Starting phenix.real_space_refine on Mon Jul 28 09:39:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jq6_61724/07_2025/9jq6_61724.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jq6_61724/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9jq6_61724/07_2025/9jq6_61724.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jq6_61724/07_2025/9jq6_61724.map" model { file = "/net/cci-nas-00/data/ceres_data/9jq6_61724/07_2025/9jq6_61724.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jq6_61724/07_2025/9jq6_61724.cif" } resolution = 3.34 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.033 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 7.35, per 1000 atoms: 0.72 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: 2.37 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.76 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: 3.06 Time building geometry restraints manager: 2.84 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 215 or resid 601 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: 7.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.430 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 26.950 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.000 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.012 0.002 TRP I 152 HIS 0.003 0.001 HIS F 24 PHE 0.021 0.002 PHE K 143 TYR 0.038 0.002 TYR H 130 ARG 0.005 0.000 ARG F 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00614 ( 10) link_NAG-ASN : angle 5.19786 ( 30) link_BETA1-4 : bond 0.00347 ( 3) link_BETA1-4 : angle 1.39356 ( 9) hydrogen bonds : bond 0.17500 ( 338) hydrogen bonds : angle 7.26082 ( 891) SS BOND : bond 0.01033 ( 12) SS BOND : angle 1.31017 ( 24) covalent geometry : bond 0.00495 (10475) covalent geometry : angle 0.79276 (14232) *********************** 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 : 1.183 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: 0.2618 time to fit residues: 71.3046 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 : 1.386 ------------------------------------------------------------------------------- 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 107 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 64 optimal weight: 0.0050 chunk 51 optimal weight: 0.9990 chunk 99 optimal weight: 0.5980 chunk 38 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 chunk 74 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 overall best weight: 0.8798 ------------------------------------------------------------------------------- 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 149 ASN I 161 ASN J 99 GLN J 172 HIS J 207 HIS K 149 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.052642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2502 r_free = 0.2502 target = 0.041141 restraints weight = 32945.652| |-----------------------------------------------------------------------------| r_work (start): 0.2496 rms_B_bonded: 2.66 r_work: 0.2393 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2280 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8920 moved from start: 0.0834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 10500 Z= 0.192 Angle : 0.710 9.807 14295 Z= 0.363 Chirality : 0.048 0.327 1611 Planarity : 0.006 0.059 1812 Dihedral : 8.222 75.035 1702 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 4.00 % Allowed : 25.62 % Favored : 70.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.23), residues: 1288 helix: -1.32 (0.95), residues: 26 sheet: 0.78 (0.21), residues: 601 loop : -1.39 (0.23), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP I 167 HIS 0.004 0.001 HIS E 24 PHE 0.017 0.002 PHE J 154 TYR 0.017 0.002 TYR E 50 ARG 0.006 0.000 ARG I 159 Details of bonding type rmsd link_NAG-ASN : bond 0.00815 ( 10) link_NAG-ASN : angle 3.72583 ( 30) link_BETA1-4 : bond 0.00264 ( 3) link_BETA1-4 : angle 1.44782 ( 9) hydrogen bonds : bond 0.04394 ( 338) hydrogen bonds : angle 6.51888 ( 891) SS BOND : bond 0.01019 ( 12) SS BOND : angle 1.26779 ( 24) covalent geometry : bond 0.00451 (10475) covalent geometry : angle 0.68802 (14232) *********************** 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 234 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 189 time to evaluate : 1.205 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: 0.9378 (OUTLIER) cc_final: 0.8055 (mmp80) REVERT: E 189 MET cc_start: 0.9014 (mmt) cc_final: 0.8471 (mmt) REVERT: F 74 ASP cc_start: 0.8770 (t0) cc_final: 0.8570 (t0) REVERT: H 130 TYR cc_start: 0.8584 (m-80) cc_final: 0.8070 (m-80) REVERT: J 217 LYS cc_start: 0.7814 (pptt) cc_final: 0.6994 (pptt) REVERT: K 147 ASP cc_start: 0.8384 (p0) cc_final: 0.8175 (p0) outliers start: 45 outliers final: 22 residues processed: 223 average time/residue: 0.2373 time to fit residues: 72.5820 Evaluate side-chains 203 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 180 time to evaluate : 1.083 ------------------------------------------------------------------------------- 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 H residue 21 SER Chi-restraints excluded: chain H residue 83 MET 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 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 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 32 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 ** 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 = 0.2809 r_free = 0.2809 target = 0.051740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2476 r_free = 0.2476 target = 0.040284 restraints weight = 33217.313| |-----------------------------------------------------------------------------| r_work (start): 0.2471 rms_B_bonded: 2.66 r_work: 0.2367 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2254 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8939 moved from start: 0.1132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 10500 Z= 0.227 Angle : 0.728 10.145 14295 Z= 0.372 Chirality : 0.049 0.320 1611 Planarity : 0.005 0.047 1812 Dihedral : 7.765 61.623 1685 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 4.72 % Allowed : 26.25 % Favored : 69.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.23), residues: 1288 helix: -1.16 (0.99), residues: 26 sheet: 0.79 (0.21), residues: 603 loop : -1.34 (0.23), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP H 33 HIS 0.004 0.001 HIS E 24 PHE 0.019 0.002 PHE I 143 TYR 0.019 0.002 TYR H 60 ARG 0.003 0.000 ARG F 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00664 ( 10) link_NAG-ASN : angle 3.82722 ( 30) link_BETA1-4 : bond 0.00226 ( 3) link_BETA1-4 : angle 1.86581 ( 9) hydrogen bonds : bond 0.04427 ( 338) hydrogen bonds : angle 6.36052 ( 891) SS BOND : bond 0.01062 ( 12) SS BOND : angle 1.40027 ( 24) covalent geometry : bond 0.00542 (10475) covalent geometry : angle 0.70372 (14232) *********************** 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 246 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 193 time to evaluate : 1.155 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: E 103 ARG cc_start: 0.9381 (OUTLIER) cc_final: 0.8057 (mmp80) REVERT: E 189 MET cc_start: 0.9000 (mmt) cc_final: 0.8323 (tpt) REVERT: F 74 ASP cc_start: 0.8770 (t0) cc_final: 0.8419 (t0) REVERT: H 181 ASP cc_start: 0.8531 (t70) cc_final: 0.8318 (t0) REVERT: I 154 ILE cc_start: 0.8534 (mm) cc_final: 0.8256 (mm) REVERT: J 51 ILE cc_start: 0.9174 (OUTLIER) cc_final: 0.8973 (tp) REVERT: J 66 ASP cc_start: 0.8542 (p0) cc_final: 0.8332 (p0) REVERT: J 90 ASP cc_start: 0.8762 (p0) cc_final: 0.8537 (p0) REVERT: K 128 GLN cc_start: 0.7621 (pt0) cc_final: 0.7367 (pt0) REVERT: K 147 ASP cc_start: 0.8366 (p0) cc_final: 0.8091 (p0) outliers start: 53 outliers final: 36 residues processed: 235 average time/residue: 0.2401 time to fit residues: 77.7236 Evaluate side-chains 217 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 179 time to evaluate : 1.156 ------------------------------------------------------------------------------- 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 F residue 61 MET Chi-restraints excluded: chain F residue 71 VAL 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 71 SER Chi-restraints excluded: chain H residue 83 MET 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 51 ILE 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 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 109 optimal weight: 0.9990 chunk 56 optimal weight: 0.9980 chunk 47 optimal weight: 0.4980 chunk 114 optimal weight: 0.0980 chunk 88 optimal weight: 0.4980 chunk 54 optimal weight: 0.9980 chunk 62 optimal weight: 0.7980 chunk 118 optimal weight: 0.9980 chunk 41 optimal weight: 0.8980 chunk 15 optimal weight: 4.9990 chunk 91 optimal weight: 0.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 85 HIS I 149 ASN ** 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 = 0.2842 r_free = 0.2842 target = 0.053048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2516 r_free = 0.2516 target = 0.041601 restraints weight = 32619.838| |-----------------------------------------------------------------------------| r_work (start): 0.2510 rms_B_bonded: 2.64 r_work: 0.2409 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2298 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8909 moved from start: 0.1261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10500 Z= 0.143 Angle : 0.664 9.860 14295 Z= 0.335 Chirality : 0.047 0.331 1611 Planarity : 0.005 0.047 1812 Dihedral : 7.304 61.747 1685 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 4.00 % Allowed : 27.05 % Favored : 68.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.23), residues: 1288 helix: -1.10 (1.00), residues: 26 sheet: 0.90 (0.21), residues: 597 loop : -1.30 (0.23), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 47 HIS 0.003 0.001 HIS E 24 PHE 0.017 0.002 PHE J 154 TYR 0.020 0.002 TYR F 50 ARG 0.004 0.000 ARG I 159 Details of bonding type rmsd link_NAG-ASN : bond 0.00654 ( 10) link_NAG-ASN : angle 3.66678 ( 30) link_BETA1-4 : bond 0.00327 ( 3) link_BETA1-4 : angle 1.69564 ( 9) hydrogen bonds : bond 0.03590 ( 338) hydrogen bonds : angle 6.01067 ( 891) SS BOND : bond 0.00765 ( 12) SS BOND : angle 0.99831 ( 24) covalent geometry : bond 0.00335 (10475) covalent geometry : angle 0.64094 (14232) *********************** 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 239 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 194 time to evaluate : 1.098 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: 0.7861 (mm-30) cc_final: 0.7491 (mp0) REVERT: E 103 ARG cc_start: 0.9366 (OUTLIER) cc_final: 0.8088 (mmp80) REVERT: E 189 MET cc_start: 0.8974 (mmt) cc_final: 0.8538 (mmt) REVERT: F 74 ASP cc_start: 0.8736 (t0) cc_final: 0.8456 (t0) REVERT: H 181 ASP cc_start: 0.8499 (t70) cc_final: 0.8266 (t0) REVERT: J 90 ASP cc_start: 0.8667 (p0) cc_final: 0.8393 (p0) REVERT: J 217 LYS cc_start: 0.7542 (pptt) cc_final: 0.7322 (pptt) REVERT: K 128 GLN cc_start: 0.7634 (pt0) cc_final: 0.7283 (pp30) REVERT: K 147 ASP cc_start: 0.8317 (p0) cc_final: 0.8012 (p0) REVERT: K 177 TYR cc_start: 0.9204 (m-80) cc_final: 0.8826 (m-80) outliers start: 45 outliers final: 34 residues processed: 230 average time/residue: 0.2441 time to fit residues: 75.7898 Evaluate side-chains 221 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 186 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 21 LEU 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 18 ASN Chi-restraints excluded: chain F residue 54 ARG Chi-restraints excluded: chain F residue 71 VAL 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 55 SER Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 93 LEU 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 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 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 140 LEU 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 103 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 68 optimal weight: 0.0000 chunk 94 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 84 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 96 optimal weight: 2.9990 overall best weight: 1.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 149 ASN ** I 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 149 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.052058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2487 r_free = 0.2487 target = 0.040674 restraints weight = 32467.864| |-----------------------------------------------------------------------------| r_work (start): 0.2481 rms_B_bonded: 2.60 r_work: 0.2380 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2267 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8949 moved from start: 0.1353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 10500 Z= 0.226 Angle : 0.722 10.125 14295 Z= 0.367 Chirality : 0.049 0.323 1611 Planarity : 0.005 0.045 1812 Dihedral : 7.254 61.270 1683 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 5.52 % Allowed : 25.98 % Favored : 68.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.23), residues: 1288 helix: -1.14 (0.99), residues: 26 sheet: 0.79 (0.21), residues: 607 loop : -1.34 (0.23), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP H 33 HIS 0.004 0.001 HIS E 24 PHE 0.020 0.002 PHE I 143 TYR 0.018 0.002 TYR H 60 ARG 0.003 0.000 ARG I 159 Details of bonding type rmsd link_NAG-ASN : bond 0.00653 ( 10) link_NAG-ASN : angle 3.79350 ( 30) link_BETA1-4 : bond 0.00213 ( 3) link_BETA1-4 : angle 2.02468 ( 9) hydrogen bonds : bond 0.04235 ( 338) hydrogen bonds : angle 6.20010 ( 891) SS BOND : bond 0.01109 ( 12) SS BOND : angle 1.46939 ( 24) covalent geometry : bond 0.00542 (10475) covalent geometry : angle 0.69772 (14232) *********************** 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 250 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 188 time to evaluate : 1.236 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: 0.7878 (mm-30) cc_final: 0.7567 (mp0) REVERT: E 103 ARG cc_start: 0.9363 (OUTLIER) cc_final: 0.8068 (mmp80) REVERT: E 189 MET cc_start: 0.9040 (mmt) cc_final: 0.8385 (tpt) REVERT: F 161 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8848 (tt) REVERT: H 181 ASP cc_start: 0.8514 (t70) cc_final: 0.8284 (t0) REVERT: I 154 ILE cc_start: 0.8543 (mm) cc_final: 0.8092 (mm) REVERT: J 51 ILE cc_start: 0.9187 (OUTLIER) cc_final: 0.8935 (tp) REVERT: K 128 GLN cc_start: 0.7811 (pt0) cc_final: 0.7506 (pp30) REVERT: K 147 ASP cc_start: 0.8300 (p0) cc_final: 0.8009 (p0) REVERT: K 177 TYR cc_start: 0.9243 (m-80) cc_final: 0.8889 (m-80) REVERT: K 198 CYS cc_start: 0.7035 (OUTLIER) cc_final: 0.6760 (t) outliers start: 62 outliers final: 45 residues processed: 240 average time/residue: 0.2393 time to fit residues: 78.6231 Evaluate side-chains 229 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 180 time to evaluate : 1.104 ------------------------------------------------------------------------------- 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 71 VAL 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 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 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 51 ILE 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 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 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 77 optimal weight: 0.8980 chunk 57 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 40 optimal weight: 0.5980 chunk 81 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 45 optimal weight: 0.5980 chunk 103 optimal weight: 0.1980 chunk 116 optimal weight: 0.0970 overall best weight: 0.4578 ------------------------------------------------------------------------------- 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** E 85 HIS F 85 HIS I 149 ASN J 204 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 = 0.2864 r_free = 0.2864 target = 0.053871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2539 r_free = 0.2539 target = 0.042421 restraints weight = 32380.255| |-----------------------------------------------------------------------------| r_work (start): 0.2532 rms_B_bonded: 2.59 r_work: 0.2433 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2322 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8908 moved from start: 0.1439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10500 Z= 0.130 Angle : 0.654 9.586 14295 Z= 0.330 Chirality : 0.047 0.335 1611 Planarity : 0.005 0.047 1812 Dihedral : 6.928 61.589 1683 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 4.89 % Allowed : 26.16 % Favored : 68.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.23), residues: 1288 helix: -1.07 (1.00), residues: 26 sheet: 0.87 (0.21), residues: 600 loop : -1.30 (0.23), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 47 HIS 0.003 0.001 HIS E 24 PHE 0.016 0.001 PHE J 154 TYR 0.020 0.002 TYR H 130 ARG 0.003 0.000 ARG J 221 Details of bonding type rmsd link_NAG-ASN : bond 0.00646 ( 10) link_NAG-ASN : angle 3.55871 ( 30) link_BETA1-4 : bond 0.00413 ( 3) link_BETA1-4 : angle 1.77067 ( 9) hydrogen bonds : bond 0.03368 ( 338) hydrogen bonds : angle 5.86014 ( 891) SS BOND : bond 0.00681 ( 12) SS BOND : angle 0.99601 ( 24) covalent geometry : bond 0.00305 (10475) covalent geometry : angle 0.63179 (14232) *********************** 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 253 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 198 time to evaluate : 1.099 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 32 GLU cc_start: 0.7841 (mm-30) cc_final: 0.7613 (mp0) REVERT: E 103 ARG cc_start: 0.9352 (OUTLIER) cc_final: 0.8085 (mmp80) REVERT: E 189 MET cc_start: 0.8969 (mmt) cc_final: 0.8394 (tpt) REVERT: F 74 ASP cc_start: 0.8705 (t0) cc_final: 0.8395 (t0) REVERT: F 164 VAL cc_start: 0.8377 (OUTLIER) cc_final: 0.8177 (t) REVERT: H 181 ASP cc_start: 0.8363 (t70) cc_final: 0.8146 (t0) REVERT: I 98 ASP cc_start: 0.8273 (t0) cc_final: 0.8046 (t0) REVERT: I 154 ILE cc_start: 0.8543 (mm) cc_final: 0.8135 (mm) REVERT: J 109 ASP cc_start: 0.8846 (p0) cc_final: 0.8644 (p0) REVERT: J 217 LYS cc_start: 0.7786 (pptt) cc_final: 0.7530 (pptt) REVERT: K 128 GLN cc_start: 0.7879 (pt0) cc_final: 0.7539 (pp30) REVERT: K 147 ASP cc_start: 0.8215 (p0) cc_final: 0.7919 (p0) REVERT: K 177 TYR cc_start: 0.9232 (m-80) cc_final: 0.8907 (m-80) REVERT: K 198 CYS cc_start: 0.7051 (OUTLIER) cc_final: 0.6791 (t) outliers start: 55 outliers final: 44 residues processed: 243 average time/residue: 0.2347 time to fit residues: 78.0352 Evaluate side-chains 233 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 186 time to evaluate : 1.089 ------------------------------------------------------------------------------- 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 54 ARG Chi-restraints excluded: chain F residue 71 VAL 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 164 VAL Chi-restraints excluded: chain F residue 211 SER Chi-restraints excluded: chain H residue 21 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 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 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 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 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 50 optimal weight: 0.6980 chunk 58 optimal weight: 2.9990 chunk 67 optimal weight: 0.6980 chunk 55 optimal weight: 0.9990 chunk 103 optimal weight: 0.9990 chunk 76 optimal weight: 0.9980 chunk 85 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 123 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 149 ASN K 149 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.052418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2497 r_free = 0.2497 target = 0.040899 restraints weight = 33355.933| |-----------------------------------------------------------------------------| r_work (start): 0.2492 rms_B_bonded: 2.69 r_work: 0.2389 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2276 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8922 moved from start: 0.1449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10500 Z= 0.178 Angle : 0.691 9.760 14295 Z= 0.350 Chirality : 0.048 0.323 1611 Planarity : 0.005 0.045 1812 Dihedral : 6.960 60.951 1682 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 5.60 % Allowed : 26.07 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.23), residues: 1288 helix: -1.00 (1.01), residues: 26 sheet: 0.88 (0.21), residues: 599 loop : -1.30 (0.23), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP H 33 HIS 0.004 0.001 HIS E 24 PHE 0.016 0.002 PHE J 154 TYR 0.025 0.002 TYR H 130 ARG 0.003 0.000 ARG I 159 Details of bonding type rmsd link_NAG-ASN : bond 0.00604 ( 10) link_NAG-ASN : angle 3.65819 ( 30) link_BETA1-4 : bond 0.00205 ( 3) link_BETA1-4 : angle 1.88231 ( 9) hydrogen bonds : bond 0.03744 ( 338) hydrogen bonds : angle 5.92529 ( 891) SS BOND : bond 0.00929 ( 12) SS BOND : angle 1.19163 ( 24) covalent geometry : bond 0.00426 (10475) covalent geometry : angle 0.66830 (14232) *********************** 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 251 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 188 time to evaluate : 1.172 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: 0.7952 (mm-30) cc_final: 0.7730 (mp0) REVERT: E 103 ARG cc_start: 0.9378 (OUTLIER) cc_final: 0.8122 (mmp80) REVERT: E 189 MET cc_start: 0.8984 (mmt) cc_final: 0.8435 (tpt) REVERT: F 74 ASP cc_start: 0.8738 (t0) cc_final: 0.8522 (t0) REVERT: H 181 ASP cc_start: 0.8397 (t70) cc_final: 0.8172 (t0) REVERT: J 115 THR cc_start: 0.8941 (OUTLIER) cc_final: 0.8637 (p) REVERT: J 217 LYS cc_start: 0.7910 (pptt) cc_final: 0.7575 (pptt) REVERT: K 128 GLN cc_start: 0.7897 (pt0) cc_final: 0.7644 (pp30) REVERT: K 147 ASP cc_start: 0.8267 (p0) cc_final: 0.7970 (p0) REVERT: K 198 CYS cc_start: 0.7062 (OUTLIER) cc_final: 0.6790 (t) outliers start: 63 outliers final: 55 residues processed: 239 average time/residue: 0.2585 time to fit residues: 84.3731 Evaluate side-chains 241 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 183 time to evaluate : 1.037 ------------------------------------------------------------------------------- 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 26 SER Chi-restraints excluded: chain F residue 41 SER Chi-restraints excluded: chain F residue 54 ARG Chi-restraints excluded: chain F residue 71 VAL 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 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 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 16 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 69 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 90 optimal weight: 0.7980 chunk 89 optimal weight: 0.6980 chunk 14 optimal weight: 0.5980 chunk 28 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 149 ASN K 149 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.052574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2502 r_free = 0.2502 target = 0.041041 restraints weight = 33133.329| |-----------------------------------------------------------------------------| r_work (start): 0.2496 rms_B_bonded: 2.69 r_work: 0.2395 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2284 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8916 moved from start: 0.1540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10500 Z= 0.169 Angle : 0.694 9.696 14295 Z= 0.352 Chirality : 0.048 0.327 1611 Planarity : 0.005 0.089 1812 Dihedral : 6.978 60.992 1682 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 5.78 % Allowed : 26.16 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.23), residues: 1288 helix: -1.01 (1.00), residues: 26 sheet: 0.92 (0.21), residues: 599 loop : -1.33 (0.23), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP H 33 HIS 0.004 0.001 HIS E 24 PHE 0.026 0.002 PHE F 70 TYR 0.021 0.002 TYR H 60 ARG 0.014 0.000 ARG I 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00610 ( 10) link_NAG-ASN : angle 3.60364 ( 30) link_BETA1-4 : bond 0.00133 ( 3) link_BETA1-4 : angle 1.93963 ( 9) hydrogen bonds : bond 0.03666 ( 338) hydrogen bonds : angle 5.89587 ( 891) SS BOND : bond 0.00890 ( 12) SS BOND : angle 1.09263 ( 24) covalent geometry : bond 0.00405 (10475) covalent geometry : angle 0.67213 (14232) *********************** 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: 65 poor density : 190 time to evaluate : 1.067 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: 0.9376 (OUTLIER) cc_final: 0.8110 (mmp80) REVERT: E 189 MET cc_start: 0.8988 (mmt) cc_final: 0.8411 (tpt) REVERT: F 58 GLU cc_start: 0.8391 (tp30) cc_final: 0.8188 (tp30) REVERT: F 74 ASP cc_start: 0.8746 (t0) cc_final: 0.8540 (t0) REVERT: F 164 VAL cc_start: 0.8427 (OUTLIER) cc_final: 0.8223 (t) REVERT: H 181 ASP cc_start: 0.8388 (t70) cc_final: 0.8165 (t0) REVERT: I 98 ASP cc_start: 0.8355 (t0) cc_final: 0.8119 (t0) REVERT: I 154 ILE cc_start: 0.8618 (mm) cc_final: 0.8197 (mm) REVERT: J 115 THR cc_start: 0.8928 (OUTLIER) cc_final: 0.8633 (p) REVERT: J 217 LYS cc_start: 0.7892 (pptt) cc_final: 0.7631 (pptt) REVERT: K 128 GLN cc_start: 0.7893 (pt0) cc_final: 0.7628 (pp30) REVERT: K 147 ASP cc_start: 0.8254 (p0) cc_final: 0.7960 (p0) REVERT: K 198 CYS cc_start: 0.7003 (OUTLIER) cc_final: 0.6750 (t) outliers start: 65 outliers final: 55 residues processed: 243 average time/residue: 0.2324 time to fit residues: 77.2631 Evaluate side-chains 245 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 186 time to evaluate : 1.162 ------------------------------------------------------------------------------- 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 26 SER Chi-restraints excluded: chain F residue 41 SER Chi-restraints excluded: chain F residue 54 ARG Chi-restraints excluded: chain F residue 71 VAL 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 164 VAL 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 98 optimal weight: 0.7980 chunk 97 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 103 optimal weight: 3.9990 chunk 125 optimal weight: 0.9990 chunk 72 optimal weight: 0.9990 chunk 71 optimal weight: 0.0770 chunk 122 optimal weight: 0.2980 chunk 6 optimal weight: 0.1980 chunk 40 optimal weight: 0.0870 chunk 55 optimal weight: 0.0020 overall best weight: 0.1324 ------------------------------------------------------------------------------- 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 17 GLN K 149 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.055254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2582 r_free = 0.2582 target = 0.043760 restraints weight = 33065.765| |-----------------------------------------------------------------------------| r_work (start): 0.2573 rms_B_bonded: 2.69 r_work: 0.2474 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2363 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8860 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10500 Z= 0.110 Angle : 0.643 9.380 14295 Z= 0.323 Chirality : 0.046 0.330 1611 Planarity : 0.005 0.048 1812 Dihedral : 6.631 60.360 1682 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 4.09 % Allowed : 28.02 % Favored : 67.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.23), residues: 1288 helix: -1.40 (0.92), residues: 26 sheet: 0.90 (0.21), residues: 604 loop : -1.17 (0.24), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP H 47 HIS 0.002 0.000 HIS F 24 PHE 0.015 0.001 PHE F 70 TYR 0.020 0.001 TYR F 50 ARG 0.009 0.000 ARG I 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00669 ( 10) link_NAG-ASN : angle 3.37029 ( 30) link_BETA1-4 : bond 0.00410 ( 3) link_BETA1-4 : angle 1.38396 ( 9) hydrogen bonds : bond 0.02881 ( 338) hydrogen bonds : angle 5.50717 ( 891) SS BOND : bond 0.00441 ( 12) SS BOND : angle 0.67817 ( 24) covalent geometry : bond 0.00256 (10475) covalent geometry : angle 0.62353 (14232) *********************** 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 246 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 200 time to evaluate : 1.234 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 189 MET cc_start: 0.8907 (mmt) cc_final: 0.8330 (tpt) REVERT: F 58 GLU cc_start: 0.8287 (tp30) cc_final: 0.8035 (tm-30) REVERT: F 74 ASP cc_start: 0.8719 (t0) cc_final: 0.8460 (t0) REVERT: I 98 ASP cc_start: 0.8260 (t0) cc_final: 0.8045 (t0) REVERT: J 66 ASP cc_start: 0.8444 (p0) cc_final: 0.8209 (p0) REVERT: J 217 LYS cc_start: 0.7950 (pptt) cc_final: 0.7723 (pptt) REVERT: K 128 GLN cc_start: 0.7906 (pt0) cc_final: 0.7606 (pp30) REVERT: K 143 PHE cc_start: 0.7168 (p90) cc_final: 0.6740 (p90) REVERT: K 147 ASP cc_start: 0.8131 (p0) cc_final: 0.7918 (p0) outliers start: 46 outliers final: 35 residues processed: 234 average time/residue: 0.2320 time to fit residues: 74.6027 Evaluate side-chains 222 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 187 time to evaluate : 1.184 ------------------------------------------------------------------------------- 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 177 THR Chi-restraints excluded: chain E residue 194 ASN Chi-restraints excluded: chain F residue 18 ASN Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 54 ARG Chi-restraints excluded: chain F residue 71 VAL 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 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 175 SER 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 100 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 26 optimal weight: 0.3980 chunk 22 optimal weight: 0.8980 chunk 106 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 chunk 9 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 85 HIS I 149 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.053565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2529 r_free = 0.2529 target = 0.041941 restraints weight = 33092.317| |-----------------------------------------------------------------------------| r_work (start): 0.2522 rms_B_bonded: 2.72 r_work: 0.2420 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2307 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8901 moved from start: 0.1692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10500 Z= 0.161 Angle : 0.694 9.473 14295 Z= 0.353 Chirality : 0.047 0.321 1611 Planarity : 0.005 0.056 1812 Dihedral : 6.769 59.669 1682 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 3.74 % Allowed : 27.67 % Favored : 68.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.23), residues: 1288 helix: -1.19 (0.97), residues: 26 sheet: 0.96 (0.21), residues: 597 loop : -1.18 (0.24), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP H 47 HIS 0.003 0.001 HIS E 24 PHE 0.027 0.002 PHE F 70 TYR 0.019 0.002 TYR H 60 ARG 0.014 0.000 ARG I 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00607 ( 10) link_NAG-ASN : angle 3.45500 ( 30) link_BETA1-4 : bond 0.00262 ( 3) link_BETA1-4 : angle 1.70631 ( 9) hydrogen bonds : bond 0.03483 ( 338) hydrogen bonds : angle 5.70338 ( 891) SS BOND : bond 0.00827 ( 12) SS BOND : angle 1.26545 ( 24) covalent geometry : bond 0.00386 (10475) covalent geometry : angle 0.67388 (14232) ********************** 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 234 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 192 time to evaluate : 1.079 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 189 MET cc_start: 0.8981 (mmt) cc_final: 0.8435 (tpt) REVERT: F 58 GLU cc_start: 0.8371 (tp30) cc_final: 0.8160 (tm-30) REVERT: F 74 ASP cc_start: 0.8757 (t0) cc_final: 0.8533 (t0) REVERT: I 154 ILE cc_start: 0.8651 (mm) cc_final: 0.8202 (mm) REVERT: J 46 GLU cc_start: 0.8623 (mt-10) cc_final: 0.8295 (pt0) REVERT: J 216 LYS cc_start: 0.9005 (mmmm) cc_final: 0.8787 (mmmm) REVERT: J 217 LYS cc_start: 0.7993 (pptt) cc_final: 0.7755 (pptt) REVERT: K 128 GLN cc_start: 0.7968 (pt0) cc_final: 0.7757 (pp30) REVERT: K 199 GLU cc_start: 0.7738 (pm20) cc_final: 0.7408 (pm20) outliers start: 42 outliers final: 39 residues processed: 224 average time/residue: 0.2533 time to fit residues: 77.4590 Evaluate side-chains 230 residues out of total 1124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 191 time to evaluate : 1.103 ------------------------------------------------------------------------------- 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 177 THR Chi-restraints excluded: chain E residue 194 ASN Chi-restraints excluded: chain F residue 18 ASN Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 54 ARG Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 76 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 93 LEU 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 175 SER 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 103 PHE 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 22 optimal weight: 0.4980 chunk 101 optimal weight: 0.4980 chunk 5 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 96 optimal weight: 4.9990 chunk 112 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 123 optimal weight: 0.9980 chunk 46 optimal weight: 0.0170 chunk 63 optimal weight: 0.9990 overall best weight: 0.5418 ------------------------------------------------------------------------------- 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 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 = 0.2866 r_free = 0.2866 target = 0.053776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2535 r_free = 0.2535 target = 0.042141 restraints weight = 32769.872| |-----------------------------------------------------------------------------| r_work (start): 0.2528 rms_B_bonded: 2.71 r_work: 0.2426 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2314 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8897 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10500 Z= 0.144 Angle : 0.692 9.449 14295 Z= 0.352 Chirality : 0.047 0.325 1611 Planarity : 0.005 0.075 1812 Dihedral : 6.817 59.767 1682 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 3.65 % Allowed : 28.29 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.23), residues: 1288 helix: -1.19 (0.97), residues: 26 sheet: 0.90 (0.21), residues: 605 loop : -1.18 (0.24), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 47 HIS 0.003 0.001 HIS E 24 PHE 0.028 0.002 PHE F 70 TYR 0.021 0.002 TYR H 60 ARG 0.012 0.000 ARG I 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00617 ( 10) link_NAG-ASN : angle 3.40754 ( 30) link_BETA1-4 : bond 0.00306 ( 3) link_BETA1-4 : angle 1.67752 ( 9) hydrogen bonds : bond 0.03362 ( 338) hydrogen bonds : angle 5.70086 ( 891) SS BOND : bond 0.00749 ( 12) SS BOND : angle 1.10226 ( 24) covalent geometry : bond 0.00342 (10475) covalent geometry : angle 0.67311 (14232) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5662.90 seconds wall clock time: 99 minutes 21.56 seconds (5961.56 seconds total)