------------- 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** I 47 GLN ** 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 = 0.3675 r_free = 0.3675 target = 0.069925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.046458 restraints weight = 66716.776| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 3.62 r_work: 0.2808 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.3440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 16592 Z= 0.215 Angle : 0.647 13.739 22569 Z= 0.331 Chirality : 0.040 0.140 2578 Planarity : 0.004 0.054 2960 Dihedral : 4.076 24.704 2379 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.44 % Allowed : 22.25 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.18), residues: 2150 helix: 1.98 (0.13), residues: 1492 sheet: 0.46 (0.45), residues: 115 loop : -1.51 (0.23), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 34 HIS 0.007 0.001 HIS B 84 PHE 0.018 0.001 PHE H 147 TYR 0.034 0.002 TYR I 126 ARG 0.011 0.000 ARG H 128 Details of bonding type rmsd hydrogen bonds : bond 0.03485 ( 1204) hydrogen bonds : angle 4.54504 ( 3582) covalent geometry : bond 0.00491 (16592) covalent geometry : angle 0.64677 (22569) *********************** 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 242 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 221 time to evaluate : 2.020 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 130 GLN cc_start: 0.9423 (mt0) cc_final: 0.9139 (mt0) REVERT: F 180 GLN cc_start: 0.9228 (tt0) cc_final: 0.8726 (tm-30) REVERT: B 47 LYS cc_start: 0.9398 (mmtt) cc_final: 0.9178 (mmmt) REVERT: B 56 GLU cc_start: 0.8840 (mt-10) cc_final: 0.8385 (pt0) REVERT: B 91 GLU cc_start: 0.7831 (mp0) cc_final: 0.6808 (pp20) REVERT: B 107 GLN cc_start: 0.9421 (mm-40) cc_final: 0.8996 (tp-100) REVERT: B 113 GLN cc_start: 0.8987 (mt0) cc_final: 0.8585 (mt0) REVERT: A 144 MET cc_start: 0.8965 (mtp) cc_final: 0.8736 (mtm) REVERT: A 262 GLN cc_start: 0.8177 (tm-30) cc_final: 0.7975 (tm-30) REVERT: C 83 GLU cc_start: 0.8987 (tm-30) cc_final: 0.8746 (pp20) REVERT: C 103 GLN cc_start: 0.9293 (tm-30) cc_final: 0.8706 (tm-30) REVERT: C 116 MET cc_start: 0.9405 (tpp) cc_final: 0.8643 (mmm) REVERT: C 126 MET cc_start: 0.9035 (OUTLIER) cc_final: 0.8112 (tmm) REVERT: C 148 ARG cc_start: 0.8648 (ttp80) cc_final: 0.8384 (tmm-80) REVERT: C 187 CYS cc_start: 0.8753 (t) cc_final: 0.8303 (p) REVERT: C 189 MET cc_start: 0.9163 (ptm) cc_final: 0.8883 (ppp) REVERT: D 74 ASP cc_start: 0.9239 (m-30) cc_final: 0.8783 (t0) REVERT: D 140 GLN cc_start: 0.9224 (OUTLIER) cc_final: 0.8499 (mp10) REVERT: D 180 GLN cc_start: 0.9099 (tt0) cc_final: 0.8809 (tm-30) REVERT: D 262 GLN cc_start: 0.8276 (pp30) cc_final: 0.7839 (pp30) REVERT: E 90 ARG cc_start: 0.7411 (OUTLIER) cc_final: 0.6984 (ttm-80) REVERT: E 113 GLN cc_start: 0.9002 (mt0) cc_final: 0.8656 (mt0) REVERT: E 116 MET cc_start: 0.9406 (tpp) cc_final: 0.8733 (mmm) REVERT: G 74 ASP cc_start: 0.9334 (m-30) cc_final: 0.8810 (t0) REVERT: G 180 GLN cc_start: 0.9228 (tt0) cc_final: 0.8790 (tm-30) REVERT: H 47 LYS cc_start: 0.9407 (mmtt) cc_final: 0.9095 (mmtp) REVERT: H 56 GLU cc_start: 0.8721 (mt-10) cc_final: 0.8380 (mp0) REVERT: H 79 GLU cc_start: 0.9273 (mm-30) cc_final: 0.9015 (pp20) REVERT: H 91 GLU cc_start: 0.8301 (mp0) cc_final: 0.7358 (pp20) REVERT: H 107 GLN cc_start: 0.9435 (mm-40) cc_final: 0.8942 (tp-100) REVERT: H 111 ASP cc_start: 0.8831 (m-30) cc_final: 0.8024 (m-30) REVERT: H 113 GLN cc_start: 0.8938 (mt0) cc_final: 0.8556 (mt0) REVERT: H 126 MET cc_start: 0.9080 (mmm) cc_final: 0.8829 (mmm) REVERT: I 180 GLN cc_start: 0.9337 (tt0) cc_final: 0.8893 (tm-30) REVERT: J 39 ASN cc_start: 0.9139 (t0) cc_final: 0.8907 (t0) REVERT: J 56 GLU cc_start: 0.9235 (tt0) cc_final: 0.8865 (mm-30) REVERT: J 103 GLN cc_start: 0.8930 (pp30) cc_final: 0.8623 (pp30) REVERT: J 120 ARG cc_start: 0.9329 (tmm-80) cc_final: 0.9083 (ptm160) outliers start: 21 outliers final: 9 residues processed: 236 average time/residue: 1.4262 time to fit residues: 376.4685 Evaluate side-chains 220 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 208 time to evaluate : 1.771 ------------------------------------------------------------------------------- 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 127 ASP Chi-restraints excluded: chain D residue 140 GLN Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 56 GLU Chi-restraints excluded: chain E residue 90 ARG Chi-restraints excluded: chain E residue 127 ASP 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 14 optimal weight: 0.9990 chunk 163 optimal weight: 0.8980 chunk 170 optimal weight: 20.0000 chunk 84 optimal weight: 10.0000 chunk 124 optimal weight: 20.0000 chunk 12 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 136 optimal weight: 0.9980 chunk 202 optimal weight: 8.9990 chunk 184 optimal weight: 0.7980 chunk 43 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: C 113 GLN ** E 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 42 GLN ** H 69 HIS ** 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 = 0.3703 r_free = 0.3703 target = 0.071148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.047718 restraints weight = 66329.722| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 3.65 r_work: 0.2844 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 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 : 0.003 0.041 16592 Z= 0.139 Angle : 0.633 14.157 22569 Z= 0.322 Chirality : 0.039 0.193 2578 Planarity : 0.004 0.054 2960 Dihedral : 4.008 24.461 2379 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.82 % Allowed : 22.86 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.18), residues: 2150 helix: 1.97 (0.13), residues: 1493 sheet: 0.50 (0.44), residues: 115 loop : -1.51 (0.23), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 34 HIS 0.006 0.001 HIS B 84 PHE 0.018 0.001 PHE H 147 TYR 0.036 0.002 TYR I 126 ARG 0.008 0.000 ARG H 128 Details of bonding type rmsd hydrogen bonds : bond 0.03233 ( 1204) hydrogen bonds : angle 4.40858 ( 3582) covalent geometry : bond 0.00320 (16592) covalent geometry : angle 0.63285 (22569) *********************** 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 250 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 238 time to evaluate : 1.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 130 GLN cc_start: 0.9379 (mt0) cc_final: 0.9012 (mt0) REVERT: F 180 GLN cc_start: 0.9233 (tt0) cc_final: 0.8692 (tm-30) REVERT: B 44 ILE cc_start: 0.8998 (pp) cc_final: 0.8762 (pp) REVERT: B 47 LYS cc_start: 0.9399 (mmtt) cc_final: 0.9175 (mmmt) REVERT: B 56 GLU cc_start: 0.8823 (mt-10) cc_final: 0.8360 (pt0) REVERT: B 79 GLU cc_start: 0.9158 (mm-30) cc_final: 0.8895 (pp20) REVERT: B 91 GLU cc_start: 0.7882 (mp0) cc_final: 0.6834 (pp20) REVERT: B 107 GLN cc_start: 0.9408 (mm-40) cc_final: 0.8967 (tp-100) REVERT: B 113 GLN cc_start: 0.8982 (mt0) cc_final: 0.8731 (mt0) REVERT: A 262 GLN cc_start: 0.8159 (tm-30) cc_final: 0.7943 (tm-30) REVERT: C 45 GLN cc_start: 0.8849 (mt0) cc_final: 0.8568 (tt0) REVERT: C 83 GLU cc_start: 0.8970 (tm-30) cc_final: 0.8763 (pp20) REVERT: C 116 MET cc_start: 0.9352 (tpp) cc_final: 0.8819 (tpp) REVERT: C 126 MET cc_start: 0.9014 (OUTLIER) cc_final: 0.8004 (tmm) REVERT: C 148 ARG cc_start: 0.8669 (ttp80) cc_final: 0.8414 (tmm-80) REVERT: C 187 CYS cc_start: 0.8723 (t) cc_final: 0.8257 (p) REVERT: D 74 ASP cc_start: 0.9161 (m-30) cc_final: 0.8766 (t0) REVERT: D 180 GLN cc_start: 0.9076 (tt0) cc_final: 0.8787 (tm-30) REVERT: D 262 GLN cc_start: 0.8224 (pp30) cc_final: 0.7772 (pp30) REVERT: E 46 ARG cc_start: 0.9169 (mtm110) cc_final: 0.8969 (ptp90) REVERT: E 83 GLU cc_start: 0.9191 (tm-30) cc_final: 0.8967 (pp20) REVERT: E 90 ARG cc_start: 0.7471 (OUTLIER) cc_final: 0.6762 (ttm-80) REVERT: E 91 GLU cc_start: 0.7669 (mp0) cc_final: 0.6430 (pp20) REVERT: E 113 GLN cc_start: 0.8949 (mt0) cc_final: 0.8656 (mt0) REVERT: E 116 MET cc_start: 0.9432 (tpp) cc_final: 0.9211 (mmm) REVERT: G 144 MET cc_start: 0.8862 (mtm) cc_final: 0.8500 (mtp) REVERT: G 180 GLN cc_start: 0.9220 (tt0) cc_final: 0.8802 (tm-30) REVERT: H 47 LYS cc_start: 0.9374 (mmtt) cc_final: 0.9117 (mmtp) REVERT: H 56 GLU cc_start: 0.8747 (mt-10) cc_final: 0.8386 (mp0) REVERT: H 79 GLU cc_start: 0.9260 (mm-30) cc_final: 0.9045 (pp20) REVERT: H 88 LYS cc_start: 0.8436 (mmmt) cc_final: 0.7879 (mmmt) REVERT: H 91 GLU cc_start: 0.8290 (mp0) cc_final: 0.7384 (pp20) REVERT: H 107 GLN cc_start: 0.9428 (mm-40) cc_final: 0.8906 (tp-100) REVERT: H 111 ASP cc_start: 0.8837 (m-30) cc_final: 0.8042 (m-30) REVERT: H 113 GLN cc_start: 0.8929 (mt0) cc_final: 0.8471 (mt0) REVERT: H 126 MET cc_start: 0.9063 (mmm) cc_final: 0.8760 (mmm) REVERT: I 130 GLN cc_start: 0.9385 (mt0) cc_final: 0.9034 (mt0) REVERT: J 39 ASN cc_start: 0.9120 (t0) cc_final: 0.8886 (t0) REVERT: J 56 GLU cc_start: 0.9248 (tt0) cc_final: 0.8853 (mm-30) REVERT: J 83 GLU cc_start: 0.9343 (tm-30) cc_final: 0.8996 (pp20) REVERT: J 103 GLN cc_start: 0.8915 (pp30) cc_final: 0.8619 (pp30) REVERT: J 120 ARG cc_start: 0.9308 (tmm-80) cc_final: 0.9058 (ptm160) outliers start: 12 outliers final: 7 residues processed: 246 average time/residue: 1.3135 time to fit residues: 357.0138 Evaluate side-chains 226 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 217 time to evaluate : 1.926 ------------------------------------------------------------------------------- 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 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 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 213 optimal weight: 30.0000 chunk 64 optimal weight: 7.9990 chunk 128 optimal weight: 50.0000 chunk 214 optimal weight: 4.9990 chunk 206 optimal weight: 9.9990 chunk 95 optimal weight: 0.0980 chunk 21 optimal weight: 0.9990 chunk 25 optimal weight: 5.9990 chunk 39 optimal weight: 50.0000 chunk 162 optimal weight: 0.9980 chunk 52 optimal weight: 0.9980 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 113 GLN ** E 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 69 HIS ** 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 = 0.3691 r_free = 0.3691 target = 0.070562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.047070 restraints weight = 66883.819| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 3.65 r_work: 0.2831 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.3613 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= 0.179 Angle : 0.657 14.293 22569 Z= 0.335 Chirality : 0.040 0.168 2578 Planarity : 0.004 0.054 2960 Dihedral : 4.044 23.970 2379 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.82 % Allowed : 23.27 % Favored : 75.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.18), residues: 2150 helix: 1.96 (0.14), residues: 1495 sheet: 0.53 (0.45), residues: 115 loop : -1.47 (0.23), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP C 109 HIS 0.006 0.001 HIS B 84 PHE 0.019 0.001 PHE H 147 TYR 0.034 0.002 TYR I 126 ARG 0.014 0.000 ARG H 46 Details of bonding type rmsd hydrogen bonds : bond 0.03330 ( 1204) hydrogen bonds : angle 4.46919 ( 3582) covalent geometry : bond 0.00415 (16592) covalent geometry : angle 0.65726 (22569) ********************** 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 232 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 220 time to evaluate : 2.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 130 GLN cc_start: 0.9379 (mt0) cc_final: 0.9070 (mt0) REVERT: F 180 GLN cc_start: 0.9220 (tt0) cc_final: 0.8725 (tm-30) REVERT: B 44 ILE cc_start: 0.9003 (pp) cc_final: 0.8738 (pp) REVERT: B 47 LYS cc_start: 0.9427 (mmtt) cc_final: 0.9216 (mmmt) REVERT: B 56 GLU cc_start: 0.8830 (mt-10) cc_final: 0.8387 (pt0) REVERT: B 79 GLU cc_start: 0.9142 (mm-30) cc_final: 0.8891 (pp20) REVERT: B 91 GLU cc_start: 0.7892 (mp0) cc_final: 0.6927 (pp20) REVERT: B 107 GLN cc_start: 0.9412 (mm-40) cc_final: 0.8985 (tp-100) REVERT: B 113 GLN cc_start: 0.8990 (mt0) cc_final: 0.8587 (mt0) REVERT: A 262 GLN cc_start: 0.8133 (tm-30) cc_final: 0.7903 (tm-30) REVERT: C 83 GLU cc_start: 0.8958 (tm-30) cc_final: 0.8734 (pp20) REVERT: C 116 MET cc_start: 0.9361 (tpp) cc_final: 0.8873 (tpp) REVERT: C 126 MET cc_start: 0.9008 (OUTLIER) cc_final: 0.8011 (tmm) REVERT: D 74 ASP cc_start: 0.9167 (m-30) cc_final: 0.8726 (t0) REVERT: D 180 GLN cc_start: 0.9068 (tt0) cc_final: 0.8785 (tm-30) REVERT: D 262 GLN cc_start: 0.8272 (pp30) cc_final: 0.7816 (pp30) REVERT: E 83 GLU cc_start: 0.9201 (tm-30) cc_final: 0.8948 (pp20) REVERT: E 90 ARG cc_start: 0.7482 (OUTLIER) cc_final: 0.7108 (ttm-80) REVERT: E 113 GLN cc_start: 0.8999 (mt0) cc_final: 0.8635 (mt0) REVERT: G 180 GLN cc_start: 0.9197 (tt0) cc_final: 0.8772 (tm-30) REVERT: H 47 LYS cc_start: 0.9344 (mmtt) cc_final: 0.9037 (mmtp) REVERT: H 56 GLU cc_start: 0.8746 (mt-10) cc_final: 0.8382 (mp0) REVERT: H 79 GLU cc_start: 0.9254 (mm-30) cc_final: 0.9035 (pp20) REVERT: H 88 LYS cc_start: 0.8408 (mmmt) cc_final: 0.7843 (mmmt) REVERT: H 91 GLU cc_start: 0.8298 (mp0) cc_final: 0.7390 (pp20) REVERT: H 107 GLN cc_start: 0.9429 (mm-40) cc_final: 0.8911 (tp-100) REVERT: H 111 ASP cc_start: 0.8824 (m-30) cc_final: 0.7976 (m-30) REVERT: H 113 GLN cc_start: 0.8926 (mt0) cc_final: 0.8473 (mt0) REVERT: H 126 MET cc_start: 0.9076 (mmm) cc_final: 0.8784 (mmm) REVERT: I 74 ASP cc_start: 0.9110 (m-30) cc_final: 0.8907 (t70) REVERT: I 130 GLN cc_start: 0.9406 (mt0) cc_final: 0.9131 (mt0) REVERT: J 39 ASN cc_start: 0.9123 (t0) cc_final: 0.8894 (t0) REVERT: J 56 GLU cc_start: 0.9251 (tt0) cc_final: 0.8857 (mm-30) REVERT: J 120 ARG cc_start: 0.9313 (tmm-80) cc_final: 0.9060 (ptm160) outliers start: 12 outliers final: 9 residues processed: 228 average time/residue: 1.2817 time to fit residues: 322.4197 Evaluate side-chains 223 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 212 time to evaluate : 2.009 ------------------------------------------------------------------------------- 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 127 ASP Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 79 GLU Chi-restraints excluded: chain E residue 90 ARG Chi-restraints excluded: chain E residue 127 ASP Chi-restraints excluded: chain H residue 131 VAL Chi-restraints excluded: chain J residue 35 ASP 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 77 optimal weight: 30.0000 chunk 18 optimal weight: 0.9980 chunk 104 optimal weight: 0.4980 chunk 74 optimal weight: 5.9990 chunk 179 optimal weight: 4.9990 chunk 180 optimal weight: 0.0060 chunk 35 optimal weight: 10.0000 chunk 177 optimal weight: 1.9990 chunk 117 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 86 optimal weight: 40.0000 overall best weight: 0.9000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 69 HIS ** 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 = 0.3704 r_free = 0.3704 target = 0.071156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.047696 restraints weight = 66114.440| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 3.66 r_work: 0.2851 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.3661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16592 Z= 0.142 Angle : 0.664 15.863 22569 Z= 0.334 Chirality : 0.039 0.157 2578 Planarity : 0.004 0.054 2960 Dihedral : 4.036 24.391 2379 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 0.82 % Allowed : 23.55 % Favored : 75.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.18), residues: 2150 helix: 1.95 (0.14), residues: 1495 sheet: 0.41 (0.45), residues: 115 loop : -1.45 (0.24), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP C 109 HIS 0.006 0.001 HIS B 84 PHE 0.016 0.001 PHE H 147 TYR 0.034 0.002 TYR I 126 ARG 0.014 0.000 ARG H 46 Details of bonding type rmsd hydrogen bonds : bond 0.03222 ( 1204) hydrogen bonds : angle 4.44179 ( 3582) covalent geometry : bond 0.00331 (16592) covalent geometry : angle 0.66395 (22569) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12644.28 seconds wall clock time: 217 minutes 26.06 seconds (13046.06 seconds total)