Starting phenix.real_space_refine on Fri Jul 3 05:21:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7vlx_32030/07_2026/7vlx_32030.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vlx_32030/07_2026/7vlx_32030.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7vlx_32030/07_2026/7vlx_32030.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7vlx_32030/07_2026/7vlx_32030.cif" model { file = "/net/cci-nas-00/data/ceres_data/7vlx_32030/07_2026/7vlx_32030.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vlx_32030/07_2026/7vlx_32030.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7vlx_32030/07_2026/7vlx_32030.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vlx_32030/07_2026/7vlx_32030.map" } resolution = 3.12 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 69 5.16 5 C 8085 2.51 5 N 2022 2.21 5 O 2127 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12303 Number of models: 1 Model: "" Number of chains: 9 Chain: "Y" Number of atoms: 1773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1773 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 9, 'TRANS': 237} Chain: "Z" Number of atoms: 2316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2316 Classifications: {'peptide': 298} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 285} Chain: "A" Number of atoms: 1773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1773 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 9, 'TRANS': 237} Chain: "B" Number of atoms: 2316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2316 Classifications: {'peptide': 298} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 285} Chain: "C" Number of atoms: 1773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1773 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 9, 'TRANS': 237} Chain: "D" Number of atoms: 2316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2316 Classifications: {'peptide': 298} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 285} Chain: "Z" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'MAN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'MAN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'MAN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.86, per 1000 atoms: 0.23 Number of scatterers: 12303 At special positions: 0 Unit cell: (125.681, 117.088, 100.975, 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 69 16.00 O 2127 8.00 N 2022 7.00 C 8085 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.80 Conformation dependent library (CDL) restraints added in 574.0 milliseconds 3246 Ramachandran restraints generated. 1623 Oldfield, 0 Emsley, 1623 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2934 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 3 sheets defined 73.6% alpha, 1.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'Y' and resid 2 through 23 removed outlier: 4.185A pdb=" N ILE Y 21 " --> pdb=" O GLY Y 17 " (cutoff:3.500A) Processing helix chain 'Y' and resid 29 through 34 Processing helix chain 'Y' and resid 35 through 40 removed outlier: 3.533A pdb=" N VAL Y 40 " --> pdb=" O LEU Y 36 " (cutoff:3.500A) Processing helix chain 'Y' and resid 44 through 59 removed outlier: 4.242A pdb=" N ILE Y 49 " --> pdb=" O THR Y 45 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N LEU Y 50 " --> pdb=" O ALA Y 46 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE Y 57 " --> pdb=" O THR Y 53 " (cutoff:3.500A) Processing helix chain 'Y' and resid 73 through 86 removed outlier: 3.571A pdb=" N VAL Y 77 " --> pdb=" O ALA Y 73 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA Y 80 " --> pdb=" O SER Y 76 " (cutoff:3.500A) Processing helix chain 'Y' and resid 92 through 101 removed outlier: 3.830A pdb=" N ILE Y 101 " --> pdb=" O ILE Y 97 " (cutoff:3.500A) Processing helix chain 'Y' and resid 103 through 117 removed outlier: 4.580A pdb=" N PHE Y 109 " --> pdb=" O VAL Y 105 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N LEU Y 110 " --> pdb=" O ALA Y 106 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL Y 114 " --> pdb=" O LEU Y 110 " (cutoff:3.500A) Processing helix chain 'Y' and resid 118 through 131 removed outlier: 4.085A pdb=" N LYS Y 131 " --> pdb=" O ARG Y 127 " (cutoff:3.500A) Processing helix chain 'Y' and resid 133 through 161 removed outlier: 4.113A pdb=" N VAL Y 137 " --> pdb=" O ASN Y 133 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N GLU Y 138 " --> pdb=" O ILE Y 134 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N TRP Y 139 " --> pdb=" O ARG Y 135 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N ILE Y 142 " --> pdb=" O GLU Y 138 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ARG Y 151 " --> pdb=" O MET Y 147 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ILE Y 152 " --> pdb=" O GLN Y 148 " (cutoff:3.500A) Proline residue: Y 155 - end of helix removed outlier: 3.696A pdb=" N LEU Y 160 " --> pdb=" O ALA Y 156 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N PHE Y 161 " --> pdb=" O ALA Y 157 " (cutoff:3.500A) Processing helix chain 'Y' and resid 177 through 187 removed outlier: 3.631A pdb=" N ALA Y 183 " --> pdb=" O THR Y 179 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY Y 187 " --> pdb=" O ALA Y 183 " (cutoff:3.500A) Processing helix chain 'Y' and resid 188 through 201 removed outlier: 4.076A pdb=" N VAL Y 192 " --> pdb=" O MET Y 188 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL Y 197 " --> pdb=" O GLY Y 193 " (cutoff:3.500A) Processing helix chain 'Y' and resid 206 through 216 Processing helix chain 'Y' and resid 223 through 246 removed outlier: 3.694A pdb=" N MET Y 244 " --> pdb=" O ASN Y 240 " (cutoff:3.500A) Processing helix chain 'Z' and resid 8 through 20 removed outlier: 3.855A pdb=" N ARG Z 14 " --> pdb=" O ARG Z 10 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR Z 20 " --> pdb=" O ALA Z 16 " (cutoff:3.500A) Processing helix chain 'Z' and resid 32 through 40 removed outlier: 3.598A pdb=" N TRP Z 36 " --> pdb=" O GLN Z 32 " (cutoff:3.500A) Processing helix chain 'Z' and resid 40 through 48 Processing helix chain 'Z' and resid 53 through 61 Processing helix chain 'Z' and resid 72 through 87 removed outlier: 3.695A pdb=" N LEU Z 80 " --> pdb=" O LEU Z 76 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU Z 85 " --> pdb=" O ALA Z 81 " (cutoff:3.500A) Processing helix chain 'Z' and resid 95 through 104 removed outlier: 3.628A pdb=" N LYS Z 101 " --> pdb=" O ILE Z 97 " (cutoff:3.500A) Processing helix chain 'Z' and resid 105 through 118 Proline residue: Z 114 - end of helix Processing helix chain 'Z' and resid 119 through 133 removed outlier: 3.584A pdb=" N MET Z 123 " --> pdb=" O THR Z 119 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU Z 131 " --> pdb=" O LEU Z 127 " (cutoff:3.500A) Processing helix chain 'Z' and resid 137 through 163 Processing helix chain 'Z' and resid 165 through 170 removed outlier: 3.714A pdb=" N ILE Z 169 " --> pdb=" O ALA Z 165 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR Z 170 " --> pdb=" O GLY Z 166 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 165 through 170' Processing helix chain 'Z' and resid 179 through 200 Processing helix chain 'Z' and resid 230 through 242 Processing helix chain 'Z' and resid 252 through 259 Processing helix chain 'Z' and resid 263 through 279 Processing helix chain 'Z' and resid 282 through 301 Processing helix chain 'A' and resid 2 through 23 removed outlier: 3.501A pdb=" N ILE A 7 " --> pdb=" O VAL A 3 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ILE A 21 " --> pdb=" O GLY A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 29 through 34 Processing helix chain 'A' and resid 35 through 40 Processing helix chain 'A' and resid 44 through 59 removed outlier: 4.255A pdb=" N ILE A 49 " --> pdb=" O THR A 45 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N LEU A 50 " --> pdb=" O ALA A 46 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE A 57 " --> pdb=" O THR A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 86 removed outlier: 3.590A pdb=" N VAL A 77 " --> pdb=" O ALA A 73 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA A 80 " --> pdb=" O SER A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 101 removed outlier: 3.806A pdb=" N ILE A 101 " --> pdb=" O ILE A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 118 removed outlier: 4.535A pdb=" N PHE A 109 " --> pdb=" O VAL A 105 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N LEU A 110 " --> pdb=" O ALA A 106 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N VAL A 114 " --> pdb=" O LEU A 110 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA A 118 " --> pdb=" O VAL A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 131 removed outlier: 4.192A pdb=" N LYS A 131 " --> pdb=" O ARG A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 161 removed outlier: 4.205A pdb=" N VAL A 137 " --> pdb=" O ASN A 133 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLU A 138 " --> pdb=" O ILE A 134 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N TRP A 139 " --> pdb=" O ARG A 135 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ILE A 142 " --> pdb=" O GLU A 138 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ARG A 151 " --> pdb=" O MET A 147 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ILE A 152 " --> pdb=" O GLN A 148 " (cutoff:3.500A) Proline residue: A 155 - end of helix removed outlier: 3.655A pdb=" N LEU A 160 " --> pdb=" O ALA A 156 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N PHE A 161 " --> pdb=" O ALA A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 187 removed outlier: 3.504A pdb=" N GLY A 181 " --> pdb=" O TRP A 177 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA A 183 " --> pdb=" O THR A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 201 removed outlier: 4.235A pdb=" N VAL A 192 " --> pdb=" O MET A 188 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLY A 193 " --> pdb=" O VAL A 189 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL A 197 " --> pdb=" O GLY A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 216 Processing helix chain 'A' and resid 223 through 246 removed outlier: 3.584A pdb=" N MET A 244 " --> pdb=" O ASN A 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 20 removed outlier: 3.880A pdb=" N ARG B 14 " --> pdb=" O ARG B 10 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N THR B 20 " --> pdb=" O ALA B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 40 removed outlier: 3.533A pdb=" N TRP B 36 " --> pdb=" O GLN B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 48 Processing helix chain 'B' and resid 53 through 61 Processing helix chain 'B' and resid 72 through 87 removed outlier: 3.928A pdb=" N LEU B 80 " --> pdb=" O LEU B 76 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLU B 85 " --> pdb=" O ALA B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 104 removed outlier: 3.624A pdb=" N LYS B 101 " --> pdb=" O ILE B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 118 Proline residue: B 114 - end of helix Processing helix chain 'B' and resid 119 through 133 removed outlier: 3.670A pdb=" N MET B 123 " --> pdb=" O THR B 119 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU B 131 " --> pdb=" O LEU B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 163 Processing helix chain 'B' and resid 165 through 170 removed outlier: 3.718A pdb=" N ILE B 169 " --> pdb=" O ALA B 165 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THR B 170 " --> pdb=" O GLY B 166 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 165 through 170' Processing helix chain 'B' and resid 179 through 200 Processing helix chain 'B' and resid 230 through 242 Processing helix chain 'B' and resid 252 through 259 Processing helix chain 'B' and resid 263 through 279 Processing helix chain 'B' and resid 282 through 301 Processing helix chain 'C' and resid 2 through 23 removed outlier: 3.514A pdb=" N ILE C 7 " --> pdb=" O VAL C 3 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ILE C 21 " --> pdb=" O GLY C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 34 Processing helix chain 'C' and resid 35 through 40 removed outlier: 3.504A pdb=" N VAL C 40 " --> pdb=" O LEU C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 59 removed outlier: 4.236A pdb=" N ILE C 49 " --> pdb=" O THR C 45 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N LEU C 50 " --> pdb=" O ALA C 46 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE C 57 " --> pdb=" O THR C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 86 removed outlier: 3.572A pdb=" N VAL C 77 " --> pdb=" O ALA C 73 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA C 80 " --> pdb=" O SER C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 101 removed outlier: 3.742A pdb=" N ILE C 101 " --> pdb=" O ILE C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 117 removed outlier: 4.581A pdb=" N PHE C 109 " --> pdb=" O VAL C 105 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N LEU C 110 " --> pdb=" O ALA C 106 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL C 114 " --> pdb=" O LEU C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 131 removed outlier: 4.150A pdb=" N LYS C 131 " --> pdb=" O ARG C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 161 removed outlier: 4.169A pdb=" N VAL C 137 " --> pdb=" O ASN C 133 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N GLU C 138 " --> pdb=" O ILE C 134 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N TRP C 139 " --> pdb=" O ARG C 135 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ILE C 142 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ARG C 151 " --> pdb=" O MET C 147 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ILE C 152 " --> pdb=" O GLN C 148 " (cutoff:3.500A) Proline residue: C 155 - end of helix removed outlier: 3.687A pdb=" N LEU C 160 " --> pdb=" O ALA C 156 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N PHE C 161 " --> pdb=" O ALA C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 187 removed outlier: 3.641A pdb=" N ALA C 183 " --> pdb=" O THR C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 201 removed outlier: 4.311A pdb=" N VAL C 192 " --> pdb=" O MET C 188 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLY C 193 " --> pdb=" O VAL C 189 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL C 197 " --> pdb=" O GLY C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 216 Processing helix chain 'C' and resid 223 through 246 removed outlier: 3.660A pdb=" N MET C 244 " --> pdb=" O ASN C 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 20 removed outlier: 3.844A pdb=" N ARG D 14 " --> pdb=" O ARG D 10 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR D 20 " --> pdb=" O ALA D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 40 Processing helix chain 'D' and resid 40 through 48 Processing helix chain 'D' and resid 53 through 61 Processing helix chain 'D' and resid 72 through 88 removed outlier: 4.009A pdb=" N LEU D 80 " --> pdb=" O LEU D 76 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLU D 85 " --> pdb=" O ALA D 81 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ASN D 88 " --> pdb=" O GLU D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 104 removed outlier: 3.775A pdb=" N LYS D 101 " --> pdb=" O ILE D 97 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N MET D 104 " --> pdb=" O VAL D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 118 Proline residue: D 114 - end of helix Processing helix chain 'D' and resid 119 through 133 removed outlier: 3.611A pdb=" N MET D 123 " --> pdb=" O THR D 119 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU D 131 " --> pdb=" O LEU D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 164 removed outlier: 3.585A pdb=" N LYS D 164 " --> pdb=" O GLU D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 170 removed outlier: 3.675A pdb=" N ILE D 169 " --> pdb=" O ALA D 165 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR D 170 " --> pdb=" O GLY D 166 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 165 through 170' Processing helix chain 'D' and resid 179 through 200 Processing helix chain 'D' and resid 230 through 242 Processing helix chain 'D' and resid 252 through 259 Processing helix chain 'D' and resid 263 through 279 Processing helix chain 'D' and resid 282 through 301 Processing sheet with id=AA1, first strand: chain 'Z' and resid 210 through 213 removed outlier: 3.888A pdb=" N SER Z 210 " --> pdb=" O THR Z 251 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N VAL Z 212 " --> pdb=" O LYS Z 249 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 210 through 213 removed outlier: 3.928A pdb=" N SER B 210 " --> pdb=" O THR B 251 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N VAL B 212 " --> pdb=" O LYS B 249 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 210 through 213 removed outlier: 3.904A pdb=" N SER D 210 " --> pdb=" O THR D 251 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N VAL D 212 " --> pdb=" O LYS D 249 " (cutoff:3.500A) 745 hydrogen bonds defined for protein. 2235 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.68 Time building geometry restraints manager: 1.13 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: 3848 1.34 - 1.46: 2715 1.46 - 1.58: 5866 1.58 - 1.70: 0 1.70 - 1.82: 126 Bond restraints: 12555 Sorted by residual: bond pdb=" C ALA Z 206 " pdb=" N PRO Z 207 " ideal model delta sigma weight residual 1.328 1.349 -0.021 1.25e-02 6.40e+03 2.92e+00 bond pdb=" C ASP B 113 " pdb=" N PRO B 114 " ideal model delta sigma weight residual 1.336 1.351 -0.015 1.20e-02 6.94e+03 1.67e+00 bond pdb=" CB GLU D 91 " pdb=" CG GLU D 91 " ideal model delta sigma weight residual 1.520 1.554 -0.034 3.00e-02 1.11e+03 1.29e+00 bond pdb=" CA ASP Z 94 " pdb=" CB ASP Z 94 " ideal model delta sigma weight residual 1.530 1.549 -0.019 1.69e-02 3.50e+03 1.28e+00 bond pdb=" CA ASP D 94 " pdb=" CB ASP D 94 " ideal model delta sigma weight residual 1.530 1.548 -0.018 1.69e-02 3.50e+03 1.14e+00 ... (remaining 12550 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.70: 16535 1.70 - 3.40: 435 3.40 - 5.11: 74 5.11 - 6.81: 29 6.81 - 8.51: 6 Bond angle restraints: 17079 Sorted by residual: angle pdb=" N VAL C 167 " pdb=" CA VAL C 167 " pdb=" C VAL C 167 " ideal model delta sigma weight residual 112.17 106.79 5.38 9.50e-01 1.11e+00 3.21e+01 angle pdb=" N VAL Y 167 " pdb=" CA VAL Y 167 " pdb=" C VAL Y 167 " ideal model delta sigma weight residual 112.17 106.92 5.25 9.50e-01 1.11e+00 3.05e+01 angle pdb=" N LYS Z 51 " pdb=" CA LYS Z 51 " pdb=" CB LYS Z 51 " ideal model delta sigma weight residual 114.17 108.46 5.71 1.14e+00 7.69e-01 2.51e+01 angle pdb=" N LYS B 51 " pdb=" CA LYS B 51 " pdb=" CB LYS B 51 " ideal model delta sigma weight residual 114.17 108.47 5.70 1.14e+00 7.69e-01 2.50e+01 angle pdb=" N LYS D 51 " pdb=" CA LYS D 51 " pdb=" CB LYS D 51 " ideal model delta sigma weight residual 114.17 108.58 5.59 1.14e+00 7.69e-01 2.40e+01 ... (remaining 17074 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.04: 6630 17.04 - 34.08: 521 34.08 - 51.13: 132 51.13 - 68.17: 12 68.17 - 85.21: 22 Dihedral angle restraints: 7317 sinusoidal: 2730 harmonic: 4587 Sorted by residual: dihedral pdb=" CA ILE Y 219 " pdb=" C ILE Y 219 " pdb=" N SER Y 220 " pdb=" CA SER Y 220 " ideal model delta harmonic sigma weight residual 180.00 150.12 29.88 0 5.00e+00 4.00e-02 3.57e+01 dihedral pdb=" CA ILE A 219 " pdb=" C ILE A 219 " pdb=" N SER A 220 " pdb=" CA SER A 220 " ideal model delta harmonic sigma weight residual 180.00 150.50 29.50 0 5.00e+00 4.00e-02 3.48e+01 dihedral pdb=" CA ILE C 219 " pdb=" C ILE C 219 " pdb=" N SER C 220 " pdb=" CA SER C 220 " ideal model delta harmonic sigma weight residual 180.00 150.80 29.20 0 5.00e+00 4.00e-02 3.41e+01 ... (remaining 7314 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1577 0.045 - 0.090: 395 0.090 - 0.135: 85 0.135 - 0.180: 4 0.180 - 0.225: 6 Chirality restraints: 2067 Sorted by residual: chirality pdb=" CB ILE B 203 " pdb=" CA ILE B 203 " pdb=" CG1 ILE B 203 " pdb=" CG2 ILE B 203 " both_signs ideal model delta sigma weight residual False 2.64 2.87 -0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CB ILE Z 203 " pdb=" CA ILE Z 203 " pdb=" CG1 ILE Z 203 " pdb=" CG2 ILE Z 203 " both_signs ideal model delta sigma weight residual False 2.64 2.85 -0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CB ILE D 203 " pdb=" CA ILE D 203 " pdb=" CG1 ILE D 203 " pdb=" CG2 ILE D 203 " both_signs ideal model delta sigma weight residual False 2.64 2.84 -0.20 2.00e-01 2.50e+01 9.68e-01 ... (remaining 2064 not shown) Planarity restraints: 2097 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP Z 93 " 0.012 2.00e-02 2.50e+03 2.51e-02 6.32e+00 pdb=" C ASP Z 93 " -0.043 2.00e-02 2.50e+03 pdb=" O ASP Z 93 " 0.016 2.00e-02 2.50e+03 pdb=" N ASP Z 94 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA D 206 " 0.039 5.00e-02 4.00e+02 5.92e-02 5.61e+00 pdb=" N PRO D 207 " -0.102 5.00e-02 4.00e+02 pdb=" CA PRO D 207 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO D 207 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 206 " -0.039 5.00e-02 4.00e+02 5.91e-02 5.58e+00 pdb=" N PRO B 207 " 0.102 5.00e-02 4.00e+02 pdb=" CA PRO B 207 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 207 " -0.033 5.00e-02 4.00e+02 ... (remaining 2094 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 224 2.69 - 3.24: 13272 3.24 - 3.79: 19720 3.79 - 4.35: 26086 4.35 - 4.90: 41718 Nonbonded interactions: 101020 Sorted by model distance: nonbonded pdb=" OE1 GLU Z 216 " pdb=" OH TYR Z 219 " model vdw 2.134 3.040 nonbonded pdb=" OH TYR B 48 " pdb=" NH2 ARG B 86 " model vdw 2.150 3.120 nonbonded pdb=" OH TYR B 48 " pdb=" OE1 GLU B 83 " model vdw 2.182 3.040 nonbonded pdb=" OH TYR Z 48 " pdb=" NH2 ARG Z 86 " model vdw 2.201 3.120 nonbonded pdb=" OH TYR D 48 " pdb=" NH2 ARG D 86 " model vdw 2.209 3.120 ... (remaining 101015 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 'C' selection = chain 'Y' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'Z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.050 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: 0.150 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.230 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12555 Z= 0.137 Angle : 0.699 8.512 17079 Z= 0.403 Chirality : 0.042 0.225 2067 Planarity : 0.005 0.059 2097 Dihedral : 13.827 85.211 4383 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.90 % Favored : 92.91 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.22), residues: 1623 helix: 0.54 (0.16), residues: 1104 sheet: None (None), residues: 0 loop : -2.01 (0.28), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 60 TYR 0.023 0.001 TYR D 48 PHE 0.021 0.001 PHE D 154 TRP 0.025 0.001 TRP D 222 HIS 0.003 0.001 HIS D 298 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.14 (12555) covalent geometry : angle 0.69943 / 0.40 (17079) hydrogen bonds : bond 0.16327 / 10.96 ( 745) hydrogen bonds : angle 6.24524 / 4.37 ( 2235) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3246 Ramachandran restraints generated. 1623 Oldfield, 0 Emsley, 1623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3246 Ramachandran restraints generated. 1623 Oldfield, 0 Emsley, 1623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 329 time to evaluate : 0.390 Fit side-chains REVERT: Y 126 ASP cc_start: 0.7944 (t70) cc_final: 0.7382 (t0) REVERT: Z 58 LEU cc_start: 0.8803 (mt) cc_final: 0.8518 (mt) REVERT: Z 86 ARG cc_start: 0.6956 (ppt170) cc_final: 0.6704 (ppt170) REVERT: Z 123 MET cc_start: 0.7826 (ptm) cc_final: 0.7614 (tmm) REVERT: A 18 ILE cc_start: 0.8875 (pt) cc_final: 0.8660 (pt) REVERT: A 126 ASP cc_start: 0.7399 (t0) cc_final: 0.7166 (t0) REVERT: B 58 LEU cc_start: 0.8651 (mt) cc_final: 0.8350 (mt) REVERT: B 93 ASP cc_start: 0.6830 (p0) cc_final: 0.6624 (p0) REVERT: B 154 PHE cc_start: 0.8675 (t80) cc_final: 0.8436 (t80) REVERT: C 126 ASP cc_start: 0.7708 (t70) cc_final: 0.7420 (t0) REVERT: C 131 LYS cc_start: 0.8900 (ptpp) cc_final: 0.8558 (tptp) REVERT: D 17 TRP cc_start: 0.8408 (t60) cc_final: 0.8183 (t-100) REVERT: D 40 MET cc_start: 0.8689 (mtp) cc_final: 0.8392 (mmm) outliers start: 0 outliers final: 0 residues processed: 329 average time/residue: 0.0982 time to fit residues: 47.6290 Evaluate side-chains 288 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 288 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.4980 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 2.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 133 ASN A 199 ASN B 255 ASN D 255 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.128888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.102046 restraints weight = 26243.292| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 2.83 r_work: 0.3334 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.1502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 12555 Z= 0.160 Angle : 0.663 8.044 17079 Z= 0.345 Chirality : 0.042 0.212 2067 Planarity : 0.005 0.053 2097 Dihedral : 5.058 34.075 1698 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.52 % Favored : 92.42 % Rotamer: Outliers : 1.19 % Allowed : 10.21 % Favored : 88.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.21), residues: 1623 helix: 0.75 (0.16), residues: 1116 sheet: None (None), residues: 0 loop : -2.56 (0.26), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 60 TYR 0.025 0.002 TYR C 194 PHE 0.017 0.001 PHE A 27 TRP 0.017 0.001 TRP Z 222 HIS 0.005 0.001 HIS B 298 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.16 (12555) covalent geometry : angle 0.66272 / 0.35 (17079) hydrogen bonds : bond 0.04330 / 2.93 ( 745) hydrogen bonds : angle 4.98514 / 3.57 ( 2235) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3246 Ramachandran restraints generated. 1623 Oldfield, 0 Emsley, 1623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3246 Ramachandran restraints generated. 1623 Oldfield, 0 Emsley, 1623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 313 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 21 ILE cc_start: 0.8451 (pt) cc_final: 0.8246 (pt) REVERT: Y 126 ASP cc_start: 0.8228 (t70) cc_final: 0.7631 (t0) REVERT: Y 131 LYS cc_start: 0.8359 (tptp) cc_final: 0.8145 (tptp) REVERT: Z 58 LEU cc_start: 0.8910 (mt) cc_final: 0.8586 (mt) REVERT: A 126 ASP cc_start: 0.7831 (t0) cc_final: 0.7467 (t0) REVERT: A 133 ASN cc_start: 0.8095 (t0) cc_final: 0.7871 (t0) REVERT: B 58 LEU cc_start: 0.8926 (mt) cc_final: 0.8612 (mt) REVERT: B 216 GLU cc_start: 0.8098 (tm-30) cc_final: 0.7781 (tm-30) REVERT: C 21 ILE cc_start: 0.8346 (pt) cc_final: 0.8070 (pt) REVERT: C 53 THR cc_start: 0.8779 (m) cc_final: 0.8519 (t) REVERT: C 127 ARG cc_start: 0.8111 (mtp-110) cc_final: 0.7423 (mtp-110) REVERT: C 131 LYS cc_start: 0.8978 (ptpp) cc_final: 0.8479 (tptp) REVERT: D 17 TRP cc_start: 0.8525 (t60) cc_final: 0.8247 (t-100) REVERT: D 86 ARG cc_start: 0.6902 (ttp80) cc_final: 0.6637 (ttp80) REVERT: D 160 GLU cc_start: 0.7765 (mm-30) cc_final: 0.7514 (pt0) outliers start: 15 outliers final: 6 residues processed: 319 average time/residue: 0.0923 time to fit residues: 43.3353 Evaluate side-chains 298 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 292 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 130 GLU Chi-restraints excluded: chain Y residue 143 SER Chi-restraints excluded: chain Z residue 219 TYR Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain C residue 143 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 121 optimal weight: 0.5980 chunk 75 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 66 optimal weight: 8.9990 chunk 49 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 chunk 125 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 94 optimal weight: 2.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Y 133 ASN Y 199 ASN A 29 GLN B 259 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.128611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.104150 restraints weight = 26473.285| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 2.50 r_work: 0.3343 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12555 Z= 0.145 Angle : 0.636 8.980 17079 Z= 0.331 Chirality : 0.041 0.183 2067 Planarity : 0.005 0.053 2097 Dihedral : 4.962 32.752 1698 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.15 % Favored : 92.79 % Rotamer: Outliers : 1.43 % Allowed : 13.62 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.22), residues: 1623 helix: 0.76 (0.16), residues: 1134 sheet: None (None), residues: 0 loop : -2.51 (0.27), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 127 TYR 0.020 0.002 TYR Y 194 PHE 0.018 0.001 PHE A 14 TRP 0.017 0.001 TRP Z 222 HIS 0.004 0.001 HIS B 298 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.15 (12555) covalent geometry : angle 0.63558 / 0.33 (17079) hydrogen bonds : bond 0.03970 / 2.71 ( 745) hydrogen bonds : angle 4.83423 / 3.46 ( 2235) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3246 Ramachandran restraints generated. 1623 Oldfield, 0 Emsley, 1623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3246 Ramachandran restraints generated. 1623 Oldfield, 0 Emsley, 1623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 307 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 21 ILE cc_start: 0.8496 (pt) cc_final: 0.8291 (pt) REVERT: Y 29 GLN cc_start: 0.8114 (mm-40) cc_final: 0.7634 (mm-40) REVERT: Y 126 ASP cc_start: 0.8207 (t70) cc_final: 0.7604 (t0) REVERT: Z 54 ARG cc_start: 0.8203 (mmt180) cc_final: 0.7360 (mmt90) REVERT: A 115 ARG cc_start: 0.8554 (mtp85) cc_final: 0.8328 (mtp85) REVERT: A 127 ARG cc_start: 0.8351 (mtp-110) cc_final: 0.8107 (ttm110) REVERT: B 58 LEU cc_start: 0.8972 (mt) cc_final: 0.8526 (mt) REVERT: B 59 LYS cc_start: 0.8513 (mmtm) cc_final: 0.8062 (mmtm) REVERT: B 216 GLU cc_start: 0.8159 (tm-30) cc_final: 0.7729 (tm-30) REVERT: D 17 TRP cc_start: 0.8538 (t60) cc_final: 0.8279 (t-100) REVERT: D 104 MET cc_start: 0.7805 (OUTLIER) cc_final: 0.7054 (ptp) REVERT: D 141 ILE cc_start: 0.8544 (mm) cc_final: 0.8113 (mp) outliers start: 18 outliers final: 10 residues processed: 315 average time/residue: 0.1050 time to fit residues: 47.4055 Evaluate side-chains 306 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 295 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 130 GLU Chi-restraints excluded: chain Y residue 143 SER Chi-restraints excluded: chain Z residue 219 TYR Chi-restraints excluded: chain Z residue 261 ILE Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 31 MET Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 188 MET Chi-restraints excluded: chain D residue 104 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 2 optimal weight: 0.9990 chunk 103 optimal weight: 0.8980 chunk 23 optimal weight: 0.5980 chunk 73 optimal weight: 0.3980 chunk 106 optimal weight: 6.9990 chunk 33 optimal weight: 5.9990 chunk 72 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 5.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** Y 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 133 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.128902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.104690 restraints weight = 26174.006| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 2.34 r_work: 0.3352 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12555 Z= 0.140 Angle : 0.628 9.431 17079 Z= 0.327 Chirality : 0.041 0.183 2067 Planarity : 0.005 0.054 2097 Dihedral : 4.961 32.177 1698 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.39 % Favored : 92.54 % Rotamer: Outliers : 1.74 % Allowed : 15.20 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.22), residues: 1623 helix: 0.80 (0.16), residues: 1134 sheet: None (None), residues: 0 loop : -2.53 (0.27), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG Z 121 TYR 0.028 0.002 TYR Y 194 PHE 0.020 0.001 PHE D 154 TRP 0.016 0.001 TRP Z 222 HIS 0.005 0.001 HIS B 298 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 (12555) covalent geometry : angle 0.62770 / 0.33 (17079) hydrogen bonds : bond 0.03784 / 2.58 ( 745) hydrogen bonds : angle 4.76295 / 3.41 ( 2235) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3246 Ramachandran restraints generated. 1623 Oldfield, 0 Emsley, 1623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3246 Ramachandran restraints generated. 1623 Oldfield, 0 Emsley, 1623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 305 time to evaluate : 0.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 29 GLN cc_start: 0.8141 (mm-40) cc_final: 0.7830 (mm-40) REVERT: Y 126 ASP cc_start: 0.8179 (t70) cc_final: 0.7576 (t0) REVERT: Z 58 LEU cc_start: 0.8730 (mt) cc_final: 0.8504 (mt) REVERT: A 180 ASP cc_start: 0.7947 (p0) cc_final: 0.7620 (p0) REVERT: B 58 LEU cc_start: 0.8996 (mt) cc_final: 0.8696 (mt) REVERT: B 59 LYS cc_start: 0.8443 (mmtm) cc_final: 0.8193 (mmtm) REVERT: B 216 GLU cc_start: 0.8198 (tm-30) cc_final: 0.7765 (tm-30) REVERT: C 24 GLU cc_start: 0.7949 (mm-30) cc_final: 0.7734 (mm-30) REVERT: C 133 ASN cc_start: 0.8260 (t0) cc_final: 0.6748 (t0) REVERT: D 17 TRP cc_start: 0.8514 (t60) cc_final: 0.8263 (t-100) REVERT: D 31 MET cc_start: 0.8107 (mtm) cc_final: 0.7779 (mtm) REVERT: D 83 GLU cc_start: 0.8428 (mt-10) cc_final: 0.8086 (mt-10) REVERT: D 104 MET cc_start: 0.7797 (OUTLIER) cc_final: 0.7173 (ptp) REVERT: D 141 ILE cc_start: 0.8567 (mm) cc_final: 0.8141 (mp) outliers start: 22 outliers final: 10 residues processed: 313 average time/residue: 0.0992 time to fit residues: 44.8844 Evaluate side-chains 303 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 292 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 143 SER Chi-restraints excluded: chain Z residue 219 TYR Chi-restraints excluded: chain Z residue 261 ILE Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 31 MET Chi-restraints excluded: chain B residue 105 MET Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 188 MET Chi-restraints excluded: chain D residue 104 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 120 optimal weight: 0.6980 chunk 89 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 153 optimal weight: 0.6980 chunk 99 optimal weight: 0.8980 chunk 76 optimal weight: 0.7980 chunk 103 optimal weight: 0.4980 chunk 134 optimal weight: 0.0270 chunk 87 optimal weight: 0.0980 chunk 5 optimal weight: 0.9980 overall best weight: 0.4038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Y 199 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.130996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.105897 restraints weight = 26224.229| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 2.78 r_work: 0.3368 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12555 Z= 0.124 Angle : 0.618 9.843 17079 Z= 0.323 Chirality : 0.040 0.193 2067 Planarity : 0.005 0.055 2097 Dihedral : 4.848 30.292 1698 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.96 % Favored : 92.98 % Rotamer: Outliers : 1.19 % Allowed : 17.26 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.22), residues: 1623 helix: 0.90 (0.16), residues: 1128 sheet: None (None), residues: 0 loop : -2.54 (0.26), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 127 TYR 0.032 0.002 TYR Y 194 PHE 0.013 0.001 PHE A 14 TRP 0.020 0.001 TRP D 222 HIS 0.004 0.001 HIS B 298 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (12555) covalent geometry : angle 0.61850 / 0.32 (17079) hydrogen bonds : bond 0.03598 / 2.46 ( 745) hydrogen bonds : angle 4.66837 / 3.34 ( 2235) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3246 Ramachandran restraints generated. 1623 Oldfield, 0 Emsley, 1623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3246 Ramachandran restraints generated. 1623 Oldfield, 0 Emsley, 1623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 325 time to evaluate : 0.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 29 GLN cc_start: 0.8068 (mm-40) cc_final: 0.7712 (mm-40) REVERT: Y 126 ASP cc_start: 0.8319 (t70) cc_final: 0.7353 (t0) REVERT: Y 243 LYS cc_start: 0.8642 (tttt) cc_final: 0.8185 (mmmm) REVERT: Z 58 LEU cc_start: 0.8782 (mt) cc_final: 0.8525 (mt) REVERT: A 133 ASN cc_start: 0.8072 (t0) cc_final: 0.7227 (t0) REVERT: A 135 ARG cc_start: 0.8047 (mpp-170) cc_final: 0.7419 (mtm-85) REVERT: B 58 LEU cc_start: 0.8990 (mt) cc_final: 0.8687 (mt) REVERT: B 59 LYS cc_start: 0.8476 (mmtm) cc_final: 0.8211 (mmtm) REVERT: B 154 PHE cc_start: 0.8718 (t80) cc_final: 0.8410 (t80) REVERT: B 216 GLU cc_start: 0.8197 (tm-30) cc_final: 0.7818 (tm-30) REVERT: C 24 GLU cc_start: 0.7787 (mm-30) cc_final: 0.7526 (mm-30) REVERT: C 131 LYS cc_start: 0.8838 (ptpp) cc_final: 0.8600 (ptpp) REVERT: C 135 ARG cc_start: 0.7645 (mpp-170) cc_final: 0.7270 (mpp-170) REVERT: D 17 TRP cc_start: 0.8507 (t60) cc_final: 0.8273 (t-100) REVERT: D 31 MET cc_start: 0.8096 (mtm) cc_final: 0.7747 (mtm) REVERT: D 104 MET cc_start: 0.7692 (OUTLIER) cc_final: 0.7086 (ptp) outliers start: 15 outliers final: 10 residues processed: 328 average time/residue: 0.1073 time to fit residues: 51.0346 Evaluate side-chains 299 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 288 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 143 SER Chi-restraints excluded: chain Z residue 219 TYR Chi-restraints excluded: chain Z residue 261 ILE Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 165 ASP Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain B residue 31 MET Chi-restraints excluded: chain B residue 105 MET Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain D residue 104 MET Chi-restraints excluded: chain D residue 222 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 105 optimal weight: 1.9990 chunk 8 optimal weight: 0.0170 chunk 156 optimal weight: 0.9990 chunk 16 optimal weight: 0.1980 chunk 38 optimal weight: 5.9990 chunk 30 optimal weight: 0.8980 chunk 2 optimal weight: 0.5980 chunk 51 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 121 optimal weight: 7.9990 overall best weight: 0.4618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Y 199 ASN C 199 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.131500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.104566 restraints weight = 26394.024| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 2.95 r_work: 0.3368 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12555 Z= 0.128 Angle : 0.641 10.149 17079 Z= 0.334 Chirality : 0.041 0.201 2067 Planarity : 0.005 0.055 2097 Dihedral : 4.838 30.916 1698 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.21 % Favored : 92.73 % Rotamer: Outliers : 1.82 % Allowed : 17.66 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.22), residues: 1623 helix: 0.92 (0.16), residues: 1128 sheet: None (None), residues: 0 loop : -2.55 (0.26), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 127 TYR 0.037 0.002 TYR Y 194 PHE 0.021 0.001 PHE D 154 TRP 0.022 0.001 TRP D 222 HIS 0.004 0.001 HIS B 298 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (12555) covalent geometry : angle 0.64124 / 0.33 (17079) hydrogen bonds : bond 0.03578 / 2.44 ( 745) hydrogen bonds : angle 4.62696 / 3.32 ( 2235) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3246 Ramachandran restraints generated. 1623 Oldfield, 0 Emsley, 1623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3246 Ramachandran restraints generated. 1623 Oldfield, 0 Emsley, 1623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 304 time to evaluate : 0.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 29 GLN cc_start: 0.8036 (mm-40) cc_final: 0.7684 (mm-40) REVERT: Y 126 ASP cc_start: 0.8208 (t70) cc_final: 0.7830 (t0) REVERT: A 29 GLN cc_start: 0.8038 (mm-40) cc_final: 0.7572 (mm-40) REVERT: A 133 ASN cc_start: 0.8086 (t0) cc_final: 0.7244 (t0) REVERT: A 135 ARG cc_start: 0.8030 (mpp-170) cc_final: 0.7415 (mtm-85) REVERT: B 52 GLU cc_start: 0.8004 (pm20) cc_final: 0.7719 (mp0) REVERT: B 54 ARG cc_start: 0.8021 (mmt180) cc_final: 0.6945 (mpt-90) REVERT: B 58 LEU cc_start: 0.9010 (mt) cc_final: 0.8731 (mt) REVERT: B 59 LYS cc_start: 0.8553 (mmtm) cc_final: 0.8284 (mmtm) REVERT: B 104 MET cc_start: 0.7539 (mtp) cc_final: 0.7078 (ptm) REVERT: B 121 ARG cc_start: 0.7798 (OUTLIER) cc_final: 0.7410 (mmm-85) REVERT: B 154 PHE cc_start: 0.8710 (t80) cc_final: 0.8359 (t80) REVERT: B 216 GLU cc_start: 0.8230 (tm-30) cc_final: 0.7759 (tm-30) REVERT: C 24 GLU cc_start: 0.7888 (mm-30) cc_final: 0.7576 (mm-30) REVERT: C 133 ASN cc_start: 0.7845 (t0) cc_final: 0.7448 (t0) REVERT: D 17 TRP cc_start: 0.8502 (t60) cc_final: 0.8271 (t-100) REVERT: D 29 GLU cc_start: 0.8263 (tm-30) cc_final: 0.7723 (tm-30) REVERT: D 31 MET cc_start: 0.7900 (mtm) cc_final: 0.7610 (mtm) REVERT: D 36 TRP cc_start: 0.8393 (t60) cc_final: 0.8190 (t-100) REVERT: D 54 ARG cc_start: 0.8193 (mmt180) cc_final: 0.7866 (mmt90) REVERT: D 83 GLU cc_start: 0.8531 (mt-10) cc_final: 0.8241 (mt-10) REVERT: D 85 GLU cc_start: 0.7484 (pp20) cc_final: 0.7233 (mm-30) outliers start: 23 outliers final: 14 residues processed: 312 average time/residue: 0.0975 time to fit residues: 44.1613 Evaluate side-chains 309 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 294 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 143 SER Chi-restraints excluded: chain Z residue 212 VAL Chi-restraints excluded: chain Z residue 219 TYR Chi-restraints excluded: chain Z residue 261 ILE Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 165 ASP Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain B residue 31 MET Chi-restraints excluded: chain B residue 105 MET Chi-restraints excluded: chain B residue 121 ARG Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 188 MET Chi-restraints excluded: chain C residue 199 ASN Chi-restraints excluded: chain D residue 222 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 22 optimal weight: 0.6980 chunk 154 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 117 optimal weight: 0.8980 chunk 112 optimal weight: 2.9990 chunk 136 optimal weight: 0.6980 chunk 74 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 chunk 59 optimal weight: 7.9990 chunk 71 optimal weight: 0.8980 chunk 56 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Y 199 ASN C 199 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.130046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.104273 restraints weight = 26259.473| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 2.67 r_work: 0.3349 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12555 Z= 0.142 Angle : 0.659 13.992 17079 Z= 0.341 Chirality : 0.041 0.207 2067 Planarity : 0.005 0.055 2097 Dihedral : 4.848 31.654 1698 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.27 % Favored : 92.61 % Rotamer: Outliers : 1.58 % Allowed : 18.37 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.22), residues: 1623 helix: 0.89 (0.16), residues: 1131 sheet: None (None), residues: 0 loop : -2.57 (0.26), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 127 TYR 0.033 0.002 TYR Y 194 PHE 0.017 0.001 PHE A 14 TRP 0.023 0.001 TRP D 222 HIS 0.004 0.001 HIS B 298 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (12555) covalent geometry : angle 0.65943 / 0.34 (17079) hydrogen bonds : bond 0.03627 / 2.46 ( 745) hydrogen bonds : angle 4.67935 / 3.36 ( 2235) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3246 Ramachandran restraints generated. 1623 Oldfield, 0 Emsley, 1623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3246 Ramachandran restraints generated. 1623 Oldfield, 0 Emsley, 1623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 302 time to evaluate : 0.277 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Y 29 GLN cc_start: 0.8115 (mm-40) cc_final: 0.7793 (mm-40) REVERT: Y 126 ASP cc_start: 0.8245 (t70) cc_final: 0.7856 (t0) REVERT: Y 243 LYS cc_start: 0.8568 (tttt) cc_final: 0.8061 (mmmm) REVERT: Z 215 ASP cc_start: 0.8327 (p0) cc_final: 0.8118 (p0) REVERT: A 135 ARG cc_start: 0.8045 (mpp-170) cc_final: 0.7419 (mtm-85) REVERT: B 54 ARG cc_start: 0.8000 (mmt180) cc_final: 0.7132 (mmt90) REVERT: B 59 LYS cc_start: 0.8562 (mmtm) cc_final: 0.8290 (mmtm) REVERT: B 104 MET cc_start: 0.7624 (mtp) cc_final: 0.7147 (ptm) REVERT: B 121 ARG cc_start: 0.7858 (OUTLIER) cc_final: 0.7608 (mmm-85) REVERT: B 154 PHE cc_start: 0.8729 (t80) cc_final: 0.8374 (t80) REVERT: B 216 GLU cc_start: 0.8150 (tm-30) cc_final: 0.7697 (tm-30) REVERT: D 17 TRP cc_start: 0.8543 (t60) cc_final: 0.8279 (t-100) REVERT: D 29 GLU cc_start: 0.8287 (tm-30) cc_final: 0.7747 (tm-30) REVERT: D 31 MET cc_start: 0.7924 (mtm) cc_final: 0.7616 (mtm) REVERT: D 36 TRP cc_start: 0.8496 (t60) cc_final: 0.8287 (t-100) REVERT: D 54 ARG cc_start: 0.8200 (mmt180) cc_final: 0.7832 (mmt90) REVERT: D 83 GLU cc_start: 0.8551 (mt-10) cc_final: 0.8206 (mt-10) REVERT: D 104 MET cc_start: 0.7744 (ptm) cc_final: 0.7293 (ptp) outliers start: 20 outliers final: 17 residues processed: 309 average time/residue: 0.0959 time to fit residues: 43.4579 Evaluate side-chains 310 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 292 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 130 GLU Chi-restraints excluded: chain Y residue 143 SER Chi-restraints excluded: chain Z residue 212 VAL Chi-restraints excluded: chain Z residue 219 TYR Chi-restraints excluded: chain Z residue 261 ILE Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 165 ASP Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 188 MET Chi-restraints excluded: chain B residue 31 MET Chi-restraints excluded: chain B residue 105 MET Chi-restraints excluded: chain B residue 121 ARG Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 182 MET Chi-restraints excluded: chain C residue 188 MET Chi-restraints excluded: chain C residue 199 ASN Chi-restraints excluded: chain D residue 222 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 97 optimal weight: 5.9990 chunk 147 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 106 optimal weight: 6.9990 chunk 152 optimal weight: 4.9990 chunk 133 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 chunk 60 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 199 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.129315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.102697 restraints weight = 26249.298| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 2.85 r_work: 0.3338 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12555 Z= 0.148 Angle : 0.667 9.788 17079 Z= 0.349 Chirality : 0.042 0.222 2067 Planarity : 0.005 0.062 2097 Dihedral : 4.999 32.169 1698 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.15 % Favored : 92.67 % Rotamer: Outliers : 1.82 % Allowed : 19.24 % Favored : 78.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.22), residues: 1623 helix: 0.90 (0.16), residues: 1125 sheet: None (None), residues: 0 loop : -2.62 (0.26), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 127 TYR 0.031 0.002 TYR Y 194 PHE 0.017 0.001 PHE A 14 TRP 0.024 0.001 TRP D 222 HIS 0.004 0.001 HIS B 298 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 (12555) covalent geometry : angle 0.66744 / 0.35 (17079) hydrogen bonds : bond 0.03683 / 2.51 ( 745) hydrogen bonds : angle 4.72153 / 3.39 ( 2235) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3246 Ramachandran restraints generated. 1623 Oldfield, 0 Emsley, 1623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3246 Ramachandran restraints generated. 1623 Oldfield, 0 Emsley, 1623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 290 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 29 GLN cc_start: 0.8117 (mm-40) cc_final: 0.7782 (mm-40) REVERT: Y 126 ASP cc_start: 0.8218 (t70) cc_final: 0.7840 (t0) REVERT: Y 146 CYS cc_start: 0.8492 (m) cc_final: 0.8126 (p) REVERT: Y 182 MET cc_start: 0.8534 (mmt) cc_final: 0.8282 (mmm) REVERT: Z 58 LEU cc_start: 0.8710 (mt) cc_final: 0.8503 (mt) REVERT: A 29 GLN cc_start: 0.8029 (mm-40) cc_final: 0.7514 (mm-40) REVERT: A 151 ARG cc_start: 0.8501 (OUTLIER) cc_final: 0.7865 (ttt90) REVERT: B 54 ARG cc_start: 0.8121 (mmt180) cc_final: 0.7402 (mmt90) REVERT: B 59 LYS cc_start: 0.8589 (mmtm) cc_final: 0.8312 (mmtm) REVERT: B 104 MET cc_start: 0.7651 (mtp) cc_final: 0.7194 (ptm) REVERT: B 121 ARG cc_start: 0.7922 (OUTLIER) cc_final: 0.7479 (mmm-85) REVERT: B 216 GLU cc_start: 0.8157 (tm-30) cc_final: 0.7689 (tm-30) REVERT: C 24 GLU cc_start: 0.7773 (mm-30) cc_final: 0.7534 (mm-30) REVERT: D 17 TRP cc_start: 0.8566 (t60) cc_final: 0.8280 (t-100) REVERT: D 29 GLU cc_start: 0.8212 (tm-30) cc_final: 0.7734 (tm-30) REVERT: D 31 MET cc_start: 0.7900 (mtm) cc_final: 0.7613 (mtm) REVERT: D 36 TRP cc_start: 0.8507 (t60) cc_final: 0.8305 (t-100) REVERT: D 54 ARG cc_start: 0.8076 (mmt180) cc_final: 0.6885 (mmt90) REVERT: D 83 GLU cc_start: 0.8560 (mt-10) cc_final: 0.8220 (mt-10) REVERT: D 104 MET cc_start: 0.7771 (ptm) cc_final: 0.7314 (ptp) outliers start: 23 outliers final: 15 residues processed: 299 average time/residue: 0.0885 time to fit residues: 38.8882 Evaluate side-chains 307 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 290 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 143 SER Chi-restraints excluded: chain Z residue 212 VAL Chi-restraints excluded: chain Z residue 261 ILE Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 165 ASP Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain B residue 31 MET Chi-restraints excluded: chain B residue 105 MET Chi-restraints excluded: chain B residue 121 ARG Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 182 MET Chi-restraints excluded: chain C residue 188 MET Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 222 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 37 optimal weight: 0.8980 chunk 75 optimal weight: 0.9980 chunk 94 optimal weight: 5.9990 chunk 118 optimal weight: 0.1980 chunk 82 optimal weight: 3.9990 chunk 69 optimal weight: 6.9990 chunk 152 optimal weight: 4.9990 chunk 132 optimal weight: 3.9990 chunk 125 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 149 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 133 ASN C 199 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.128862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.102153 restraints weight = 26226.013| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 2.86 r_work: 0.3338 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.2491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12555 Z= 0.143 Angle : 0.669 9.324 17079 Z= 0.347 Chirality : 0.041 0.233 2067 Planarity : 0.005 0.055 2097 Dihedral : 4.933 31.946 1698 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.21 % Favored : 92.61 % Rotamer: Outliers : 1.90 % Allowed : 19.48 % Favored : 78.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.22), residues: 1623 helix: 0.89 (0.16), residues: 1125 sheet: None (None), residues: 0 loop : -2.61 (0.26), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 127 TYR 0.040 0.002 TYR Y 194 PHE 0.016 0.001 PHE A 14 TRP 0.023 0.001 TRP D 222 HIS 0.004 0.001 HIS B 298 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (12555) covalent geometry : angle 0.66869 / 0.35 (17079) hydrogen bonds : bond 0.03701 / 2.51 ( 745) hydrogen bonds : angle 4.71982 / 3.39 ( 2235) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3246 Ramachandran restraints generated. 1623 Oldfield, 0 Emsley, 1623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3246 Ramachandran restraints generated. 1623 Oldfield, 0 Emsley, 1623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 297 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 29 GLN cc_start: 0.8126 (mm-40) cc_final: 0.7792 (mm-40) REVERT: Y 126 ASP cc_start: 0.8258 (t70) cc_final: 0.7906 (t0) REVERT: Y 146 CYS cc_start: 0.8513 (m) cc_final: 0.8122 (p) REVERT: Y 182 MET cc_start: 0.8552 (mmt) cc_final: 0.8309 (mmm) REVERT: Z 58 LEU cc_start: 0.8713 (mt) cc_final: 0.8502 (mt) REVERT: A 133 ASN cc_start: 0.8105 (t0) cc_final: 0.7118 (t0) REVERT: A 135 ARG cc_start: 0.7964 (mpp-170) cc_final: 0.7514 (mtm-85) REVERT: B 59 LYS cc_start: 0.8584 (mmtm) cc_final: 0.8309 (mmtm) REVERT: B 104 MET cc_start: 0.7655 (mtp) cc_final: 0.7198 (ptm) REVERT: B 121 ARG cc_start: 0.7938 (OUTLIER) cc_final: 0.7672 (mmm-85) REVERT: B 154 PHE cc_start: 0.8750 (t80) cc_final: 0.8395 (t80) REVERT: B 159 GLN cc_start: 0.9086 (tm-30) cc_final: 0.8749 (tm-30) REVERT: B 216 GLU cc_start: 0.8162 (tm-30) cc_final: 0.7685 (tm-30) REVERT: C 24 GLU cc_start: 0.7749 (mm-30) cc_final: 0.7508 (mm-30) REVERT: D 17 TRP cc_start: 0.8567 (t60) cc_final: 0.8291 (t-100) REVERT: D 29 GLU cc_start: 0.8202 (tm-30) cc_final: 0.7728 (tm-30) REVERT: D 31 MET cc_start: 0.7884 (OUTLIER) cc_final: 0.7594 (mtm) REVERT: D 36 TRP cc_start: 0.8479 (t60) cc_final: 0.8244 (t-100) REVERT: D 83 GLU cc_start: 0.8565 (mt-10) cc_final: 0.8230 (mt-10) REVERT: D 104 MET cc_start: 0.7747 (ptm) cc_final: 0.7280 (ptp) REVERT: D 141 ILE cc_start: 0.8537 (mm) cc_final: 0.8167 (mp) outliers start: 24 outliers final: 15 residues processed: 308 average time/residue: 0.0943 time to fit residues: 42.6196 Evaluate side-chains 310 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 293 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 130 GLU Chi-restraints excluded: chain Y residue 143 SER Chi-restraints excluded: chain Z residue 212 VAL Chi-restraints excluded: chain Z residue 261 ILE Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 165 ASP Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain B residue 31 MET Chi-restraints excluded: chain B residue 105 MET Chi-restraints excluded: chain B residue 121 ARG Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 188 MET Chi-restraints excluded: chain C residue 199 ASN Chi-restraints excluded: chain D residue 31 MET Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 222 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 4 optimal weight: 0.9980 chunk 56 optimal weight: 0.5980 chunk 2 optimal weight: 0.6980 chunk 104 optimal weight: 0.7980 chunk 6 optimal weight: 0.9980 chunk 125 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 chunk 34 optimal weight: 3.9990 chunk 144 optimal weight: 0.7980 chunk 151 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 199 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.129135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.104209 restraints weight = 26185.884| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 2.47 r_work: 0.3360 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.2519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12555 Z= 0.143 Angle : 0.689 9.578 17079 Z= 0.356 Chirality : 0.041 0.240 2067 Planarity : 0.005 0.055 2097 Dihedral : 4.962 31.774 1698 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.46 % Favored : 92.36 % Rotamer: Outliers : 1.58 % Allowed : 20.19 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.22), residues: 1623 helix: 0.86 (0.16), residues: 1131 sheet: None (None), residues: 0 loop : -2.59 (0.26), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 127 TYR 0.040 0.002 TYR Y 194 PHE 0.016 0.001 PHE A 14 TRP 0.024 0.001 TRP D 222 HIS 0.006 0.001 HIS Z 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 (12555) covalent geometry : angle 0.68909 / 0.36 (17079) hydrogen bonds : bond 0.03679 / 2.50 ( 745) hydrogen bonds : angle 4.72354 / 3.40 ( 2235) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3246 Ramachandran restraints generated. 1623 Oldfield, 0 Emsley, 1623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3246 Ramachandran restraints generated. 1623 Oldfield, 0 Emsley, 1623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 296 time to evaluate : 0.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 29 GLN cc_start: 0.8094 (mm-40) cc_final: 0.7769 (mm-40) REVERT: Y 126 ASP cc_start: 0.8244 (t70) cc_final: 0.7894 (t0) REVERT: Y 146 CYS cc_start: 0.8490 (m) cc_final: 0.8076 (p) REVERT: Y 182 MET cc_start: 0.8571 (mmt) cc_final: 0.8328 (mmm) REVERT: Y 243 LYS cc_start: 0.8584 (tttt) cc_final: 0.8099 (mmmm) REVERT: Z 58 LEU cc_start: 0.8696 (mt) cc_final: 0.8489 (mt) REVERT: A 117 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.8204 (tt) REVERT: A 133 ASN cc_start: 0.7995 (t0) cc_final: 0.6951 (t0) REVERT: A 135 ARG cc_start: 0.7946 (mpp-170) cc_final: 0.7446 (mtm-85) REVERT: B 59 LYS cc_start: 0.8584 (mmtm) cc_final: 0.8296 (mmtm) REVERT: B 104 MET cc_start: 0.7620 (mtp) cc_final: 0.7156 (ptm) REVERT: B 121 ARG cc_start: 0.7910 (OUTLIER) cc_final: 0.7649 (mmm-85) REVERT: B 154 PHE cc_start: 0.8751 (t80) cc_final: 0.8376 (t80) REVERT: B 159 GLN cc_start: 0.9074 (tm-30) cc_final: 0.8719 (tm-30) REVERT: B 216 GLU cc_start: 0.8217 (tm-30) cc_final: 0.7775 (tm-30) REVERT: B 246 SER cc_start: 0.8068 (t) cc_final: 0.7604 (m) REVERT: C 24 GLU cc_start: 0.7783 (mm-30) cc_final: 0.7525 (mm-30) REVERT: C 199 ASN cc_start: 0.8866 (OUTLIER) cc_final: 0.8468 (t0) REVERT: D 17 TRP cc_start: 0.8526 (t60) cc_final: 0.8233 (t-100) REVERT: D 29 GLU cc_start: 0.8220 (tm-30) cc_final: 0.7720 (tm-30) REVERT: D 31 MET cc_start: 0.7921 (OUTLIER) cc_final: 0.7607 (mtm) REVERT: D 36 TRP cc_start: 0.8474 (t60) cc_final: 0.8271 (t-100) REVERT: D 44 ILE cc_start: 0.9140 (mm) cc_final: 0.8363 (mm) REVERT: D 54 ARG cc_start: 0.8145 (mmt180) cc_final: 0.6818 (mmt90) REVERT: D 83 GLU cc_start: 0.8563 (mt-10) cc_final: 0.8233 (mt-10) REVERT: D 104 MET cc_start: 0.7541 (ptm) cc_final: 0.7091 (ptp) REVERT: D 105 MET cc_start: 0.6391 (mmt) cc_final: 0.6187 (mmt) REVERT: D 141 ILE cc_start: 0.8473 (mm) cc_final: 0.8100 (mp) outliers start: 20 outliers final: 16 residues processed: 304 average time/residue: 0.0976 time to fit residues: 43.5986 Evaluate side-chains 313 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 293 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 130 GLU Chi-restraints excluded: chain Y residue 143 SER Chi-restraints excluded: chain Z residue 212 VAL Chi-restraints excluded: chain Z residue 261 ILE Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 165 ASP Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain B residue 31 MET Chi-restraints excluded: chain B residue 105 MET Chi-restraints excluded: chain B residue 121 ARG Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 182 MET Chi-restraints excluded: chain C residue 188 MET Chi-restraints excluded: chain C residue 199 ASN Chi-restraints excluded: chain D residue 31 MET Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 222 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 8 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 96 optimal weight: 0.7980 chunk 33 optimal weight: 0.0770 chunk 127 optimal weight: 0.0970 chunk 138 optimal weight: 0.0670 chunk 149 optimal weight: 0.9990 chunk 125 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 overall best weight: 0.4076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 199 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.131093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.104500 restraints weight = 26035.750| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 2.93 r_work: 0.3365 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.2570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12555 Z= 0.130 Angle : 0.670 9.334 17079 Z= 0.347 Chirality : 0.041 0.240 2067 Planarity : 0.005 0.055 2097 Dihedral : 4.865 30.462 1698 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.15 % Favored : 92.67 % Rotamer: Outliers : 1.58 % Allowed : 20.35 % Favored : 78.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.22), residues: 1623 helix: 0.88 (0.16), residues: 1131 sheet: None (None), residues: 0 loop : -2.57 (0.26), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 127 TYR 0.038 0.002 TYR Y 194 PHE 0.015 0.001 PHE A 14 TRP 0.036 0.001 TRP B 222 HIS 0.004 0.001 HIS Z 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (12555) covalent geometry : angle 0.66957 / 0.35 (17079) hydrogen bonds : bond 0.03592 / 2.45 ( 745) hydrogen bonds : angle 4.65347 / 3.35 ( 2235) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2834.51 seconds wall clock time: 49 minutes 13.28 seconds (2953.28 seconds total)