Starting phenix.real_space_refine on Wed Mar 4 08:49:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vlx_32030/03_2026/7vlx_32030.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vlx_32030/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/7vlx_32030/03_2026/7vlx_32030.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vlx_32030/03_2026/7vlx_32030.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7vlx_32030/03_2026/7vlx_32030.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vlx_32030/03_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-5986/lib/python3.9/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: 3.08, per 1000 atoms: 0.25 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: 1.03 Conformation dependent library (CDL) restraints added in 647.6 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: 0.29 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: 1.84 Time building geometry restraints manager: 1.42 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: 6696 17.04 - 34.08: 521 34.08 - 51.13: 132 51.13 - 68.17: 12 68.17 - 85.21: 22 Dihedral angle restraints: 7383 sinusoidal: 2796 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 7380 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: 0.01 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: 1.200 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: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.540 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 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 : 13.740 85.211 4449 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 covalent geometry : bond 0.00277 (12555) covalent geometry : angle 0.69943 (17079) hydrogen bonds : bond 0.16327 ( 745) hydrogen bonds : angle 6.24524 ( 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 : 0.486 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: 0.1026 time to fit residues: 49.4896 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 : 0.457 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.128599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.101730 restraints weight = 26207.420| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 2.83 r_work: 0.3336 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.1458 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 : 0.661 8.061 17079 Z= 0.345 Chirality : 0.042 0.211 2067 Planarity : 0.005 0.053 2097 Dihedral : 5.123 33.941 1764 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.39 % Favored : 92.54 % Rotamer: Outliers : 1.19 % Allowed : 10.37 % Favored : 88.44 % 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: -0.37 (0.22), residues: 1623 helix: 0.76 (0.16), residues: 1116 sheet: None (None), residues: 0 loop : -2.56 (0.27), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 60 TYR 0.024 0.002 TYR C 194 PHE 0.018 0.001 PHE A 27 TRP 0.016 0.001 TRP Z 222 HIS 0.006 0.001 HIS B 298 Details of bonding type rmsd covalent geometry : bond 0.00357 (12555) covalent geometry : angle 0.66146 (17079) hydrogen bonds : bond 0.04447 ( 745) hydrogen bonds : angle 5.01220 ( 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 326 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 311 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 21 ILE cc_start: 0.8420 (pt) cc_final: 0.8206 (pt) REVERT: Y 127 ARG cc_start: 0.8170 (ttm110) cc_final: 0.7460 (ttm110) REVERT: A 126 ASP cc_start: 0.7829 (t0) cc_final: 0.7468 (t0) REVERT: A 133 ASN cc_start: 0.8093 (t0) cc_final: 0.7873 (t0) REVERT: B 58 LEU cc_start: 0.8925 (mt) cc_final: 0.8612 (mt) REVERT: B 216 GLU cc_start: 0.8044 (tm-30) cc_final: 0.7737 (tm-30) REVERT: C 21 ILE cc_start: 0.8333 (pt) cc_final: 0.8069 (pt) REVERT: C 127 ARG cc_start: 0.8104 (mtp-110) cc_final: 0.7419 (mtp-110) REVERT: C 131 LYS cc_start: 0.8976 (ptpp) cc_final: 0.8481 (tptp) REVERT: D 17 TRP cc_start: 0.8523 (t60) cc_final: 0.8242 (t-100) REVERT: D 86 ARG cc_start: 0.6888 (ttp80) cc_final: 0.6634 (ttp80) outliers start: 15 outliers final: 6 residues processed: 318 average time/residue: 0.1014 time to fit residues: 47.4665 Evaluate side-chains 300 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 294 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 6 ILE 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: 0.9990 chunk 75 optimal weight: 0.0670 chunk 38 optimal weight: 0.8980 chunk 66 optimal weight: 0.0670 chunk 49 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 125 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 94 optimal weight: 2.9990 overall best weight: 0.6060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 133 ASN Z 255 ASN Z 259 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.129931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.104200 restraints weight = 26413.478| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 2.67 r_work: 0.3363 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12555 Z= 0.130 Angle : 0.626 8.935 17079 Z= 0.325 Chirality : 0.041 0.182 2067 Planarity : 0.005 0.053 2097 Dihedral : 4.943 31.406 1764 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.90 % Favored : 93.04 % Rotamer: Outliers : 1.43 % Allowed : 13.46 % Favored : 85.11 % 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: -0.29 (0.22), residues: 1623 helix: 0.77 (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 B 60 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 covalent geometry : bond 0.00283 (12555) covalent geometry : angle 0.62578 (17079) hydrogen bonds : bond 0.03892 ( 745) hydrogen bonds : angle 4.77187 ( 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 331 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 313 time to evaluate : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Y 21 ILE cc_start: 0.8482 (pt) cc_final: 0.8268 (pt) REVERT: Y 29 GLN cc_start: 0.8066 (mm-40) cc_final: 0.7750 (mm-40) REVERT: Z 54 ARG cc_start: 0.8080 (mmt180) cc_final: 0.7759 (mmt90) REVERT: Z 58 LEU cc_start: 0.8827 (mt) cc_final: 0.8618 (mt) REVERT: A 115 ARG cc_start: 0.8535 (mtp85) cc_final: 0.8325 (mtp85) REVERT: A 127 ARG cc_start: 0.8356 (mtp-110) cc_final: 0.8072 (ttm110) REVERT: A 148 GLN cc_start: 0.8705 (tp40) cc_final: 0.8459 (tp40) REVERT: B 58 LEU cc_start: 0.8947 (mt) cc_final: 0.8503 (mt) REVERT: B 59 LYS cc_start: 0.8511 (mmtm) cc_final: 0.8045 (mmtm) REVERT: B 216 GLU cc_start: 0.8154 (tm-30) cc_final: 0.7726 (tm-30) REVERT: D 17 TRP cc_start: 0.8479 (t60) cc_final: 0.8253 (t-100) REVERT: D 31 MET cc_start: 0.8080 (mtm) cc_final: 0.7834 (mtm) REVERT: D 83 GLU cc_start: 0.8446 (mt-10) cc_final: 0.8085 (mt-10) REVERT: D 86 ARG cc_start: 0.7020 (ttp80) cc_final: 0.6820 (ttp80) REVERT: D 104 MET cc_start: 0.7815 (OUTLIER) cc_final: 0.7085 (ptp) REVERT: D 141 ILE cc_start: 0.8532 (mm) cc_final: 0.8107 (mp) outliers start: 18 outliers final: 9 residues processed: 322 average time/residue: 0.1099 time to fit residues: 50.8490 Evaluate side-chains 304 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 294 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 143 SER Chi-restraints excluded: chain Z residue 59 LYS 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 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: 0.6980 chunk 23 optimal weight: 0.9980 chunk 73 optimal weight: 0.0470 chunk 106 optimal weight: 6.9990 chunk 33 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 75 optimal weight: 0.5980 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 0.8980 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 199 ASN C 133 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.130097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.103060 restraints weight = 26150.038| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 2.94 r_work: 0.3351 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.1944 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= 0.132 Angle : 0.622 9.436 17079 Z= 0.323 Chirality : 0.041 0.184 2067 Planarity : 0.005 0.054 2097 Dihedral : 4.938 31.101 1764 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.33 % Favored : 92.61 % Rotamer: Outliers : 1.50 % Allowed : 15.04 % Favored : 83.45 % 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: -0.23 (0.22), residues: 1623 helix: 0.84 (0.16), residues: 1131 sheet: None (None), residues: 0 loop : -2.53 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 127 TYR 0.028 0.002 TYR Y 194 PHE 0.019 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 covalent geometry : bond 0.00294 (12555) covalent geometry : angle 0.62167 (17079) hydrogen bonds : bond 0.03736 ( 745) hydrogen bonds : angle 4.70095 ( 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 328 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 309 time to evaluate : 0.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 29 GLN cc_start: 0.8176 (mm-40) cc_final: 0.7858 (mm-40) REVERT: Z 52 GLU cc_start: 0.8167 (pm20) cc_final: 0.7672 (mp0) REVERT: Z 53 ASP cc_start: 0.8848 (p0) cc_final: 0.8344 (p0) REVERT: Z 58 LEU cc_start: 0.8787 (mt) cc_final: 0.8523 (mt) REVERT: A 135 ARG cc_start: 0.8030 (mpp-170) cc_final: 0.7395 (mtm-85) REVERT: A 180 ASP cc_start: 0.7946 (p0) cc_final: 0.7641 (p0) REVERT: B 58 LEU cc_start: 0.9009 (mt) cc_final: 0.8691 (mt) REVERT: B 59 LYS cc_start: 0.8436 (mmtm) cc_final: 0.8177 (mmtm) REVERT: B 216 GLU cc_start: 0.8246 (tm-30) cc_final: 0.7807 (tm-30) REVERT: C 24 GLU cc_start: 0.7966 (mm-30) cc_final: 0.7735 (mm-30) REVERT: C 133 ASN cc_start: 0.8282 (t0) cc_final: 0.6750 (t0) REVERT: D 17 TRP cc_start: 0.8501 (t60) cc_final: 0.8261 (t-100) REVERT: D 31 MET cc_start: 0.8158 (mtm) cc_final: 0.7837 (mtm) REVERT: D 104 MET cc_start: 0.7719 (OUTLIER) cc_final: 0.7104 (ptp) REVERT: D 141 ILE cc_start: 0.8522 (mm) cc_final: 0.8088 (mp) outliers start: 19 outliers final: 11 residues processed: 315 average time/residue: 0.1071 time to fit residues: 48.3209 Evaluate side-chains 306 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 294 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 143 SER Chi-restraints excluded: chain Y residue 148 GLN Chi-restraints excluded: chain Z residue 59 LYS 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 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: 0.9990 chunk 4 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 153 optimal weight: 0.0770 chunk 99 optimal weight: 5.9990 chunk 76 optimal weight: 0.7980 chunk 103 optimal weight: 0.1980 chunk 134 optimal weight: 0.5980 chunk 87 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 199 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.131577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.104499 restraints weight = 26217.723| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 2.96 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: 0.8193 moved from start: 0.2093 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= 0.125 Angle : 0.623 9.895 17079 Z= 0.325 Chirality : 0.041 0.192 2067 Planarity : 0.005 0.054 2097 Dihedral : 4.870 30.138 1764 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.96 % Favored : 92.98 % Rotamer: Outliers : 1.27 % Allowed : 16.94 % Favored : 81.79 % 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: -0.17 (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 0.036 0.002 TYR Y 194 PHE 0.019 0.001 PHE A 14 TRP 0.014 0.001 TRP Z 222 HIS 0.004 0.001 HIS B 298 Details of bonding type rmsd covalent geometry : bond 0.00272 (12555) covalent geometry : angle 0.62320 (17079) hydrogen bonds : bond 0.03600 ( 745) hydrogen bonds : angle 4.63079 ( 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 331 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 315 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Y 29 GLN cc_start: 0.8114 (mm-40) cc_final: 0.7808 (mm-40) REVERT: Y 243 LYS cc_start: 0.8589 (tttt) cc_final: 0.8093 (mmmm) REVERT: Z 54 ARG cc_start: 0.8121 (mmt180) cc_final: 0.7223 (mmt90) REVERT: A 133 ASN cc_start: 0.8082 (t0) cc_final: 0.7195 (t0) REVERT: A 135 ARG cc_start: 0.8018 (mpp-170) cc_final: 0.7429 (mtm-85) REVERT: A 242 SER cc_start: 0.8943 (t) cc_final: 0.8703 (p) REVERT: B 58 LEU cc_start: 0.8983 (mt) cc_final: 0.8678 (mt) REVERT: B 59 LYS cc_start: 0.8450 (mmtm) cc_final: 0.8189 (mmtm) REVERT: B 154 PHE cc_start: 0.8715 (t80) cc_final: 0.8361 (t80) REVERT: B 216 GLU cc_start: 0.8202 (tm-30) cc_final: 0.7843 (tm-30) REVERT: C 24 GLU cc_start: 0.7830 (mm-30) cc_final: 0.7574 (mm-30) REVERT: C 133 ASN cc_start: 0.7858 (t0) cc_final: 0.7464 (t0) REVERT: D 17 TRP cc_start: 0.8482 (t60) cc_final: 0.8242 (t-100) REVERT: D 31 MET cc_start: 0.8067 (mtm) cc_final: 0.7732 (mtm) REVERT: D 54 ARG cc_start: 0.8271 (mmt180) cc_final: 0.7375 (mpt-90) REVERT: D 83 GLU cc_start: 0.8458 (mt-10) cc_final: 0.8080 (mt-10) REVERT: D 104 MET cc_start: 0.7723 (OUTLIER) cc_final: 0.7107 (ptp) outliers start: 16 outliers final: 10 residues processed: 319 average time/residue: 0.1073 time to fit residues: 49.0880 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 : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 143 SER Chi-restraints excluded: chain Z residue 59 LYS 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 31 MET Chi-restraints excluded: chain B residue 105 MET Chi-restraints excluded: chain C residue 188 MET Chi-restraints excluded: chain C residue 199 ASN Chi-restraints excluded: chain D residue 104 MET 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: 0.0980 chunk 156 optimal weight: 0.3980 chunk 16 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 30 optimal weight: 0.9990 chunk 2 optimal weight: 0.2980 chunk 51 optimal weight: 0.6980 chunk 34 optimal weight: 0.9980 chunk 74 optimal weight: 0.5980 chunk 121 optimal weight: 0.0030 overall best weight: 0.2790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3922 r_free = 0.3922 target = 0.132492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.105664 restraints weight = 26314.402| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 2.97 r_work: 0.3389 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.2316 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= 0.121 Angle : 0.632 10.134 17079 Z= 0.328 Chirality : 0.040 0.195 2067 Planarity : 0.005 0.053 2097 Dihedral : 4.793 30.295 1764 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.96 % Favored : 92.98 % Rotamer: Outliers : 1.43 % Allowed : 17.58 % Favored : 81.00 % 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: -0.14 (0.22), residues: 1623 helix: 0.92 (0.16), residues: 1128 sheet: None (None), residues: 0 loop : -2.53 (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 0.015 0.001 PHE A 14 TRP 0.014 0.001 TRP Z 222 HIS 0.004 0.001 HIS B 298 Details of bonding type rmsd covalent geometry : bond 0.00262 (12555) covalent geometry : angle 0.63157 (17079) hydrogen bonds : bond 0.03485 ( 745) hydrogen bonds : angle 4.56396 ( 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 326 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 308 time to evaluate : 0.357 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Y 29 GLN cc_start: 0.8051 (mm-40) cc_final: 0.7698 (mm-40) REVERT: Y 146 CYS cc_start: 0.8545 (m) cc_final: 0.8121 (p) REVERT: Y 243 LYS cc_start: 0.8472 (tttt) cc_final: 0.8013 (mmmm) REVERT: A 133 ASN cc_start: 0.8092 (t0) cc_final: 0.7225 (t0) REVERT: A 135 ARG cc_start: 0.7999 (mpp-170) cc_final: 0.7423 (mtm-85) REVERT: A 242 SER cc_start: 0.9054 (t) cc_final: 0.8774 (p) REVERT: B 52 GLU cc_start: 0.7993 (pm20) cc_final: 0.7732 (mp0) REVERT: B 54 ARG cc_start: 0.8027 (mmt180) cc_final: 0.6965 (mpt-90) REVERT: B 58 LEU cc_start: 0.8983 (mt) cc_final: 0.8700 (mt) REVERT: B 59 LYS cc_start: 0.8559 (mmtm) cc_final: 0.8286 (mmtm) REVERT: B 104 MET cc_start: 0.7499 (mtp) cc_final: 0.7150 (ptm) REVERT: B 148 ASN cc_start: 0.8118 (m-40) cc_final: 0.7862 (m110) REVERT: B 154 PHE cc_start: 0.8691 (t80) cc_final: 0.8427 (t80) REVERT: B 216 GLU cc_start: 0.8260 (tm-30) cc_final: 0.7752 (tm-30) REVERT: C 24 GLU cc_start: 0.7853 (mm-30) cc_final: 0.7557 (mm-30) REVERT: D 17 TRP cc_start: 0.8426 (t60) cc_final: 0.8219 (t-100) REVERT: D 31 MET cc_start: 0.7873 (mtm) cc_final: 0.7578 (mtm) REVERT: D 54 ARG cc_start: 0.8168 (mmt180) cc_final: 0.7877 (mmt90) outliers start: 18 outliers final: 11 residues processed: 315 average time/residue: 0.1028 time to fit residues: 47.1769 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 : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 143 SER Chi-restraints excluded: chain Z residue 59 LYS 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 31 MET Chi-restraints excluded: chain B residue 105 MET Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 188 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 22 optimal weight: 2.9990 chunk 154 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 117 optimal weight: 0.5980 chunk 112 optimal weight: 0.8980 chunk 136 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 chunk 89 optimal weight: 4.9990 chunk 59 optimal weight: 0.7980 chunk 71 optimal weight: 3.9990 chunk 56 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 199 ASN A 199 ASN C 199 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.130247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.104463 restraints weight = 26226.111| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 2.65 r_work: 0.3362 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.2362 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= 0.142 Angle : 0.657 13.828 17079 Z= 0.340 Chirality : 0.041 0.199 2067 Planarity : 0.005 0.053 2097 Dihedral : 4.843 31.190 1764 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.33 % Favored : 92.61 % Rotamer: Outliers : 1.66 % Allowed : 18.61 % Favored : 79.73 % 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: -0.13 (0.22), residues: 1623 helix: 0.92 (0.16), residues: 1131 sheet: None (None), residues: 0 loop : -2.52 (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 0.020 0.001 PHE A 14 TRP 0.014 0.001 TRP Z 222 HIS 0.004 0.001 HIS B 298 Details of bonding type rmsd covalent geometry : bond 0.00323 (12555) covalent geometry : angle 0.65714 (17079) hydrogen bonds : bond 0.03579 ( 745) hydrogen bonds : angle 4.62240 ( 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 325 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 304 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Y 29 GLN cc_start: 0.8150 (mm-40) cc_final: 0.7827 (mm-40) REVERT: Y 146 CYS cc_start: 0.8548 (m) cc_final: 0.8120 (p) REVERT: Y 182 MET cc_start: 0.8559 (mmt) cc_final: 0.8312 (mmm) REVERT: Y 243 LYS cc_start: 0.8388 (tttt) cc_final: 0.7935 (mmmm) REVERT: Z 215 ASP cc_start: 0.8308 (p0) cc_final: 0.8083 (p0) REVERT: A 29 GLN cc_start: 0.7862 (mm-40) cc_final: 0.7479 (mm-40) REVERT: A 133 ASN cc_start: 0.8138 (t0) cc_final: 0.7218 (t0) REVERT: A 135 ARG cc_start: 0.8016 (mpp-170) cc_final: 0.7428 (mtm-85) REVERT: A 242 SER cc_start: 0.9038 (t) cc_final: 0.8749 (p) REVERT: B 54 ARG cc_start: 0.8002 (mmt180) cc_final: 0.7073 (mmt90) REVERT: B 58 LEU cc_start: 0.9015 (mt) cc_final: 0.8730 (mt) REVERT: B 59 LYS cc_start: 0.8580 (mmtm) cc_final: 0.8296 (mmtm) REVERT: B 104 MET cc_start: 0.7583 (mtp) cc_final: 0.7113 (ptm) REVERT: B 154 PHE cc_start: 0.8719 (t80) cc_final: 0.8375 (t80) REVERT: B 216 GLU cc_start: 0.8169 (tm-30) cc_final: 0.7812 (tm-30) REVERT: C 133 ASN cc_start: 0.7692 (t0) cc_final: 0.7176 (t0) REVERT: C 242 SER cc_start: 0.8978 (t) cc_final: 0.8642 (p) REVERT: D 17 TRP cc_start: 0.8510 (t60) cc_final: 0.8242 (t-100) REVERT: D 31 MET cc_start: 0.7872 (OUTLIER) cc_final: 0.7571 (mtm) REVERT: D 54 ARG cc_start: 0.8210 (mmt180) cc_final: 0.7876 (mmt90) REVERT: D 83 GLU cc_start: 0.8576 (mt-10) cc_final: 0.8312 (mt-10) REVERT: D 85 GLU cc_start: 0.7487 (pp20) cc_final: 0.7248 (mm-30) REVERT: D 104 MET cc_start: 0.7701 (ptm) cc_final: 0.7269 (ptp) outliers start: 21 outliers final: 13 residues processed: 312 average time/residue: 0.1054 time to fit residues: 47.5577 Evaluate side-chains 309 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 295 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 143 SER Chi-restraints excluded: chain Z residue 59 LYS 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 167 VAL Chi-restraints excluded: chain B residue 31 MET Chi-restraints excluded: chain B residue 105 MET 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 D residue 31 MET Chi-restraints excluded: chain D residue 290 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 97 optimal weight: 0.5980 chunk 147 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 106 optimal weight: 6.9990 chunk 152 optimal weight: 0.7980 chunk 133 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 chunk 58 optimal weight: 0.9990 chunk 60 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.3885 r_free = 0.3885 target = 0.130005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.102933 restraints weight = 26306.743| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 2.97 r_work: 0.3345 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12555 Z= 0.142 Angle : 0.657 10.620 17079 Z= 0.342 Chirality : 0.041 0.213 2067 Planarity : 0.005 0.058 2097 Dihedral : 4.910 31.304 1764 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.02 % Favored : 92.79 % Rotamer: Outliers : 1.82 % Allowed : 18.76 % Favored : 79.41 % 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: -0.14 (0.22), residues: 1623 helix: 0.91 (0.16), residues: 1131 sheet: None (None), residues: 0 loop : -2.52 (0.26), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 127 TYR 0.032 0.002 TYR Y 194 PHE 0.018 0.001 PHE A 14 TRP 0.028 0.001 TRP D 36 HIS 0.005 0.001 HIS Z 61 Details of bonding type rmsd covalent geometry : bond 0.00324 (12555) covalent geometry : angle 0.65713 (17079) hydrogen bonds : bond 0.03595 ( 745) hydrogen bonds : angle 4.62886 ( 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 324 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 301 time to evaluate : 0.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 29 GLN cc_start: 0.8171 (mm-40) cc_final: 0.7846 (mm-40) REVERT: Y 146 CYS cc_start: 0.8544 (m) cc_final: 0.8133 (p) REVERT: Y 182 MET cc_start: 0.8539 (mmt) cc_final: 0.8301 (mmm) REVERT: Z 40 MET cc_start: 0.9065 (mmm) cc_final: 0.8653 (mmm) REVERT: A 133 ASN cc_start: 0.8173 (t0) cc_final: 0.7252 (t0) REVERT: A 135 ARG cc_start: 0.8007 (mpp-170) cc_final: 0.7435 (mtm-85) REVERT: A 242 SER cc_start: 0.9103 (t) cc_final: 0.8860 (p) REVERT: B 54 ARG cc_start: 0.8127 (mmt180) cc_final: 0.7367 (mmt90) REVERT: B 58 LEU cc_start: 0.9020 (mt) cc_final: 0.8756 (mt) REVERT: B 59 LYS cc_start: 0.8598 (mmtm) cc_final: 0.8328 (mmtm) REVERT: B 104 MET cc_start: 0.7614 (mtp) cc_final: 0.7157 (ptm) REVERT: B 154 PHE cc_start: 0.8720 (t80) cc_final: 0.8388 (t80) REVERT: B 216 GLU cc_start: 0.8205 (tm-30) cc_final: 0.7669 (tm-30) REVERT: C 133 ASN cc_start: 0.7882 (t0) cc_final: 0.7184 (t0) REVERT: C 242 SER cc_start: 0.8818 (t) cc_final: 0.8604 (p) REVERT: D 17 TRP cc_start: 0.8536 (t60) cc_final: 0.8262 (t-100) REVERT: D 29 GLU cc_start: 0.8266 (tm-30) cc_final: 0.7769 (tm-30) REVERT: D 31 MET cc_start: 0.7961 (OUTLIER) cc_final: 0.7647 (mtm) REVERT: D 54 ARG cc_start: 0.8149 (mmt180) cc_final: 0.7845 (mmt90) REVERT: D 83 GLU cc_start: 0.8608 (mt-10) cc_final: 0.8318 (mt-10) outliers start: 23 outliers final: 16 residues processed: 311 average time/residue: 0.1064 time to fit residues: 47.9264 Evaluate side-chains 312 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 295 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 143 SER Chi-restraints excluded: chain Z residue 47 LEU Chi-restraints excluded: chain Z residue 59 LYS Chi-restraints excluded: chain Z residue 212 VAL Chi-restraints excluded: chain Z residue 261 ILE Chi-restraints excluded: chain Z residue 285 ILE Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain B residue 31 MET Chi-restraints excluded: chain B residue 105 MET 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 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 261 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 37 optimal weight: 0.7980 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: 0.2980 chunk 152 optimal weight: 0.0270 chunk 132 optimal weight: 0.0770 chunk 125 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 149 optimal weight: 1.9990 overall best weight: 0.2796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN A 199 ASN C 199 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.132505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.106204 restraints weight = 26139.307| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 2.88 r_work: 0.3394 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12555 Z= 0.125 Angle : 0.657 10.251 17079 Z= 0.339 Chirality : 0.041 0.233 2067 Planarity : 0.005 0.053 2097 Dihedral : 4.817 29.225 1764 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.09 % Favored : 92.73 % Rotamer: Outliers : 1.50 % Allowed : 19.32 % Favored : 79.18 % 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: -0.14 (0.22), residues: 1623 helix: 0.93 (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 0.009 0.001 ARG A 127 TYR 0.040 0.002 TYR Y 194 PHE 0.018 0.001 PHE A 14 TRP 0.018 0.001 TRP D 200 HIS 0.003 0.001 HIS Z 61 Details of bonding type rmsd covalent geometry : bond 0.00275 (12555) covalent geometry : angle 0.65656 (17079) hydrogen bonds : bond 0.03497 ( 745) hydrogen bonds : angle 4.57717 ( 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 322 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 303 time to evaluate : 0.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 29 GLN cc_start: 0.8018 (mm-40) cc_final: 0.7681 (mm-40) REVERT: Y 90 VAL cc_start: 0.9058 (t) cc_final: 0.8849 (m) REVERT: Y 146 CYS cc_start: 0.8551 (m) cc_final: 0.8100 (p) REVERT: Y 182 MET cc_start: 0.8552 (mmt) cc_final: 0.8316 (mmm) REVERT: Z 40 MET cc_start: 0.9061 (mmm) cc_final: 0.8624 (mmm) REVERT: A 135 ARG cc_start: 0.7948 (mpp-170) cc_final: 0.7328 (mtm-85) REVERT: A 242 SER cc_start: 0.9002 (t) cc_final: 0.8752 (p) REVERT: B 54 ARG cc_start: 0.8033 (mmt180) cc_final: 0.7224 (mmt90) REVERT: B 58 LEU cc_start: 0.8962 (mt) cc_final: 0.8644 (mt) REVERT: B 59 LYS cc_start: 0.8578 (mmtm) cc_final: 0.8289 (mmtm) REVERT: B 104 MET cc_start: 0.7612 (mtp) cc_final: 0.7240 (ptm) REVERT: B 154 PHE cc_start: 0.8678 (t80) cc_final: 0.8380 (t80) REVERT: B 160 GLU cc_start: 0.7834 (mm-30) cc_final: 0.7319 (pt0) REVERT: B 216 GLU cc_start: 0.8184 (tm-30) cc_final: 0.7733 (tm-30) REVERT: B 246 SER cc_start: 0.8090 (t) cc_final: 0.7722 (m) REVERT: C 146 CYS cc_start: 0.8650 (t) cc_final: 0.7796 (p) REVERT: C 199 ASN cc_start: 0.8768 (OUTLIER) cc_final: 0.8486 (t0) REVERT: C 242 SER cc_start: 0.8966 (t) cc_final: 0.8644 (p) REVERT: D 17 TRP cc_start: 0.8459 (t60) cc_final: 0.8235 (t-100) REVERT: D 29 GLU cc_start: 0.8210 (tm-30) cc_final: 0.7655 (tm-30) REVERT: D 31 MET cc_start: 0.7903 (OUTLIER) cc_final: 0.7596 (mtm) REVERT: D 54 ARG cc_start: 0.8088 (mmt180) cc_final: 0.6816 (mmt90) REVERT: D 83 GLU cc_start: 0.8610 (mt-10) cc_final: 0.8326 (mt-10) REVERT: D 104 MET cc_start: 0.6310 (ptm) cc_final: 0.6077 (ptp) outliers start: 19 outliers final: 14 residues processed: 311 average time/residue: 0.1007 time to fit residues: 45.6449 Evaluate side-chains 309 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 293 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 143 SER Chi-restraints excluded: chain Z residue 47 LEU Chi-restraints excluded: chain Z residue 59 LYS Chi-restraints excluded: chain Z residue 212 VAL Chi-restraints excluded: chain Z residue 261 ILE Chi-restraints excluded: chain A residue 29 GLN Chi-restraints excluded: chain A residue 95 SER 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 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 261 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 4 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 2 optimal weight: 0.0770 chunk 104 optimal weight: 0.5980 chunk 6 optimal weight: 2.9990 chunk 125 optimal weight: 3.9990 chunk 1 optimal weight: 0.9980 chunk 42 optimal weight: 0.5980 chunk 34 optimal weight: 0.7980 chunk 144 optimal weight: 0.7980 chunk 151 optimal weight: 1.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.131489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.105016 restraints weight = 26142.506| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 2.87 r_work: 0.3381 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.2603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12555 Z= 0.133 Angle : 0.675 15.502 17079 Z= 0.347 Chirality : 0.041 0.240 2067 Planarity : 0.005 0.054 2097 Dihedral : 4.803 29.042 1764 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.27 % Favored : 92.54 % Rotamer: Outliers : 1.35 % Allowed : 19.56 % Favored : 79.10 % 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: -0.16 (0.22), residues: 1623 helix: 0.91 (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 0.009 0.001 ARG C 127 TYR 0.039 0.002 TYR Y 194 PHE 0.021 0.001 PHE A 14 TRP 0.022 0.001 TRP Z 147 HIS 0.004 0.001 HIS B 298 Details of bonding type rmsd covalent geometry : bond 0.00302 (12555) covalent geometry : angle 0.67537 (17079) hydrogen bonds : bond 0.03508 ( 745) hydrogen bonds : angle 4.60394 ( 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 319 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 302 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 29 GLN cc_start: 0.8063 (mm-40) cc_final: 0.7696 (mm-40) REVERT: Y 90 VAL cc_start: 0.9065 (t) cc_final: 0.8855 (m) REVERT: Y 146 CYS cc_start: 0.8596 (m) cc_final: 0.8164 (p) REVERT: Y 182 MET cc_start: 0.8530 (mmt) cc_final: 0.8294 (mmm) REVERT: Z 40 MET cc_start: 0.9084 (mmm) cc_final: 0.8648 (mmm) REVERT: A 135 ARG cc_start: 0.8020 (mpp-170) cc_final: 0.7367 (mtm-85) REVERT: A 242 SER cc_start: 0.9061 (t) cc_final: 0.8839 (p) REVERT: B 54 ARG cc_start: 0.8020 (mmt180) cc_final: 0.7226 (mmt90) REVERT: B 58 LEU cc_start: 0.8958 (mt) cc_final: 0.8642 (mt) REVERT: B 59 LYS cc_start: 0.8541 (mmtm) cc_final: 0.8281 (mmtm) REVERT: B 104 MET cc_start: 0.7616 (mtp) cc_final: 0.7243 (ptm) REVERT: B 154 PHE cc_start: 0.8683 (t80) cc_final: 0.8410 (t80) REVERT: B 160 GLU cc_start: 0.7962 (mm-30) cc_final: 0.7465 (pt0) REVERT: B 216 GLU cc_start: 0.8187 (tm-30) cc_final: 0.7743 (tm-30) REVERT: B 246 SER cc_start: 0.8159 (t) cc_final: 0.7718 (m) REVERT: C 90 VAL cc_start: 0.8938 (t) cc_final: 0.8694 (m) REVERT: C 146 CYS cc_start: 0.8658 (t) cc_final: 0.7810 (p) REVERT: D 17 TRP cc_start: 0.8486 (t60) cc_final: 0.8222 (t-100) REVERT: D 29 GLU cc_start: 0.8189 (tm-30) cc_final: 0.7647 (tm-30) REVERT: D 31 MET cc_start: 0.7881 (OUTLIER) cc_final: 0.7580 (mtm) REVERT: D 54 ARG cc_start: 0.8129 (mmt180) cc_final: 0.6806 (mmt90) REVERT: D 83 GLU cc_start: 0.8541 (mt-10) cc_final: 0.8182 (mt-10) outliers start: 17 outliers final: 16 residues processed: 310 average time/residue: 0.1015 time to fit residues: 45.6538 Evaluate side-chains 316 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 299 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 143 SER Chi-restraints excluded: chain Z residue 47 LEU Chi-restraints excluded: chain Z residue 59 LYS Chi-restraints excluded: chain Z residue 212 VAL Chi-restraints excluded: chain Z residue 215 ASP 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 31 MET Chi-restraints excluded: chain B residue 105 MET 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 188 MET Chi-restraints excluded: chain D residue 31 MET Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 261 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 8 optimal weight: 7.9990 chunk 85 optimal weight: 9.9990 chunk 96 optimal weight: 0.9980 chunk 33 optimal weight: 0.3980 chunk 127 optimal weight: 0.0870 chunk 138 optimal weight: 0.2980 chunk 149 optimal weight: 0.7980 chunk 125 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 74 optimal weight: 0.2980 overall best weight: 0.3758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 199 ASN A 29 GLN A 240 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.132912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.106390 restraints weight = 26028.140| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 2.94 r_work: 0.3397 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.2684 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= 0.127 Angle : 0.670 14.728 17079 Z= 0.344 Chirality : 0.041 0.237 2067 Planarity : 0.005 0.053 2097 Dihedral : 4.737 27.861 1764 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.21 % Favored : 92.61 % Rotamer: Outliers : 1.27 % Allowed : 20.19 % Favored : 78.54 % 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: -0.14 (0.22), residues: 1623 helix: 0.93 (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 0.010 0.001 ARG D 86 TYR 0.038 0.002 TYR Y 194 PHE 0.022 0.001 PHE Z 154 TRP 0.014 0.001 TRP Z 222 HIS 0.003 0.001 HIS B 298 Details of bonding type rmsd covalent geometry : bond 0.00282 (12555) covalent geometry : angle 0.67048 (17079) hydrogen bonds : bond 0.03443 ( 745) hydrogen bonds : angle 4.53832 ( 2235) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3155.49 seconds wall clock time: 54 minutes 34.22 seconds (3274.22 seconds total)