Starting phenix.real_space_refine on Wed Sep 17 17:56:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jq6_61724/09_2025/9jq6_61724.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jq6_61724/09_2025/9jq6_61724.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9jq6_61724/09_2025/9jq6_61724.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jq6_61724/09_2025/9jq6_61724.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9jq6_61724/09_2025/9jq6_61724.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jq6_61724/09_2025/9jq6_61724.map" } resolution = 3.34 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.033 sd= 0.279 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 48 5.16 5 C 6428 2.51 5 N 1725 2.21 5 O 2035 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10236 Number of models: 1 Model: "" Number of chains: 11 Chain: "E" Number of atoms: 1691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1691 Classifications: {'peptide': 215} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 202} Chain: "F" Number of atoms: 1691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1691 Classifications: {'peptide': 215} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 202} Chain: "H" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1670 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 13, 'TRANS': 205} Chain breaks: 1 Chain: "I" Number of atoms: 1659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1659 Classifications: {'peptide': 216} Link IDs: {'PCIS': 4, 'PTRANS': 8, 'TRANS': 203} Chain: "J" Number of atoms: 1684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1684 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 13, 'TRANS': 207} Chain: "K" Number of atoms: 1659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1659 Classifications: {'peptide': 216} Link IDs: {'PCIS': 4, 'PTRANS': 8, 'TRANS': 203} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 2.95, per 1000 atoms: 0.29 Number of scatterers: 10236 At special positions: 0 Unit cell: (62.7, 114.95, 243.2, 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 48 16.00 O 2035 8.00 N 1725 7.00 C 6428 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 97 " distance=2.03 Simple disulfide: pdb=" SG CYS E 137 " - pdb=" SG CYS E 191 " distance=2.04 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 97 " distance=2.04 Simple disulfide: pdb=" SG CYS F 137 " - pdb=" SG CYS F 191 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS H 148 " - pdb=" SG CYS H 203 " distance=2.04 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 92 " distance=2.04 Simple disulfide: pdb=" SG CYS I 138 " - pdb=" SG CYS I 198 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.04 Simple disulfide: pdb=" SG CYS J 148 " - pdb=" SG CYS J 203 " distance=2.05 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 92 " distance=2.04 Simple disulfide: pdb=" SG CYS K 138 " - pdb=" SG CYS K 198 " distance=2.04 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 Links applied BETA1-4 " NAG A 1 " - " NAG A 2 " " NAG B 1 " - " NAG B 2 " " NAG C 1 " - " NAG C 2 " NAG-ASN " NAG A 1 " - " ASN E 92 " " NAG B 1 " - " ASN E 194 " " NAG C 1 " - " ASN F 92 " " NAG E 601 " - " ASN E 18 " " NAG E 602 " - " ASN E 86 " " NAG E 603 " - " ASN E 188 " " NAG F 601 " - " ASN F 18 " " NAG F 602 " - " ASN F 86 " " NAG F 603 " - " ASN F 188 " " NAG F 604 " - " ASN F 194 " Time building additional restraints: 1.17 Conformation dependent library (CDL) restraints added in 464.2 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2400 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 34 sheets defined 7.3% alpha, 44.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'E' and resid 56 through 60 Processing helix chain 'E' and resid 74 through 78 Processing helix chain 'E' and resid 88 through 92 removed outlier: 3.830A pdb=" N ASN E 92 " --> pdb=" O ALA E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 209 through 213 removed outlier: 3.551A pdb=" N PHE E 212 " --> pdb=" O PRO E 209 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N MET E 213 " --> pdb=" O GLU E 210 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 209 through 213' Processing helix chain 'F' and resid 88 through 92 Processing helix chain 'F' and resid 209 through 213 removed outlier: 4.008A pdb=" N MET F 213 " --> pdb=" O GLU F 210 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.748A pdb=" N ARG H 31 " --> pdb=" O ASP H 28 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 66 removed outlier: 4.003A pdb=" N LYS H 65 " --> pdb=" O PRO H 62 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ASP H 66 " --> pdb=" O SER H 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 62 through 66' Processing helix chain 'H' and resid 194 through 199 Processing helix chain 'I' and resid 83 through 87 removed outlier: 3.802A pdb=" N ASP I 86 " --> pdb=" O GLU I 83 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ALA I 87 " --> pdb=" O GLU I 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 83 through 87' Processing helix chain 'I' and resid 125 through 131 removed outlier: 4.046A pdb=" N SER I 131 " --> pdb=" O GLU I 127 " (cutoff:3.500A) Processing helix chain 'I' and resid 187 through 193 removed outlier: 4.154A pdb=" N HIS I 193 " --> pdb=" O GLU I 189 " (cutoff:3.500A) Processing helix chain 'J' and resid 28 through 32 removed outlier: 3.538A pdb=" N ARG J 31 " --> pdb=" O ASP J 28 " (cutoff:3.500A) Processing helix chain 'J' and resid 62 through 65 removed outlier: 3.729A pdb=" N LYS J 65 " --> pdb=" O PRO J 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 62 through 65' Processing helix chain 'J' and resid 135 through 139 removed outlier: 3.724A pdb=" N THR J 139 " --> pdb=" O CYS J 136 " (cutoff:3.500A) Processing helix chain 'J' and resid 164 through 166 No H-bonds generated for 'chain 'J' and resid 164 through 166' Processing helix chain 'K' and resid 83 through 87 removed outlier: 3.502A pdb=" N ASP K 86 " --> pdb=" O GLU K 83 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ALA K 87 " --> pdb=" O GLU K 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 83 through 87' Processing helix chain 'K' and resid 125 through 132 removed outlier: 3.704A pdb=" N LEU K 129 " --> pdb=" O SER K 125 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 4 through 5 Processing sheet with id=AA2, first strand: chain 'E' and resid 11 through 14 removed outlier: 3.619A pdb=" N ALA E 108 " --> pdb=" O CYS E 97 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N VAL E 36 " --> pdb=" O TYR E 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 122 through 128 removed outlier: 6.468A pdb=" N ARG E 134 " --> pdb=" O ARG E 126 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N PHE E 173 " --> pdb=" O GLY E 141 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA E 178 " --> pdb=" O LYS E 162 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS E 162 " --> pdb=" O ALA E 178 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 122 through 128 removed outlier: 6.468A pdb=" N ARG E 134 " --> pdb=" O ARG E 126 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N PHE E 173 " --> pdb=" O GLY E 141 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 157 through 158 removed outlier: 4.705A pdb=" N TRP E 150 " --> pdb=" O ALA E 158 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 4 through 5 removed outlier: 4.216A pdb=" N ALA F 81 " --> pdb=" O VAL F 71 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 11 through 14 Processing sheet with id=AA8, first strand: chain 'F' and resid 122 through 129 removed outlier: 6.587A pdb=" N ARG F 134 " --> pdb=" O ARG F 126 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N HIS F 128 " --> pdb=" O GLY F 132 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N GLY F 132 " --> pdb=" O HIS F 128 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N ARG F 134 " --> pdb=" O ILE F 181 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N ILE F 181 " --> pdb=" O ARG F 134 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N GLU F 136 " --> pdb=" O VAL F 179 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N VAL F 179 " --> pdb=" O GLU F 136 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N ILE F 138 " --> pdb=" O THR F 177 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N THR F 177 " --> pdb=" O ILE F 138 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N ARG F 140 " --> pdb=" O VAL F 175 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N VAL F 175 " --> pdb=" O ARG F 140 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N TRP F 142 " --> pdb=" O PHE F 173 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ALA F 178 " --> pdb=" O LYS F 162 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LYS F 162 " --> pdb=" O ALA F 178 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 122 through 129 removed outlier: 6.587A pdb=" N ARG F 134 " --> pdb=" O ARG F 126 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N HIS F 128 " --> pdb=" O GLY F 132 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N GLY F 132 " --> pdb=" O HIS F 128 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N ARG F 134 " --> pdb=" O ILE F 181 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N ILE F 181 " --> pdb=" O ARG F 134 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N GLU F 136 " --> pdb=" O VAL F 179 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N VAL F 179 " --> pdb=" O GLU F 136 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N ILE F 138 " --> pdb=" O THR F 177 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N THR F 177 " --> pdb=" O ILE F 138 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N ARG F 140 " --> pdb=" O VAL F 175 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N VAL F 175 " --> pdb=" O ARG F 140 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N TRP F 142 " --> pdb=" O PHE F 173 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 147 through 150 removed outlier: 3.708A pdb=" N GLN F 200 " --> pdb=" O ASN F 195 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 147 through 150 Processing sheet with id=AB3, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AB4, first strand: chain 'H' and resid 11 through 12 removed outlier: 4.093A pdb=" N TRP H 33 " --> pdb=" O GLN H 99 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N MET H 34 " --> pdb=" O GLU H 50 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N GLU H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 11 through 12 removed outlier: 7.058A pdb=" N CYS H 96 " --> pdb=" O TRP H 111 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N TRP H 111 " --> pdb=" O CYS H 96 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ARG H 98 " --> pdb=" O ASP H 109 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA H 107 " --> pdb=" O ARG H 100 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 128 through 131 removed outlier: 6.471A pdb=" N THR H 184 " --> pdb=" O ALA H 176 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ALA H 176 " --> pdb=" O THR H 184 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N SER H 186 " --> pdb=" O PHE H 174 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 143 through 145 Processing sheet with id=AB8, first strand: chain 'H' and resid 159 through 162 removed outlier: 3.940A pdb=" N LYS H 216 " --> pdb=" O CYS H 203 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 5 through 7 Processing sheet with id=AC1, first strand: chain 'I' and resid 10 through 14 removed outlier: 6.454A pdb=" N TRP I 39 " --> pdb=" O LEU I 51 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 118 through 122 removed outlier: 6.009A pdb=" N TYR I 177 " --> pdb=" O ASN I 142 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER I 180 " --> pdb=" O SER I 166 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 133 through 134 Processing sheet with id=AC4, first strand: chain 'I' and resid 148 through 153 removed outlier: 3.651A pdb=" N GLU I 199 " --> pdb=" O LYS I 151 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA I 200 " --> pdb=" O ILE I 209 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ILE I 209 " --> pdb=" O ALA I 200 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N HIS I 202 " --> pdb=" O SER I 207 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N SER I 207 " --> pdb=" O HIS I 202 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'J' and resid 3 through 7 Processing sheet with id=AC6, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.099A pdb=" N GLY J 10 " --> pdb=" O THR J 118 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N TRP J 33 " --> pdb=" O GLN J 99 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY J 49 " --> pdb=" O TRP J 36 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ARG J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N TRP J 47 " --> pdb=" O ARG J 38 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.099A pdb=" N GLY J 10 " --> pdb=" O THR J 118 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N CYS J 96 " --> pdb=" O TRP J 111 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N TRP J 111 " --> pdb=" O CYS J 96 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ARG J 98 " --> pdb=" O ASP J 109 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'J' and resid 129 through 130 Processing sheet with id=AC9, first strand: chain 'J' and resid 129 through 130 removed outlier: 6.524A pdb=" N LEU J 182 " --> pdb=" O LEU J 178 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N LEU J 178 " --> pdb=" O LEU J 182 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N THR J 184 " --> pdb=" O ALA J 176 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ALA J 176 " --> pdb=" O THR J 184 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N SER J 186 " --> pdb=" O PHE J 174 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'J' and resid 159 through 162 Processing sheet with id=AD2, first strand: chain 'J' and resid 159 through 162 removed outlier: 3.871A pdb=" N ILE J 201 " --> pdb=" O ILE J 218 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'K' and resid 4 through 7 Processing sheet with id=AD4, first strand: chain 'K' and resid 11 through 14 removed outlier: 6.315A pdb=" N TRP K 39 " --> pdb=" O LEU K 51 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'K' and resid 30 through 31 Processing sheet with id=AD6, first strand: chain 'K' and resid 118 through 122 removed outlier: 5.077A pdb=" N PHE K 139 " --> pdb=" O SER K 181 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N SER K 181 " --> pdb=" O PHE K 139 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N ASN K 141 " --> pdb=" O MET K 179 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N MET K 179 " --> pdb=" O ASN K 141 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'K' and resid 151 through 153 379 hydrogen bonds defined for protein. 891 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.83 Time building geometry restraints manager: 1.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3280 1.34 - 1.46: 2461 1.46 - 1.58: 4664 1.58 - 1.70: 0 1.70 - 1.82: 70 Bond restraints: 10475 Sorted by residual: bond pdb=" CA PRO J 127 " pdb=" C PRO J 127 " ideal model delta sigma weight residual 1.526 1.496 0.030 1.13e-02 7.83e+03 6.83e+00 bond pdb=" CA GLU I 158 " pdb=" C GLU I 158 " ideal model delta sigma weight residual 1.526 1.498 0.029 1.21e-02 6.83e+03 5.58e+00 bond pdb=" CA SER J 128 " pdb=" C SER J 128 " ideal model delta sigma weight residual 1.520 1.493 0.028 1.22e-02 6.72e+03 5.25e+00 bond pdb=" CA ASP I 155 " pdb=" C ASP I 155 " ideal model delta sigma weight residual 1.527 1.498 0.029 1.30e-02 5.92e+03 5.06e+00 bond pdb=" CA ARG J 100 " pdb=" C ARG J 100 " ideal model delta sigma weight residual 1.525 1.499 0.025 1.25e-02 6.40e+03 4.09e+00 ... (remaining 10470 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.03: 13760 2.03 - 4.07: 415 4.07 - 6.10: 44 6.10 - 8.13: 10 8.13 - 10.16: 3 Bond angle restraints: 14232 Sorted by residual: angle pdb=" N THR K 130 " pdb=" CA THR K 130 " pdb=" C THR K 130 " ideal model delta sigma weight residual 111.14 100.98 10.16 1.08e+00 8.57e-01 8.85e+01 angle pdb=" N GLY E 155 " pdb=" CA GLY E 155 " pdb=" C GLY E 155 " ideal model delta sigma weight residual 113.58 121.10 -7.52 1.07e+00 8.73e-01 4.93e+01 angle pdb=" N THR H 195 " pdb=" CA THR H 195 " pdb=" C THR H 195 " ideal model delta sigma weight residual 113.02 105.77 7.25 1.20e+00 6.94e-01 3.65e+01 angle pdb=" N TRP H 196 " pdb=" CA TRP H 196 " pdb=" C TRP H 196 " ideal model delta sigma weight residual 112.75 105.14 7.61 1.36e+00 5.41e-01 3.13e+01 angle pdb=" N GLY E 156 " pdb=" CA GLY E 156 " pdb=" C GLY E 156 " ideal model delta sigma weight residual 112.54 119.62 -7.08 1.28e+00 6.10e-01 3.06e+01 ... (remaining 14227 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.90: 5553 16.90 - 33.81: 655 33.81 - 50.71: 185 50.71 - 67.62: 47 67.62 - 84.52: 12 Dihedral angle restraints: 6452 sinusoidal: 2705 harmonic: 3747 Sorted by residual: dihedral pdb=" CB CYS K 23 " pdb=" SG CYS K 23 " pdb=" SG CYS K 92 " pdb=" CB CYS K 92 " ideal model delta sinusoidal sigma weight residual 93.00 172.29 -79.29 1 1.00e+01 1.00e-02 7.82e+01 dihedral pdb=" CB CYS J 148 " pdb=" SG CYS J 148 " pdb=" SG CYS J 203 " pdb=" CB CYS J 203 " ideal model delta sinusoidal sigma weight residual 93.00 138.68 -45.68 1 1.00e+01 1.00e-02 2.89e+01 dihedral pdb=" CB CYS K 138 " pdb=" SG CYS K 138 " pdb=" SG CYS K 198 " pdb=" CB CYS K 198 " ideal model delta sinusoidal sigma weight residual -86.00 -50.77 -35.23 1 1.00e+01 1.00e-02 1.76e+01 ... (remaining 6449 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1307 0.060 - 0.121: 279 0.121 - 0.181: 21 0.181 - 0.241: 3 0.241 - 0.301: 1 Chirality restraints: 1611 Sorted by residual: chirality pdb=" C1 NAG F 603 " pdb=" ND2 ASN F 188 " pdb=" C2 NAG F 603 " pdb=" O5 NAG F 603 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.27e+00 chirality pdb=" C1 NAG B 1 " pdb=" ND2 ASN E 194 " pdb=" C2 NAG B 1 " pdb=" O5 NAG B 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.63 0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" C1 NAG F 602 " pdb=" ND2 ASN F 86 " pdb=" C2 NAG F 602 " pdb=" O5 NAG F 602 " both_signs ideal model delta sigma weight residual False -2.40 -2.19 -0.21 2.00e-01 2.50e+01 1.07e+00 ... (remaining 1608 not shown) Planarity restraints: 1822 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 601 " 0.351 2.00e-02 2.50e+03 3.03e-01 1.15e+03 pdb=" C7 NAG E 601 " -0.083 2.00e-02 2.50e+03 pdb=" C8 NAG E 601 " 0.108 2.00e-02 2.50e+03 pdb=" N2 NAG E 601 " -0.540 2.00e-02 2.50e+03 pdb=" O7 NAG E 601 " 0.163 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 604 " -0.291 2.00e-02 2.50e+03 2.46e-01 7.58e+02 pdb=" C7 NAG F 604 " 0.076 2.00e-02 2.50e+03 pdb=" C8 NAG F 604 " -0.183 2.00e-02 2.50e+03 pdb=" N2 NAG F 604 " 0.422 2.00e-02 2.50e+03 pdb=" O7 NAG F 604 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN E 194 " -0.000 2.00e-02 2.50e+03 3.39e-02 1.44e+01 pdb=" CG ASN E 194 " -0.032 2.00e-02 2.50e+03 pdb=" OD1 ASN E 194 " 0.039 2.00e-02 2.50e+03 pdb=" ND2 ASN E 194 " -0.043 2.00e-02 2.50e+03 pdb=" C1 NAG B 1 " 0.037 2.00e-02 2.50e+03 ... (remaining 1819 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1022 2.74 - 3.28: 9507 3.28 - 3.82: 15805 3.82 - 4.36: 18518 4.36 - 4.90: 33037 Nonbonded interactions: 77889 Sorted by model distance: nonbonded pdb=" OE2 GLU H 156 " pdb=" OH TYR H 183 " model vdw 2.201 3.040 nonbonded pdb=" N GLU J 1 " pdb=" OE1 GLU J 1 " model vdw 2.207 3.120 nonbonded pdb=" OD1 ASN K 214 " pdb=" N ARG K 215 " model vdw 2.210 3.120 nonbonded pdb=" NZ LYS I 151 " pdb=" OE2 GLU I 199 " model vdw 2.224 3.120 nonbonded pdb=" O SER J 88 " pdb=" OG SER J 88 " model vdw 2.235 3.040 ... (remaining 77884 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' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'E' selection = (chain 'F' and resid 1 through 603) } ncs_group { reference = chain 'H' selection = (chain 'J' and (resid 1 through 138 or resid 141 through 221)) } ncs_group { reference = chain 'I' selection = chain 'K' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 7.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.580 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8868 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 : 0.005 0.051 10500 Z= 0.262 Angle : 0.829 18.520 14295 Z= 0.464 Chirality : 0.049 0.301 1611 Planarity : 0.011 0.303 1812 Dihedral : 16.108 84.519 4016 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 1.69 % Allowed : 28.38 % Favored : 69.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.60 (0.23), residues: 1288 helix: -1.56 (1.18), residues: 19 sheet: 0.69 (0.21), residues: 607 loop : -1.48 (0.23), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 54 TYR 0.038 0.002 TYR H 130 PHE 0.021 0.002 PHE K 143 TRP 0.012 0.002 TRP I 152 HIS 0.003 0.001 HIS F 24 Details of bonding type rmsd covalent geometry : bond 0.00495 (10475) covalent geometry : angle 0.79276 (14232) SS BOND : bond 0.01033 ( 12) SS BOND : angle 1.31017 ( 24) hydrogen bonds : bond 0.17500 ( 338) hydrogen bonds : angle 7.26082 ( 891) link_BETA1-4 : bond 0.00347 ( 3) link_BETA1-4 : angle 1.39356 ( 9) link_NAG-ASN : bond 0.00614 ( 10) link_NAG-ASN : angle 5.19786 ( 30) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 196 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 72 ARG cc_start: 0.9382 (OUTLIER) cc_final: 0.8646 (ptm160) REVERT: I 161 ASN cc_start: 0.6878 (t0) cc_final: 0.6626 (t0) outliers start: 19 outliers final: 7 residues processed: 203 average time/residue: 0.1182 time to fit residues: 32.3547 Evaluate side-chains 195 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 187 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 86 ASN Chi-restraints excluded: chain H residue 72 ARG Chi-restraints excluded: chain I residue 57 ASN Chi-restraints excluded: chain I residue 128 GLN Chi-restraints excluded: chain I residue 159 ARG Chi-restraints excluded: chain I residue 180 SER Chi-restraints excluded: chain J residue 216 LYS Chi-restraints excluded: chain K residue 154 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 113 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 123 optimal weight: 0.8980 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 85 HIS I 42 GLN I 149 ASN I 161 ASN J 99 GLN J 172 HIS J 204 ASN J 207 HIS K 149 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.051155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2454 r_free = 0.2454 target = 0.039623 restraints weight = 33073.949| |-----------------------------------------------------------------------------| r_work (start): 0.2449 rms_B_bonded: 2.71 r_work: 0.2343 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2229 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8944 moved from start: 0.1026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 10500 Z= 0.304 Angle : 0.801 10.392 14295 Z= 0.412 Chirality : 0.051 0.321 1611 Planarity : 0.006 0.058 1812 Dihedral : 8.533 72.252 1702 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 4.80 % Allowed : 25.27 % Favored : 69.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.64 (0.23), residues: 1288 helix: -1.14 (0.99), residues: 26 sheet: 0.63 (0.21), residues: 605 loop : -1.47 (0.23), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG I 159 TYR 0.020 0.003 TYR F 98 PHE 0.022 0.003 PHE I 143 TRP 0.017 0.003 TRP H 33 HIS 0.005 0.001 HIS E 24 Details of bonding type rmsd covalent geometry : bond 0.00725 (10475) covalent geometry : angle 0.77672 (14232) SS BOND : bond 0.01346 ( 12) SS BOND : angle 1.75075 ( 24) hydrogen bonds : bond 0.05267 ( 338) hydrogen bonds : angle 6.75212 ( 891) link_BETA1-4 : bond 0.00212 ( 3) link_BETA1-4 : angle 1.73628 ( 9) link_NAG-ASN : bond 0.00650 ( 10) link_NAG-ASN : angle 4.04032 ( 30) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 190 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 103 ARG cc_start: 0.9392 (OUTLIER) cc_final: 0.8082 (mmp80) REVERT: F 74 ASP cc_start: 0.8822 (t0) cc_final: 0.8606 (t0) REVERT: H 128 SER cc_start: 0.8439 (OUTLIER) cc_final: 0.7984 (t) REVERT: H 130 TYR cc_start: 0.8641 (m-80) cc_final: 0.7852 (m-80) outliers start: 54 outliers final: 24 residues processed: 231 average time/residue: 0.1003 time to fit residues: 32.3372 Evaluate side-chains 209 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 183 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 34 MET Chi-restraints excluded: chain E residue 86 ASN Chi-restraints excluded: chain E residue 103 ARG Chi-restraints excluded: chain E residue 177 THR Chi-restraints excluded: chain E residue 194 ASN Chi-restraints excluded: chain F residue 124 SER Chi-restraints excluded: chain F residue 211 SER Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 128 SER Chi-restraints excluded: chain I residue 126 SER Chi-restraints excluded: chain I residue 169 ASP Chi-restraints excluded: chain I residue 180 SER Chi-restraints excluded: chain J residue 46 GLU Chi-restraints excluded: chain J residue 76 LYS Chi-restraints excluded: chain J residue 83 MET Chi-restraints excluded: chain J residue 93 LEU Chi-restraints excluded: chain J residue 118 THR Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain J residue 135 VAL Chi-restraints excluded: chain J residue 146 LEU Chi-restraints excluded: chain J residue 190 THR Chi-restraints excluded: chain K residue 140 LEU Chi-restraints excluded: chain K residue 154 ILE Chi-restraints excluded: chain K residue 209 ILE Chi-restraints excluded: chain K residue 210 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 106 optimal weight: 0.8980 chunk 57 optimal weight: 0.9980 chunk 116 optimal weight: 0.9980 chunk 73 optimal weight: 0.9980 chunk 75 optimal weight: 0.6980 chunk 61 optimal weight: 0.9990 chunk 126 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 87 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 93 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 85 HIS I 6 GLN ** I 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 149 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.052223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2490 r_free = 0.2490 target = 0.040761 restraints weight = 33180.108| |-----------------------------------------------------------------------------| r_work (start): 0.2483 rms_B_bonded: 2.66 r_work: 0.2379 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2267 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8929 moved from start: 0.1136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10500 Z= 0.177 Angle : 0.695 10.186 14295 Z= 0.354 Chirality : 0.048 0.331 1611 Planarity : 0.005 0.045 1812 Dihedral : 7.655 62.351 1685 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 4.27 % Allowed : 26.42 % Favored : 69.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.45 (0.23), residues: 1288 helix: -1.13 (1.00), residues: 26 sheet: 0.78 (0.21), residues: 603 loop : -1.36 (0.23), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 159 TYR 0.018 0.002 TYR H 60 PHE 0.017 0.002 PHE J 154 TRP 0.014 0.002 TRP H 33 HIS 0.004 0.001 HIS E 24 Details of bonding type rmsd covalent geometry : bond 0.00415 (10475) covalent geometry : angle 0.67221 (14232) SS BOND : bond 0.00899 ( 12) SS BOND : angle 1.13763 ( 24) hydrogen bonds : bond 0.04040 ( 338) hydrogen bonds : angle 6.30924 ( 891) link_BETA1-4 : bond 0.00311 ( 3) link_BETA1-4 : angle 1.78074 ( 9) link_NAG-ASN : bond 0.00668 ( 10) link_NAG-ASN : angle 3.73106 ( 30) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 194 time to evaluate : 0.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 103 ARG cc_start: 0.9379 (OUTLIER) cc_final: 0.8045 (mmp80) REVERT: E 189 MET cc_start: 0.9002 (mmt) cc_final: 0.8312 (tpt) REVERT: F 74 ASP cc_start: 0.8772 (t0) cc_final: 0.8433 (t0) REVERT: H 128 SER cc_start: 0.8524 (OUTLIER) cc_final: 0.7908 (t) REVERT: H 130 TYR cc_start: 0.8587 (m-80) cc_final: 0.7879 (m-80) REVERT: H 181 ASP cc_start: 0.8518 (t70) cc_final: 0.8305 (t0) REVERT: I 128 GLN cc_start: 0.9057 (tp-100) cc_final: 0.8364 (tp40) REVERT: I 154 ILE cc_start: 0.8637 (mm) cc_final: 0.8144 (mm) REVERT: J 66 ASP cc_start: 0.8538 (p0) cc_final: 0.8337 (p0) outliers start: 48 outliers final: 31 residues processed: 231 average time/residue: 0.1086 time to fit residues: 34.9299 Evaluate side-chains 213 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 180 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 34 MET Chi-restraints excluded: chain E residue 86 ASN Chi-restraints excluded: chain E residue 103 ARG Chi-restraints excluded: chain E residue 177 THR Chi-restraints excluded: chain E residue 194 ASN Chi-restraints excluded: chain F residue 41 SER Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 128 SER Chi-restraints excluded: chain H residue 184 THR Chi-restraints excluded: chain H residue 196 TRP Chi-restraints excluded: chain I residue 136 VAL Chi-restraints excluded: chain I residue 169 ASP Chi-restraints excluded: chain I residue 180 SER Chi-restraints excluded: chain J residue 46 GLU Chi-restraints excluded: chain J residue 76 LYS Chi-restraints excluded: chain J residue 83 MET Chi-restraints excluded: chain J residue 93 LEU Chi-restraints excluded: chain J residue 118 THR Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain J residue 135 VAL Chi-restraints excluded: chain J residue 149 LEU Chi-restraints excluded: chain J residue 190 THR Chi-restraints excluded: chain J residue 218 ILE Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 77 LEU Chi-restraints excluded: chain K residue 120 SER Chi-restraints excluded: chain K residue 140 LEU Chi-restraints excluded: chain K residue 209 ILE Chi-restraints excluded: chain K residue 210 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 34 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 124 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 chunk 114 optimal weight: 2.9990 chunk 118 optimal weight: 0.7980 chunk 63 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 85 HIS I 128 GLN I 149 ASN ** I 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 149 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.052025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2484 r_free = 0.2484 target = 0.040567 restraints weight = 33340.743| |-----------------------------------------------------------------------------| r_work (start): 0.2480 rms_B_bonded: 2.68 r_work: 0.2376 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2264 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8932 moved from start: 0.1276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10500 Z= 0.186 Angle : 0.697 10.111 14295 Z= 0.353 Chirality : 0.048 0.328 1611 Planarity : 0.005 0.046 1812 Dihedral : 7.310 61.836 1683 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 4.63 % Allowed : 26.69 % Favored : 68.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.43 (0.23), residues: 1288 helix: -1.12 (1.00), residues: 26 sheet: 0.78 (0.21), residues: 605 loop : -1.34 (0.23), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 105 TYR 0.019 0.002 TYR F 50 PHE 0.017 0.002 PHE J 154 TRP 0.014 0.002 TRP H 33 HIS 0.004 0.001 HIS E 24 Details of bonding type rmsd covalent geometry : bond 0.00446 (10475) covalent geometry : angle 0.67270 (14232) SS BOND : bond 0.00942 ( 12) SS BOND : angle 1.22066 ( 24) hydrogen bonds : bond 0.03984 ( 338) hydrogen bonds : angle 6.17289 ( 891) link_BETA1-4 : bond 0.00260 ( 3) link_BETA1-4 : angle 1.87539 ( 9) link_NAG-ASN : bond 0.00673 ( 10) link_NAG-ASN : angle 3.77510 ( 30) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 192 time to evaluate : 0.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 32 GLU cc_start: 0.7856 (mm-30) cc_final: 0.7389 (mp0) REVERT: E 103 ARG cc_start: 0.9379 (OUTLIER) cc_final: 0.8128 (mmp80) REVERT: E 189 MET cc_start: 0.9001 (mmt) cc_final: 0.8316 (tpt) REVERT: F 74 ASP cc_start: 0.8768 (t0) cc_final: 0.8475 (t0) REVERT: H 130 TYR cc_start: 0.8612 (m-80) cc_final: 0.8129 (m-80) REVERT: H 181 ASP cc_start: 0.8547 (t70) cc_final: 0.8321 (t0) REVERT: I 128 GLN cc_start: 0.9072 (tp40) cc_final: 0.8535 (tp40) REVERT: J 217 LYS cc_start: 0.7639 (pptt) cc_final: 0.7192 (pptt) REVERT: K 177 TYR cc_start: 0.9209 (m-80) cc_final: 0.8864 (m-80) REVERT: K 198 CYS cc_start: 0.7380 (OUTLIER) cc_final: 0.7154 (t) outliers start: 52 outliers final: 36 residues processed: 234 average time/residue: 0.1088 time to fit residues: 34.9723 Evaluate side-chains 220 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 182 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 34 MET Chi-restraints excluded: chain E residue 86 ASN Chi-restraints excluded: chain E residue 103 ARG Chi-restraints excluded: chain E residue 194 ASN Chi-restraints excluded: chain E residue 197 LEU Chi-restraints excluded: chain F residue 18 ASN Chi-restraints excluded: chain F residue 41 SER Chi-restraints excluded: chain F residue 124 SER Chi-restraints excluded: chain F residue 211 SER Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 184 THR Chi-restraints excluded: chain H residue 196 TRP Chi-restraints excluded: chain I residue 169 ASP Chi-restraints excluded: chain J residue 31 ARG Chi-restraints excluded: chain J residue 46 GLU Chi-restraints excluded: chain J residue 76 LYS Chi-restraints excluded: chain J residue 83 MET Chi-restraints excluded: chain J residue 93 LEU Chi-restraints excluded: chain J residue 118 THR Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain J residue 135 VAL Chi-restraints excluded: chain J residue 146 LEU Chi-restraints excluded: chain J residue 149 LEU Chi-restraints excluded: chain J residue 190 THR Chi-restraints excluded: chain J residue 218 ILE Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 77 LEU Chi-restraints excluded: chain K residue 120 SER Chi-restraints excluded: chain K residue 140 LEU Chi-restraints excluded: chain K residue 154 ILE Chi-restraints excluded: chain K residue 165 ASN Chi-restraints excluded: chain K residue 198 CYS Chi-restraints excluded: chain K residue 209 ILE Chi-restraints excluded: chain K residue 210 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 109 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 110 optimal weight: 0.5980 chunk 106 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 chunk 111 optimal weight: 0.8980 chunk 103 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 149 ASN K 149 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.052748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2508 r_free = 0.2508 target = 0.041354 restraints weight = 32679.975| |-----------------------------------------------------------------------------| r_work (start): 0.2502 rms_B_bonded: 2.60 r_work: 0.2401 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2289 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8932 moved from start: 0.1361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 10500 Z= 0.176 Angle : 0.689 9.979 14295 Z= 0.349 Chirality : 0.048 0.330 1611 Planarity : 0.005 0.047 1812 Dihedral : 7.101 61.638 1682 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 5.52 % Allowed : 25.71 % Favored : 68.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.42 (0.23), residues: 1288 helix: -1.11 (1.01), residues: 26 sheet: 0.80 (0.21), residues: 605 loop : -1.34 (0.23), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 159 TYR 0.020 0.002 TYR H 60 PHE 0.016 0.002 PHE J 154 TRP 0.014 0.002 TRP H 33 HIS 0.004 0.001 HIS E 24 Details of bonding type rmsd covalent geometry : bond 0.00421 (10475) covalent geometry : angle 0.66545 (14232) SS BOND : bond 0.00936 ( 12) SS BOND : angle 1.26733 ( 24) hydrogen bonds : bond 0.03843 ( 338) hydrogen bonds : angle 6.06258 ( 891) link_BETA1-4 : bond 0.00254 ( 3) link_BETA1-4 : angle 1.90087 ( 9) link_NAG-ASN : bond 0.00652 ( 10) link_NAG-ASN : angle 3.71319 ( 30) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 194 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 32 GLU cc_start: 0.7845 (mm-30) cc_final: 0.7530 (mp0) REVERT: E 103 ARG cc_start: 0.9354 (OUTLIER) cc_final: 0.8111 (mmp80) REVERT: E 189 MET cc_start: 0.9026 (mmt) cc_final: 0.8374 (tpt) REVERT: F 74 ASP cc_start: 0.8752 (t0) cc_final: 0.8466 (t0) REVERT: F 161 LEU cc_start: 0.9038 (OUTLIER) cc_final: 0.8837 (tt) REVERT: H 130 TYR cc_start: 0.8570 (m-80) cc_final: 0.8227 (m-80) REVERT: I 128 GLN cc_start: 0.9000 (tp40) cc_final: 0.8573 (tp40) REVERT: I 149 ASN cc_start: 0.8594 (m-40) cc_final: 0.8386 (m110) REVERT: I 154 ILE cc_start: 0.8609 (mm) cc_final: 0.8216 (mm) REVERT: J 90 ASP cc_start: 0.8669 (p0) cc_final: 0.8443 (p0) REVERT: J 109 ASP cc_start: 0.8906 (p0) cc_final: 0.8705 (p0) REVERT: J 217 LYS cc_start: 0.7751 (pptt) cc_final: 0.7520 (pptt) REVERT: K 128 GLN cc_start: 0.7547 (pt0) cc_final: 0.7175 (pt0) REVERT: K 147 ASP cc_start: 0.8254 (p0) cc_final: 0.7988 (p0) REVERT: K 198 CYS cc_start: 0.7357 (OUTLIER) cc_final: 0.7131 (t) outliers start: 62 outliers final: 47 residues processed: 246 average time/residue: 0.1075 time to fit residues: 36.7237 Evaluate side-chains 239 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 189 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 34 MET Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain E residue 86 ASN Chi-restraints excluded: chain E residue 103 ARG Chi-restraints excluded: chain E residue 177 THR Chi-restraints excluded: chain E residue 194 ASN Chi-restraints excluded: chain E residue 197 LEU Chi-restraints excluded: chain F residue 18 ASN Chi-restraints excluded: chain F residue 41 SER Chi-restraints excluded: chain F residue 76 SER Chi-restraints excluded: chain F residue 104 SER Chi-restraints excluded: chain F residue 124 SER Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 211 SER Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 184 THR Chi-restraints excluded: chain H residue 196 TRP Chi-restraints excluded: chain H residue 215 ASP Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain I residue 136 VAL Chi-restraints excluded: chain I residue 169 ASP Chi-restraints excluded: chain I residue 175 SER Chi-restraints excluded: chain I residue 180 SER Chi-restraints excluded: chain J residue 31 ARG Chi-restraints excluded: chain J residue 46 GLU Chi-restraints excluded: chain J residue 76 LYS Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 83 MET Chi-restraints excluded: chain J residue 93 LEU Chi-restraints excluded: chain J residue 118 THR Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain J residue 135 VAL Chi-restraints excluded: chain J residue 146 LEU Chi-restraints excluded: chain J residue 149 LEU Chi-restraints excluded: chain J residue 190 THR Chi-restraints excluded: chain J residue 218 ILE Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 77 LEU Chi-restraints excluded: chain K residue 120 SER Chi-restraints excluded: chain K residue 140 LEU Chi-restraints excluded: chain K residue 154 ILE Chi-restraints excluded: chain K residue 165 ASN Chi-restraints excluded: chain K residue 198 CYS Chi-restraints excluded: chain K residue 209 ILE Chi-restraints excluded: chain K residue 210 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 52 optimal weight: 0.9990 chunk 91 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 112 optimal weight: 2.9990 chunk 55 optimal weight: 6.9990 chunk 115 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 125 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 85 optimal weight: 0.3980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 85 HIS F 85 HIS F 90 GLN K 149 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.052124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2486 r_free = 0.2486 target = 0.040630 restraints weight = 33427.590| |-----------------------------------------------------------------------------| r_work (start): 0.2481 rms_B_bonded: 2.66 r_work: 0.2378 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2265 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8932 moved from start: 0.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10500 Z= 0.185 Angle : 0.695 9.934 14295 Z= 0.353 Chirality : 0.048 0.329 1611 Planarity : 0.005 0.045 1812 Dihedral : 7.076 61.384 1682 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 4.98 % Allowed : 26.25 % Favored : 68.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.45 (0.23), residues: 1288 helix: -1.08 (1.01), residues: 26 sheet: 0.81 (0.21), residues: 603 loop : -1.39 (0.23), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 98 TYR 0.019 0.002 TYR H 60 PHE 0.017 0.002 PHE J 154 TRP 0.015 0.002 TRP H 33 HIS 0.004 0.001 HIS E 24 Details of bonding type rmsd covalent geometry : bond 0.00444 (10475) covalent geometry : angle 0.67191 (14232) SS BOND : bond 0.00970 ( 12) SS BOND : angle 1.22541 ( 24) hydrogen bonds : bond 0.03893 ( 338) hydrogen bonds : angle 6.06863 ( 891) link_BETA1-4 : bond 0.00250 ( 3) link_BETA1-4 : angle 1.96297 ( 9) link_NAG-ASN : bond 0.00629 ( 10) link_NAG-ASN : angle 3.69934 ( 30) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 194 time to evaluate : 0.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 32 GLU cc_start: 0.7921 (mm-30) cc_final: 0.7646 (mp0) REVERT: E 103 ARG cc_start: 0.9379 (OUTLIER) cc_final: 0.8131 (mmp80) REVERT: E 189 MET cc_start: 0.8988 (mmt) cc_final: 0.8333 (tpt) REVERT: F 74 ASP cc_start: 0.8771 (t0) cc_final: 0.8494 (t0) REVERT: F 161 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8817 (tt) REVERT: H 130 TYR cc_start: 0.8575 (m-80) cc_final: 0.8202 (m-80) REVERT: I 98 ASP cc_start: 0.8353 (t0) cc_final: 0.8113 (t0) REVERT: I 128 GLN cc_start: 0.9025 (tp40) cc_final: 0.8583 (tp40) REVERT: I 149 ASN cc_start: 0.8624 (m-40) cc_final: 0.8413 (m110) REVERT: J 66 ASP cc_start: 0.8571 (p0) cc_final: 0.8323 (p0) REVERT: J 90 ASP cc_start: 0.8716 (p0) cc_final: 0.8472 (p0) REVERT: K 128 GLN cc_start: 0.7669 (pt0) cc_final: 0.7270 (pt0) REVERT: K 147 ASP cc_start: 0.8279 (p0) cc_final: 0.7994 (p0) REVERT: K 198 CYS cc_start: 0.7317 (OUTLIER) cc_final: 0.7045 (t) outliers start: 56 outliers final: 50 residues processed: 240 average time/residue: 0.1122 time to fit residues: 37.0054 Evaluate side-chains 238 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 185 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 34 MET Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain E residue 86 ASN Chi-restraints excluded: chain E residue 103 ARG Chi-restraints excluded: chain E residue 177 THR Chi-restraints excluded: chain E residue 194 ASN Chi-restraints excluded: chain E residue 197 LEU Chi-restraints excluded: chain F residue 18 ASN Chi-restraints excluded: chain F residue 41 SER Chi-restraints excluded: chain F residue 54 ARG Chi-restraints excluded: chain F residue 90 GLN Chi-restraints excluded: chain F residue 104 SER Chi-restraints excluded: chain F residue 124 SER Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 211 SER Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 171 VAL Chi-restraints excluded: chain H residue 184 THR Chi-restraints excluded: chain H residue 196 TRP Chi-restraints excluded: chain H residue 215 ASP Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain I residue 136 VAL Chi-restraints excluded: chain I residue 169 ASP Chi-restraints excluded: chain I residue 180 SER Chi-restraints excluded: chain J residue 31 ARG Chi-restraints excluded: chain J residue 46 GLU Chi-restraints excluded: chain J residue 76 LYS Chi-restraints excluded: chain J residue 83 MET Chi-restraints excluded: chain J residue 93 LEU Chi-restraints excluded: chain J residue 118 THR Chi-restraints excluded: chain J residue 120 SER Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain J residue 135 VAL Chi-restraints excluded: chain J residue 149 LEU Chi-restraints excluded: chain J residue 190 THR Chi-restraints excluded: chain J residue 202 THR Chi-restraints excluded: chain J residue 218 ILE Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 34 ASP Chi-restraints excluded: chain K residue 77 LEU Chi-restraints excluded: chain K residue 120 SER Chi-restraints excluded: chain K residue 140 LEU Chi-restraints excluded: chain K residue 154 ILE Chi-restraints excluded: chain K residue 165 ASN Chi-restraints excluded: chain K residue 198 CYS Chi-restraints excluded: chain K residue 209 ILE Chi-restraints excluded: chain K residue 210 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 53 optimal weight: 0.6980 chunk 98 optimal weight: 0.7980 chunk 102 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 chunk 86 optimal weight: 0.9980 chunk 75 optimal weight: 0.1980 chunk 85 optimal weight: 0.9980 chunk 118 optimal weight: 0.7980 chunk 55 optimal weight: 4.9990 chunk 14 optimal weight: 0.9990 chunk 73 optimal weight: 0.2980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 85 HIS J 204 ASN K 149 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.052733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2508 r_free = 0.2508 target = 0.041252 restraints weight = 32958.115| |-----------------------------------------------------------------------------| r_work (start): 0.2501 rms_B_bonded: 2.67 r_work: 0.2399 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2287 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8914 moved from start: 0.1490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10500 Z= 0.146 Angle : 0.677 9.625 14295 Z= 0.343 Chirality : 0.047 0.333 1611 Planarity : 0.005 0.046 1812 Dihedral : 6.959 61.264 1682 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 5.52 % Allowed : 26.16 % Favored : 68.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.40 (0.23), residues: 1288 helix: -1.09 (1.00), residues: 26 sheet: 0.85 (0.21), residues: 597 loop : -1.34 (0.23), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 159 TYR 0.021 0.002 TYR H 60 PHE 0.021 0.002 PHE F 70 TRP 0.014 0.001 TRP H 47 HIS 0.003 0.001 HIS E 24 Details of bonding type rmsd covalent geometry : bond 0.00347 (10475) covalent geometry : angle 0.65518 (14232) SS BOND : bond 0.00784 ( 12) SS BOND : angle 0.97620 ( 24) hydrogen bonds : bond 0.03549 ( 338) hydrogen bonds : angle 5.91137 ( 891) link_BETA1-4 : bond 0.00287 ( 3) link_BETA1-4 : angle 1.84666 ( 9) link_NAG-ASN : bond 0.00643 ( 10) link_NAG-ASN : angle 3.58934 ( 30) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 194 time to evaluate : 0.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 32 GLU cc_start: 0.7964 (mm-30) cc_final: 0.7725 (mp0) REVERT: E 103 ARG cc_start: 0.9374 (OUTLIER) cc_final: 0.8101 (mmp80) REVERT: E 189 MET cc_start: 0.9000 (mmt) cc_final: 0.8423 (tpt) REVERT: F 74 ASP cc_start: 0.8759 (t0) cc_final: 0.8437 (t0) REVERT: F 161 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8801 (tt) REVERT: H 130 TYR cc_start: 0.8576 (m-80) cc_final: 0.8181 (m-80) REVERT: I 128 GLN cc_start: 0.8999 (tp40) cc_final: 0.8552 (tp40) REVERT: I 154 ILE cc_start: 0.8177 (mm) cc_final: 0.7841 (mm) REVERT: J 66 ASP cc_start: 0.8578 (p0) cc_final: 0.8328 (p0) REVERT: J 90 ASP cc_start: 0.8643 (p0) cc_final: 0.8365 (p0) REVERT: J 217 LYS cc_start: 0.7793 (pptt) cc_final: 0.7560 (pptt) REVERT: K 128 GLN cc_start: 0.7667 (pt0) cc_final: 0.7230 (pt0) REVERT: K 147 ASP cc_start: 0.8238 (p0) cc_final: 0.7882 (p0) REVERT: K 198 CYS cc_start: 0.7386 (OUTLIER) cc_final: 0.7105 (t) outliers start: 62 outliers final: 51 residues processed: 246 average time/residue: 0.1135 time to fit residues: 38.4197 Evaluate side-chains 242 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 188 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain E residue 86 ASN Chi-restraints excluded: chain E residue 103 ARG Chi-restraints excluded: chain E residue 177 THR Chi-restraints excluded: chain E residue 194 ASN Chi-restraints excluded: chain E residue 197 LEU Chi-restraints excluded: chain F residue 18 ASN Chi-restraints excluded: chain F residue 41 SER Chi-restraints excluded: chain F residue 54 ARG Chi-restraints excluded: chain F residue 76 SER Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain F residue 104 SER Chi-restraints excluded: chain F residue 124 SER Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 211 SER Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 171 VAL Chi-restraints excluded: chain H residue 184 THR Chi-restraints excluded: chain H residue 196 TRP Chi-restraints excluded: chain H residue 215 ASP Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain I residue 136 VAL Chi-restraints excluded: chain I residue 169 ASP Chi-restraints excluded: chain I residue 175 SER Chi-restraints excluded: chain I residue 180 SER Chi-restraints excluded: chain J residue 31 ARG Chi-restraints excluded: chain J residue 46 GLU Chi-restraints excluded: chain J residue 76 LYS Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 83 MET Chi-restraints excluded: chain J residue 93 LEU Chi-restraints excluded: chain J residue 118 THR Chi-restraints excluded: chain J residue 120 SER Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain J residue 135 VAL Chi-restraints excluded: chain J residue 149 LEU Chi-restraints excluded: chain J residue 190 THR Chi-restraints excluded: chain J residue 202 THR Chi-restraints excluded: chain J residue 218 ILE Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 34 ASP Chi-restraints excluded: chain K residue 77 LEU Chi-restraints excluded: chain K residue 120 SER Chi-restraints excluded: chain K residue 140 LEU Chi-restraints excluded: chain K residue 154 ILE Chi-restraints excluded: chain K residue 165 ASN Chi-restraints excluded: chain K residue 198 CYS Chi-restraints excluded: chain K residue 209 ILE Chi-restraints excluded: chain K residue 210 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 112 optimal weight: 0.9980 chunk 102 optimal weight: 2.9990 chunk 73 optimal weight: 0.0870 chunk 22 optimal weight: 1.9990 chunk 119 optimal weight: 0.4980 chunk 47 optimal weight: 0.4980 chunk 15 optimal weight: 3.9990 chunk 90 optimal weight: 0.9990 chunk 96 optimal weight: 4.9990 chunk 92 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 42 GLN I 149 ASN K 149 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.052833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2510 r_free = 0.2510 target = 0.041314 restraints weight = 32917.658| |-----------------------------------------------------------------------------| r_work (start): 0.2503 rms_B_bonded: 2.68 r_work: 0.2401 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2289 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8912 moved from start: 0.1553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 10500 Z= 0.153 Angle : 0.685 9.601 14295 Z= 0.347 Chirality : 0.048 0.328 1611 Planarity : 0.005 0.071 1812 Dihedral : 6.944 60.891 1682 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 5.52 % Allowed : 26.42 % Favored : 68.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.39 (0.23), residues: 1288 helix: -1.06 (1.01), residues: 26 sheet: 0.86 (0.21), residues: 599 loop : -1.35 (0.23), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG I 18 TYR 0.021 0.002 TYR F 50 PHE 0.020 0.002 PHE F 70 TRP 0.013 0.001 TRP H 47 HIS 0.003 0.001 HIS E 24 Details of bonding type rmsd covalent geometry : bond 0.00366 (10475) covalent geometry : angle 0.66297 (14232) SS BOND : bond 0.00832 ( 12) SS BOND : angle 1.03841 ( 24) hydrogen bonds : bond 0.03571 ( 338) hydrogen bonds : angle 5.86129 ( 891) link_BETA1-4 : bond 0.00290 ( 3) link_BETA1-4 : angle 1.82093 ( 9) link_NAG-ASN : bond 0.00623 ( 10) link_NAG-ASN : angle 3.62031 ( 30) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 193 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 103 ARG cc_start: 0.9368 (OUTLIER) cc_final: 0.8097 (mmp80) REVERT: E 189 MET cc_start: 0.9000 (mmt) cc_final: 0.8442 (tpt) REVERT: F 74 ASP cc_start: 0.8768 (t0) cc_final: 0.8463 (t0) REVERT: H 130 TYR cc_start: 0.8548 (m-80) cc_final: 0.8143 (m-80) REVERT: I 98 ASP cc_start: 0.8307 (t0) cc_final: 0.8066 (t0) REVERT: I 128 GLN cc_start: 0.9018 (tp40) cc_final: 0.8572 (tp40) REVERT: I 154 ILE cc_start: 0.8319 (mm) cc_final: 0.7861 (mm) REVERT: J 66 ASP cc_start: 0.8581 (p0) cc_final: 0.8345 (p0) REVERT: J 90 ASP cc_start: 0.8655 (p0) cc_final: 0.8369 (p0) REVERT: J 217 LYS cc_start: 0.7916 (pptt) cc_final: 0.7536 (pptt) REVERT: K 128 GLN cc_start: 0.7694 (pt0) cc_final: 0.7249 (pt0) REVERT: K 143 PHE cc_start: 0.7450 (p90) cc_final: 0.7206 (p90) REVERT: K 198 CYS cc_start: 0.7294 (OUTLIER) cc_final: 0.7016 (t) outliers start: 62 outliers final: 52 residues processed: 245 average time/residue: 0.1075 time to fit residues: 36.2418 Evaluate side-chains 242 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 188 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain E residue 86 ASN Chi-restraints excluded: chain E residue 103 ARG Chi-restraints excluded: chain E residue 177 THR Chi-restraints excluded: chain E residue 194 ASN Chi-restraints excluded: chain E residue 197 LEU Chi-restraints excluded: chain F residue 18 ASN Chi-restraints excluded: chain F residue 41 SER Chi-restraints excluded: chain F residue 54 ARG Chi-restraints excluded: chain F residue 76 SER Chi-restraints excluded: chain F residue 104 SER Chi-restraints excluded: chain F residue 124 SER Chi-restraints excluded: chain F residue 211 SER Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 171 VAL Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain H residue 184 THR Chi-restraints excluded: chain H residue 196 TRP Chi-restraints excluded: chain H residue 215 ASP Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain I residue 136 VAL Chi-restraints excluded: chain I residue 169 ASP Chi-restraints excluded: chain I residue 175 SER Chi-restraints excluded: chain I residue 180 SER Chi-restraints excluded: chain J residue 31 ARG Chi-restraints excluded: chain J residue 46 GLU Chi-restraints excluded: chain J residue 76 LYS Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 83 MET Chi-restraints excluded: chain J residue 93 LEU Chi-restraints excluded: chain J residue 118 THR Chi-restraints excluded: chain J residue 120 SER Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain J residue 135 VAL Chi-restraints excluded: chain J residue 149 LEU Chi-restraints excluded: chain J residue 190 THR Chi-restraints excluded: chain J residue 202 THR Chi-restraints excluded: chain J residue 218 ILE Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 34 ASP Chi-restraints excluded: chain K residue 77 LEU Chi-restraints excluded: chain K residue 120 SER Chi-restraints excluded: chain K residue 140 LEU Chi-restraints excluded: chain K residue 154 ILE Chi-restraints excluded: chain K residue 165 ASN Chi-restraints excluded: chain K residue 198 CYS Chi-restraints excluded: chain K residue 209 ILE Chi-restraints excluded: chain K residue 210 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 65 optimal weight: 1.9990 chunk 110 optimal weight: 0.4980 chunk 89 optimal weight: 0.5980 chunk 100 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 108 optimal weight: 3.9990 chunk 85 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 85 HIS F 90 GLN I 42 GLN I 149 ASN K 149 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.052614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2505 r_free = 0.2505 target = 0.041123 restraints weight = 33086.657| |-----------------------------------------------------------------------------| r_work (start): 0.2499 rms_B_bonded: 2.68 r_work: 0.2397 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2286 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8916 moved from start: 0.1613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 10500 Z= 0.168 Angle : 0.708 9.681 14295 Z= 0.360 Chirality : 0.048 0.325 1611 Planarity : 0.005 0.043 1812 Dihedral : 6.989 60.591 1682 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 5.43 % Allowed : 26.60 % Favored : 67.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.40 (0.23), residues: 1288 helix: -1.10 (1.00), residues: 26 sheet: 0.81 (0.21), residues: 603 loop : -1.32 (0.23), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG I 18 TYR 0.020 0.002 TYR H 60 PHE 0.016 0.002 PHE J 154 TRP 0.013 0.002 TRP H 33 HIS 0.004 0.001 HIS E 24 Details of bonding type rmsd covalent geometry : bond 0.00404 (10475) covalent geometry : angle 0.68693 (14232) SS BOND : bond 0.00861 ( 12) SS BOND : angle 1.07900 ( 24) hydrogen bonds : bond 0.03677 ( 338) hydrogen bonds : angle 5.90920 ( 891) link_BETA1-4 : bond 0.00273 ( 3) link_BETA1-4 : angle 1.89044 ( 9) link_NAG-ASN : bond 0.00616 ( 10) link_NAG-ASN : angle 3.58794 ( 30) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 193 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 103 ARG cc_start: 0.9371 (OUTLIER) cc_final: 0.8099 (mmp80) REVERT: E 189 MET cc_start: 0.8991 (mmt) cc_final: 0.8430 (tpt) REVERT: F 74 ASP cc_start: 0.8790 (t0) cc_final: 0.8507 (t0) REVERT: H 130 TYR cc_start: 0.8524 (m-80) cc_final: 0.8124 (m-80) REVERT: I 98 ASP cc_start: 0.8334 (t0) cc_final: 0.8090 (t0) REVERT: I 128 GLN cc_start: 0.9066 (tp40) cc_final: 0.8623 (tp40) REVERT: I 154 ILE cc_start: 0.8356 (mm) cc_final: 0.7897 (mm) REVERT: J 66 ASP cc_start: 0.8567 (p0) cc_final: 0.8309 (p0) REVERT: J 90 ASP cc_start: 0.8696 (p0) cc_final: 0.8434 (p0) REVERT: J 115 THR cc_start: 0.8906 (OUTLIER) cc_final: 0.8618 (p) REVERT: J 217 LYS cc_start: 0.7965 (pptt) cc_final: 0.7604 (pptt) REVERT: K 128 GLN cc_start: 0.7697 (pt0) cc_final: 0.7221 (pp30) REVERT: K 198 CYS cc_start: 0.7266 (OUTLIER) cc_final: 0.6791 (t) REVERT: K 199 GLU cc_start: 0.7688 (pm20) cc_final: 0.7359 (pm20) outliers start: 61 outliers final: 55 residues processed: 243 average time/residue: 0.1016 time to fit residues: 34.4271 Evaluate side-chains 247 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 189 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain E residue 86 ASN Chi-restraints excluded: chain E residue 103 ARG Chi-restraints excluded: chain E residue 177 THR Chi-restraints excluded: chain E residue 194 ASN Chi-restraints excluded: chain E residue 197 LEU Chi-restraints excluded: chain F residue 18 ASN Chi-restraints excluded: chain F residue 41 SER Chi-restraints excluded: chain F residue 54 ARG Chi-restraints excluded: chain F residue 76 SER Chi-restraints excluded: chain F residue 90 GLN Chi-restraints excluded: chain F residue 104 SER Chi-restraints excluded: chain F residue 124 SER Chi-restraints excluded: chain F residue 211 SER Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 171 VAL Chi-restraints excluded: chain H residue 184 THR Chi-restraints excluded: chain H residue 196 TRP Chi-restraints excluded: chain H residue 215 ASP Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain I residue 136 VAL Chi-restraints excluded: chain I residue 169 ASP Chi-restraints excluded: chain I residue 175 SER Chi-restraints excluded: chain I residue 180 SER Chi-restraints excluded: chain J residue 31 ARG Chi-restraints excluded: chain J residue 46 GLU Chi-restraints excluded: chain J residue 50 GLU Chi-restraints excluded: chain J residue 76 LYS Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 83 MET Chi-restraints excluded: chain J residue 93 LEU Chi-restraints excluded: chain J residue 115 THR Chi-restraints excluded: chain J residue 118 THR Chi-restraints excluded: chain J residue 120 SER Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain J residue 135 VAL Chi-restraints excluded: chain J residue 149 LEU Chi-restraints excluded: chain J residue 190 THR Chi-restraints excluded: chain J residue 202 THR Chi-restraints excluded: chain J residue 218 ILE Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 34 ASP Chi-restraints excluded: chain K residue 77 LEU Chi-restraints excluded: chain K residue 120 SER Chi-restraints excluded: chain K residue 140 LEU Chi-restraints excluded: chain K residue 154 ILE Chi-restraints excluded: chain K residue 161 ASN Chi-restraints excluded: chain K residue 165 ASN Chi-restraints excluded: chain K residue 198 CYS Chi-restraints excluded: chain K residue 209 ILE Chi-restraints excluded: chain K residue 210 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 52 optimal weight: 0.9990 chunk 84 optimal weight: 0.0970 chunk 70 optimal weight: 2.9990 chunk 85 optimal weight: 0.1980 chunk 45 optimal weight: 0.9990 chunk 114 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 41 optimal weight: 0.6980 chunk 13 optimal weight: 0.9980 chunk 87 optimal weight: 0.5980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 85 HIS I 149 ASN K 149 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.053048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2521 r_free = 0.2521 target = 0.041657 restraints weight = 32775.398| |-----------------------------------------------------------------------------| r_work (start): 0.2512 rms_B_bonded: 2.66 r_work: 0.2411 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2300 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8904 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 10500 Z= 0.145 Angle : 0.699 9.461 14295 Z= 0.356 Chirality : 0.048 0.328 1611 Planarity : 0.005 0.091 1812 Dihedral : 6.941 60.523 1682 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 5.07 % Allowed : 26.87 % Favored : 68.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.36 (0.23), residues: 1288 helix: -1.18 (0.98), residues: 26 sheet: 0.86 (0.21), residues: 602 loop : -1.31 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 18 TYR 0.021 0.002 TYR H 60 PHE 0.024 0.002 PHE F 70 TRP 0.013 0.001 TRP H 47 HIS 0.004 0.001 HIS I 80 Details of bonding type rmsd covalent geometry : bond 0.00348 (10475) covalent geometry : angle 0.67924 (14232) SS BOND : bond 0.00749 ( 12) SS BOND : angle 0.93878 ( 24) hydrogen bonds : bond 0.03449 ( 338) hydrogen bonds : angle 5.81980 ( 891) link_BETA1-4 : bond 0.00354 ( 3) link_BETA1-4 : angle 1.79542 ( 9) link_NAG-ASN : bond 0.00637 ( 10) link_NAG-ASN : angle 3.50604 ( 30) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 193 time to evaluate : 0.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 103 ARG cc_start: 0.9365 (OUTLIER) cc_final: 0.8080 (mmp80) REVERT: E 189 MET cc_start: 0.8990 (mmt) cc_final: 0.8431 (tpt) REVERT: F 74 ASP cc_start: 0.8773 (t0) cc_final: 0.8461 (t0) REVERT: I 98 ASP cc_start: 0.8299 (t0) cc_final: 0.8061 (t0) REVERT: I 154 ILE cc_start: 0.8372 (mm) cc_final: 0.7918 (mm) REVERT: J 66 ASP cc_start: 0.8566 (p0) cc_final: 0.8299 (p0) REVERT: J 90 ASP cc_start: 0.8679 (p0) cc_final: 0.8427 (p0) REVERT: J 115 THR cc_start: 0.8881 (OUTLIER) cc_final: 0.8565 (p) REVERT: J 216 LYS cc_start: 0.8960 (mmmm) cc_final: 0.8717 (mmmm) REVERT: J 217 LYS cc_start: 0.7927 (pptt) cc_final: 0.7525 (pptt) REVERT: J 221 ARG cc_start: 0.8089 (mmt-90) cc_final: 0.7716 (mmt-90) REVERT: K 128 GLN cc_start: 0.7731 (pt0) cc_final: 0.7356 (pp30) REVERT: K 143 PHE cc_start: 0.7480 (p90) cc_final: 0.7269 (p90) REVERT: K 198 CYS cc_start: 0.7240 (OUTLIER) cc_final: 0.6983 (t) outliers start: 57 outliers final: 53 residues processed: 241 average time/residue: 0.1085 time to fit residues: 36.1546 Evaluate side-chains 243 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 187 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain E residue 86 ASN Chi-restraints excluded: chain E residue 103 ARG Chi-restraints excluded: chain E residue 177 THR Chi-restraints excluded: chain E residue 194 ASN Chi-restraints excluded: chain E residue 197 LEU Chi-restraints excluded: chain F residue 18 ASN Chi-restraints excluded: chain F residue 41 SER Chi-restraints excluded: chain F residue 54 ARG Chi-restraints excluded: chain F residue 76 SER Chi-restraints excluded: chain F residue 104 SER Chi-restraints excluded: chain F residue 124 SER Chi-restraints excluded: chain F residue 211 SER Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 171 VAL Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain H residue 184 THR Chi-restraints excluded: chain H residue 196 TRP Chi-restraints excluded: chain H residue 215 ASP Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain I residue 136 VAL Chi-restraints excluded: chain I residue 169 ASP Chi-restraints excluded: chain I residue 175 SER Chi-restraints excluded: chain I residue 180 SER Chi-restraints excluded: chain J residue 46 GLU Chi-restraints excluded: chain J residue 50 GLU Chi-restraints excluded: chain J residue 76 LYS Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 83 MET Chi-restraints excluded: chain J residue 93 LEU Chi-restraints excluded: chain J residue 115 THR Chi-restraints excluded: chain J residue 118 THR Chi-restraints excluded: chain J residue 120 SER Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain J residue 135 VAL Chi-restraints excluded: chain J residue 149 LEU Chi-restraints excluded: chain J residue 190 THR Chi-restraints excluded: chain J residue 202 THR Chi-restraints excluded: chain J residue 218 ILE Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 34 ASP Chi-restraints excluded: chain K residue 77 LEU Chi-restraints excluded: chain K residue 120 SER Chi-restraints excluded: chain K residue 140 LEU Chi-restraints excluded: chain K residue 154 ILE Chi-restraints excluded: chain K residue 165 ASN Chi-restraints excluded: chain K residue 198 CYS Chi-restraints excluded: chain K residue 209 ILE Chi-restraints excluded: chain K residue 210 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 99 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 45 optimal weight: 0.0670 chunk 17 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 121 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 overall best weight: 1.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 85 HIS F 90 GLN I 149 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.051416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2471 r_free = 0.2471 target = 0.039953 restraints weight = 33174.088| |-----------------------------------------------------------------------------| r_work (start): 0.2465 rms_B_bonded: 2.68 r_work: 0.2361 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2249 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8942 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 10500 Z= 0.247 Angle : 0.788 10.073 14295 Z= 0.403 Chirality : 0.050 0.322 1611 Planarity : 0.006 0.080 1812 Dihedral : 7.298 60.666 1682 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 5.34 % Allowed : 26.51 % Favored : 68.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.45 (0.23), residues: 1288 helix: -1.08 (1.00), residues: 26 sheet: 0.76 (0.21), residues: 609 loop : -1.36 (0.23), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG I 18 TYR 0.020 0.003 TYR H 95 PHE 0.024 0.003 PHE F 70 TRP 0.015 0.002 TRP J 33 HIS 0.009 0.001 HIS I 80 Details of bonding type rmsd covalent geometry : bond 0.00598 (10475) covalent geometry : angle 0.76659 (14232) SS BOND : bond 0.01149 ( 12) SS BOND : angle 1.49123 ( 24) hydrogen bonds : bond 0.04290 ( 338) hydrogen bonds : angle 6.16088 ( 891) link_BETA1-4 : bond 0.00214 ( 3) link_BETA1-4 : angle 2.19150 ( 9) link_NAG-ASN : bond 0.00620 ( 10) link_NAG-ASN : angle 3.69175 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2490.62 seconds wall clock time: 43 minutes 35.14 seconds (2615.14 seconds total)