Starting phenix.real_space_refine on Wed Jul 30 11:25:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vlx_32030/07_2025/7vlx_32030.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vlx_32030/07_2025/7vlx_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7vlx_32030/07_2025/7vlx_32030.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vlx_32030/07_2025/7vlx_32030.map" model { file = "/net/cci-nas-00/data/ceres_data/7vlx_32030/07_2025/7vlx_32030.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vlx_32030/07_2025/7vlx_32030.cif" } resolution = 3.12 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 7.90, per 1000 atoms: 0.64 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: 3.17 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 1.19 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: 3.21 Time building geometry restraints manager: 3.74 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: 0.02 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: 1.300 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: 0.020 Extract box with map and model: 0.470 Check model and map are aligned: 0.090 Set scattering table: 0.140 Process input model: 29.960 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.280 ------------------------------------------------------------------------------- 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 : 12.56 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.22), 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 TRP 0.025 0.001 TRP D 222 HIS 0.003 0.001 HIS D 298 PHE 0.021 0.001 PHE D 154 TYR 0.023 0.001 TYR D 48 ARG 0.015 0.001 ARG B 60 Details of bonding type rmsd hydrogen bonds : bond 0.16327 ( 745) hydrogen bonds : angle 6.24524 ( 2235) covalent geometry : bond 0.00277 (12555) covalent geometry : angle 0.69943 (17079) *********************** 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 : 1.320 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: 0.8517 (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: 0.2282 time to fit residues: 108.4424 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 : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 134 optimal weight: 5.9990 chunk 120 optimal weight: 1.9990 chunk 66 optimal weight: 0.4980 chunk 41 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 75 optimal weight: 0.7980 chunk 92 optimal weight: 3.9990 chunk 144 optimal weight: 0.9980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN A 133 ASN A 199 ASN B 255 ASN D 255 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.127614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.101841 restraints weight = 26124.619| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 2.57 r_work: 0.3328 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12555 Z= 0.184 Angle : 0.680 8.381 17079 Z= 0.355 Chirality : 0.042 0.214 2067 Planarity : 0.005 0.053 2097 Dihedral : 5.202 34.896 1764 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.58 % Favored : 92.36 % Rotamer: Outliers : 1.19 % Allowed : 11.01 % Favored : 87.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.22), residues: 1623 helix: 0.71 (0.16), residues: 1119 sheet: None (None), residues: 0 loop : -2.55 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP Z 222 HIS 0.006 0.001 HIS B 298 PHE 0.017 0.001 PHE A 27 TYR 0.024 0.002 TYR C 194 ARG 0.009 0.001 ARG B 60 Details of bonding type rmsd hydrogen bonds : bond 0.04345 ( 745) hydrogen bonds : angle 5.04971 ( 2235) covalent geometry : bond 0.00411 (12555) covalent geometry : angle 0.67991 (17079) *********************** 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 : 1.414 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Y 21 ILE cc_start: 0.8502 (pt) cc_final: 0.8286 (pt) REVERT: Y 127 ARG cc_start: 0.8174 (ttm110) cc_final: 0.7437 (ttm110) REVERT: Z 58 LEU cc_start: 0.8920 (mt) cc_final: 0.8596 (mt) REVERT: Z 86 ARG cc_start: 0.7036 (ppt170) cc_final: 0.6809 (ppt170) REVERT: A 126 ASP cc_start: 0.7828 (t0) cc_final: 0.7473 (t0) REVERT: A 133 ASN cc_start: 0.8090 (t0) cc_final: 0.7867 (t0) REVERT: B 58 LEU cc_start: 0.8934 (mt) cc_final: 0.8617 (mt) REVERT: B 216 GLU cc_start: 0.8054 (tm-30) cc_final: 0.7755 (tm-30) REVERT: C 21 ILE cc_start: 0.8418 (pt) cc_final: 0.8147 (pt) REVERT: C 53 THR cc_start: 0.8776 (m) cc_final: 0.8499 (t) REVERT: C 127 ARG cc_start: 0.8198 (mtp-110) cc_final: 0.7526 (mtp-110) REVERT: C 131 LYS cc_start: 0.8996 (ptpp) cc_final: 0.8483 (tptp) REVERT: D 17 TRP cc_start: 0.8535 (t60) cc_final: 0.8226 (t-100) REVERT: D 86 ARG cc_start: 0.6928 (ttp80) cc_final: 0.6656 (ttp80) REVERT: D 200 TRP cc_start: 0.8160 (m-10) cc_final: 0.7954 (m-10) outliers start: 15 outliers final: 6 residues processed: 318 average time/residue: 0.2623 time to fit residues: 122.5589 Evaluate side-chains 301 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 295 time to evaluate : 1.688 ------------------------------------------------------------------------------- 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 118 optimal weight: 3.9990 chunk 122 optimal weight: 0.0270 chunk 153 optimal weight: 3.9990 chunk 43 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 47 optimal weight: 0.7980 chunk 21 optimal weight: 0.2980 chunk 157 optimal weight: 0.0570 chunk 12 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 overall best weight: 0.4356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 133 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.130295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.103605 restraints weight = 26293.925| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 2.85 r_work: 0.3363 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12555 Z= 0.125 Angle : 0.625 9.008 17079 Z= 0.324 Chirality : 0.041 0.182 2067 Planarity : 0.005 0.053 2097 Dihedral : 4.937 31.003 1764 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.78 % Favored : 93.16 % Rotamer: Outliers : 1.27 % Allowed : 13.86 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (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 TRP 0.016 0.001 TRP Z 222 HIS 0.003 0.001 HIS B 298 PHE 0.018 0.001 PHE A 14 TYR 0.021 0.002 TYR Z 48 ARG 0.006 0.001 ARG A 127 Details of bonding type rmsd hydrogen bonds : bond 0.03865 ( 745) hydrogen bonds : angle 4.77633 ( 2235) covalent geometry : bond 0.00266 (12555) covalent geometry : angle 0.62525 (17079) *********************** 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 332 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 316 time to evaluate : 1.274 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Y 21 ILE cc_start: 0.8459 (pt) cc_final: 0.8216 (pt) REVERT: Y 29 GLN cc_start: 0.8053 (mm-40) cc_final: 0.7707 (mm-40) REVERT: Z 48 TYR cc_start: 0.6242 (m-10) cc_final: 0.5811 (m-80) REVERT: Z 53 ASP cc_start: 0.8592 (p0) cc_final: 0.8336 (p0) REVERT: Z 54 ARG cc_start: 0.8082 (mmt180) cc_final: 0.7296 (mmt90) REVERT: A 115 ARG cc_start: 0.8536 (mtp85) cc_final: 0.8323 (mtp85) REVERT: A 127 ARG cc_start: 0.8343 (mtp-110) cc_final: 0.8108 (ttm110) REVERT: B 58 LEU cc_start: 0.8940 (mt) cc_final: 0.8500 (mt) REVERT: B 59 LYS cc_start: 0.8506 (mmtm) cc_final: 0.8041 (mmtm) REVERT: B 216 GLU cc_start: 0.8219 (tm-30) cc_final: 0.7779 (tm-30) REVERT: C 131 LYS cc_start: 0.8781 (ptpp) cc_final: 0.8554 (tptp) REVERT: D 17 TRP cc_start: 0.8479 (t60) cc_final: 0.8271 (t-100) REVERT: D 31 MET cc_start: 0.8069 (mtm) cc_final: 0.7836 (mtm) REVERT: D 141 ILE cc_start: 0.8544 (mm) cc_final: 0.8118 (mp) REVERT: D 200 TRP cc_start: 0.8157 (m-10) cc_final: 0.7955 (m-10) outliers start: 16 outliers final: 10 residues processed: 325 average time/residue: 0.2414 time to fit residues: 111.7975 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 : 1.247 ------------------------------------------------------------------------------- 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 117 LEU 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 85 optimal weight: 6.9990 chunk 47 optimal weight: 2.9990 chunk 117 optimal weight: 0.9990 chunk 103 optimal weight: 0.5980 chunk 143 optimal weight: 0.9980 chunk 74 optimal weight: 0.5980 chunk 58 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 137 optimal weight: 4.9990 chunk 135 optimal weight: 0.5980 chunk 0 optimal weight: 6.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3884 r_free = 0.3884 target = 0.129518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.102761 restraints weight = 25965.432| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 2.84 r_work: 0.3349 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 12555 Z= 0.136 Angle : 0.625 9.435 17079 Z= 0.326 Chirality : 0.041 0.186 2067 Planarity : 0.005 0.055 2097 Dihedral : 4.980 31.481 1764 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.33 % Favored : 92.61 % Rotamer: Outliers : 1.58 % Allowed : 15.28 % Favored : 83.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.22), residues: 1623 helix: 0.82 (0.16), residues: 1134 sheet: None (None), residues: 0 loop : -2.53 (0.27), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP Z 222 HIS 0.004 0.001 HIS B 298 PHE 0.019 0.001 PHE D 154 TYR 0.028 0.002 TYR Y 194 ARG 0.006 0.001 ARG C 127 Details of bonding type rmsd hydrogen bonds : bond 0.03756 ( 745) hydrogen bonds : angle 4.71215 ( 2235) covalent geometry : bond 0.00306 (12555) covalent geometry : angle 0.62489 (17079) *********************** 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 329 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 309 time to evaluate : 1.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 29 GLN cc_start: 0.8184 (mm-40) cc_final: 0.7868 (mm-40) REVERT: Z 52 GLU cc_start: 0.8076 (pm20) cc_final: 0.7796 (mp0) REVERT: Z 54 ARG cc_start: 0.8086 (mmt180) cc_final: 0.7080 (mmt90) REVERT: Z 58 LEU cc_start: 0.8812 (mt) cc_final: 0.8611 (mt) REVERT: A 135 ARG cc_start: 0.8022 (mpp-170) cc_final: 0.7374 (mtm-85) REVERT: B 58 LEU cc_start: 0.9009 (mt) cc_final: 0.8699 (mt) REVERT: B 59 LYS cc_start: 0.8448 (mmtm) cc_final: 0.8195 (mmtm) REVERT: B 216 GLU cc_start: 0.8209 (tm-30) cc_final: 0.7755 (tm-30) REVERT: C 24 GLU cc_start: 0.7893 (mm-30) cc_final: 0.7686 (mm-30) REVERT: C 133 ASN cc_start: 0.8245 (t0) cc_final: 0.6708 (t0) REVERT: D 17 TRP cc_start: 0.8511 (t60) cc_final: 0.8275 (t-100) REVERT: D 31 MET cc_start: 0.8134 (mtm) cc_final: 0.7829 (mtm) REVERT: D 83 GLU cc_start: 0.8416 (mt-10) cc_final: 0.8039 (mt-10) REVERT: D 104 MET cc_start: 0.7768 (OUTLIER) cc_final: 0.6991 (ptp) REVERT: D 141 ILE cc_start: 0.8572 (mm) cc_final: 0.8130 (mp) outliers start: 20 outliers final: 12 residues processed: 317 average time/residue: 0.3923 time to fit residues: 175.7445 Evaluate side-chains 308 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 295 time to evaluate : 2.023 ------------------------------------------------------------------------------- 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 117 LEU Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 31 MET Chi-restraints excluded: chain B residue 105 MET Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 188 MET Chi-restraints excluded: chain D residue 104 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 151 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 66 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 63 optimal weight: 5.9990 chunk 48 optimal weight: 0.5980 chunk 19 optimal weight: 0.9980 chunk 96 optimal weight: 0.3980 chunk 122 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 148 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.128585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.104186 restraints weight = 26265.719| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 2.47 r_work: 0.3338 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12555 Z= 0.154 Angle : 0.645 9.813 17079 Z= 0.336 Chirality : 0.041 0.196 2067 Planarity : 0.005 0.053 2097 Dihedral : 5.021 32.595 1764 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.21 % Favored : 92.73 % Rotamer: Outliers : 1.35 % Allowed : 17.26 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.22), residues: 1623 helix: 0.86 (0.16), residues: 1131 sheet: None (None), residues: 0 loop : -2.54 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP Z 222 HIS 0.005 0.001 HIS B 298 PHE 0.019 0.001 PHE A 14 TYR 0.036 0.002 TYR Y 194 ARG 0.006 0.001 ARG D 121 Details of bonding type rmsd hydrogen bonds : bond 0.03784 ( 745) hydrogen bonds : angle 4.74548 ( 2235) covalent geometry : bond 0.00350 (12555) covalent geometry : angle 0.64487 (17079) *********************** 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 328 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 311 time to evaluate : 1.295 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Y 29 GLN cc_start: 0.8221 (mm-40) cc_final: 0.7915 (mm-40) REVERT: Y 243 LYS cc_start: 0.8678 (tttt) cc_final: 0.8238 (mmmm) REVERT: Z 53 ASP cc_start: 0.8783 (p0) cc_final: 0.8563 (p0) REVERT: Z 58 LEU cc_start: 0.8781 (mt) cc_final: 0.8518 (mt) REVERT: A 133 ASN cc_start: 0.8044 (t0) cc_final: 0.7221 (t0) REVERT: A 135 ARG cc_start: 0.8043 (mpp-170) cc_final: 0.7413 (mtm-85) REVERT: B 54 ARG cc_start: 0.8164 (mmt180) cc_final: 0.7068 (mpt-90) REVERT: B 58 LEU cc_start: 0.8996 (mt) cc_final: 0.8700 (mt) REVERT: B 59 LYS cc_start: 0.8485 (mmtm) cc_final: 0.8228 (mmtm) REVERT: B 216 GLU cc_start: 0.8114 (tm-30) cc_final: 0.7769 (tm-30) REVERT: C 24 GLU cc_start: 0.7916 (mm-30) cc_final: 0.7703 (mm-30) REVERT: C 133 ASN cc_start: 0.7881 (t0) cc_final: 0.7483 (t0) REVERT: D 17 TRP cc_start: 0.8553 (t60) cc_final: 0.8276 (t-100) REVERT: D 31 MET cc_start: 0.8099 (mtm) cc_final: 0.7766 (mtm) REVERT: D 54 ARG cc_start: 0.8271 (mmt180) cc_final: 0.7666 (mmt90) REVERT: D 85 GLU cc_start: 0.7500 (pp20) cc_final: 0.7256 (mm-30) REVERT: D 104 MET cc_start: 0.7791 (OUTLIER) cc_final: 0.7124 (ptp) outliers start: 17 outliers final: 13 residues processed: 316 average time/residue: 0.2394 time to fit residues: 107.6871 Evaluate side-chains 312 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 298 time to evaluate : 1.245 ------------------------------------------------------------------------------- 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 117 LEU Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 188 MET Chi-restraints excluded: chain B residue 31 MET Chi-restraints excluded: chain B residue 105 MET Chi-restraints excluded: chain B residue 212 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 102 optimal weight: 0.7980 chunk 114 optimal weight: 4.9990 chunk 94 optimal weight: 0.8980 chunk 47 optimal weight: 0.9990 chunk 104 optimal weight: 0.9990 chunk 112 optimal weight: 0.3980 chunk 66 optimal weight: 3.9990 chunk 151 optimal weight: 0.7980 chunk 93 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 chunk 152 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 199 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.129066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.103528 restraints weight = 26508.929| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 2.53 r_work: 0.3350 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.2278 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 : 0.654 10.023 17079 Z= 0.340 Chirality : 0.041 0.207 2067 Planarity : 0.005 0.053 2097 Dihedral : 5.031 32.074 1764 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.33 % Favored : 92.61 % Rotamer: Outliers : 1.50 % Allowed : 18.45 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.32 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.22), residues: 1623 helix: 0.87 (0.16), residues: 1131 sheet: None (None), residues: 0 loop : -2.54 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP Z 36 HIS 0.004 0.001 HIS B 298 PHE 0.021 0.001 PHE D 154 TYR 0.040 0.002 TYR Y 194 ARG 0.007 0.001 ARG A 127 Details of bonding type rmsd hydrogen bonds : bond 0.03696 ( 745) hydrogen bonds : angle 4.70375 ( 2235) covalent geometry : bond 0.00320 (12555) covalent geometry : angle 0.65351 (17079) *********************** 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 324 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 305 time to evaluate : 1.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 29 GLN cc_start: 0.8215 (mm-40) cc_final: 0.7920 (mm-40) REVERT: Y 146 CYS cc_start: 0.8493 (m) cc_final: 0.8110 (p) REVERT: Y 243 LYS cc_start: 0.8613 (tttt) cc_final: 0.8154 (mmmm) REVERT: Z 58 LEU cc_start: 0.8842 (mt) cc_final: 0.8572 (mt) REVERT: A 135 ARG cc_start: 0.8035 (mpp-170) cc_final: 0.7385 (mtm-85) REVERT: B 36 TRP cc_start: 0.8159 (t60) cc_final: 0.7952 (t-100) REVERT: B 52 GLU cc_start: 0.8053 (pm20) cc_final: 0.7728 (mp0) REVERT: B 54 ARG cc_start: 0.8059 (mmt180) cc_final: 0.7171 (mmt90) REVERT: B 58 LEU cc_start: 0.9025 (mt) cc_final: 0.8754 (mt) REVERT: B 59 LYS cc_start: 0.8525 (mmtm) cc_final: 0.8258 (mmtm) REVERT: B 216 GLU cc_start: 0.8199 (tm-30) cc_final: 0.7711 (tm-30) REVERT: C 24 GLU cc_start: 0.7904 (mm-30) cc_final: 0.7650 (mm-30) REVERT: D 17 TRP cc_start: 0.8546 (t60) cc_final: 0.8285 (t-100) REVERT: D 29 GLU cc_start: 0.8234 (tm-30) cc_final: 0.7695 (tm-30) REVERT: D 31 MET cc_start: 0.7952 (mtm) cc_final: 0.7646 (mtm) REVERT: D 54 ARG cc_start: 0.8197 (mmt180) cc_final: 0.7866 (mmt90) REVERT: D 83 GLU cc_start: 0.8556 (mt-10) cc_final: 0.8312 (mt-10) REVERT: D 85 GLU cc_start: 0.7406 (pp20) cc_final: 0.7166 (mm-30) REVERT: D 104 MET cc_start: 0.7728 (OUTLIER) cc_final: 0.7123 (ptp) outliers start: 19 outliers final: 13 residues processed: 314 average time/residue: 0.2449 time to fit residues: 109.4173 Evaluate side-chains 306 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 292 time to evaluate : 1.287 ------------------------------------------------------------------------------- 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 117 LEU 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 104 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 40 optimal weight: 0.2980 chunk 36 optimal weight: 4.9990 chunk 83 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 132 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 155 optimal weight: 0.5980 chunk 111 optimal weight: 0.7980 chunk 125 optimal weight: 1.9990 chunk 127 optimal weight: 0.9980 chunk 113 optimal weight: 0.0970 overall best weight: 0.4978 ------------------------------------------------------------------------------- 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 = 0.3893 r_free = 0.3893 target = 0.130398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.103876 restraints weight = 26076.462| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 2.84 r_work: 0.3362 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.2337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12555 Z= 0.127 Angle : 0.646 9.724 17079 Z= 0.335 Chirality : 0.041 0.204 2067 Planarity : 0.005 0.054 2097 Dihedral : 4.898 30.738 1764 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.02 % Favored : 92.79 % Rotamer: Outliers : 1.82 % Allowed : 19.00 % Favored : 79.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.22), residues: 1623 helix: 0.89 (0.16), residues: 1134 sheet: None (None), residues: 0 loop : -2.63 (0.26), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP Z 200 HIS 0.004 0.001 HIS B 298 PHE 0.015 0.001 PHE A 14 TYR 0.033 0.002 TYR Y 194 ARG 0.007 0.001 ARG C 127 Details of bonding type rmsd hydrogen bonds : bond 0.03559 ( 745) hydrogen bonds : angle 4.62930 ( 2235) covalent geometry : bond 0.00284 (12555) covalent geometry : angle 0.64557 (17079) *********************** 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 335 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 312 time to evaluate : 1.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 29 GLN cc_start: 0.8123 (mm-40) cc_final: 0.7814 (mm-40) REVERT: Y 146 CYS cc_start: 0.8609 (m) cc_final: 0.8192 (p) REVERT: Y 243 LYS cc_start: 0.8524 (tttt) cc_final: 0.8084 (mmmm) REVERT: Z 123 MET cc_start: 0.8133 (ptm) cc_final: 0.7904 (ptt) REVERT: A 29 GLN cc_start: 0.8086 (mm-40) cc_final: 0.7546 (mm-40) REVERT: B 36 TRP cc_start: 0.8146 (t60) cc_final: 0.7869 (t-100) REVERT: B 54 ARG cc_start: 0.7992 (mmt180) cc_final: 0.6986 (mmt90) REVERT: B 59 LYS cc_start: 0.8565 (mmtm) cc_final: 0.8288 (mmtm) REVERT: B 121 ARG cc_start: 0.7838 (OUTLIER) cc_final: 0.7391 (mmm-85) REVERT: B 154 PHE cc_start: 0.8709 (t80) cc_final: 0.8380 (t80) REVERT: B 159 GLN cc_start: 0.9084 (tm-30) cc_final: 0.8780 (tm-30) REVERT: B 216 GLU cc_start: 0.8138 (tm-30) cc_final: 0.7643 (tm-30) REVERT: C 133 ASN cc_start: 0.7654 (t0) cc_final: 0.7055 (t0) REVERT: D 17 TRP cc_start: 0.8543 (t60) cc_final: 0.8314 (t-100) REVERT: D 29 GLU cc_start: 0.8254 (tm-30) cc_final: 0.7714 (tm-30) REVERT: D 31 MET cc_start: 0.7900 (mtm) cc_final: 0.7622 (mtm) REVERT: D 54 ARG cc_start: 0.8170 (mmt180) cc_final: 0.7826 (mmt90) REVERT: D 83 GLU cc_start: 0.8572 (mt-10) cc_final: 0.8279 (mt-10) REVERT: D 104 MET cc_start: 0.7740 (OUTLIER) cc_final: 0.7178 (ptp) outliers start: 23 outliers final: 15 residues processed: 321 average time/residue: 0.2494 time to fit residues: 114.3536 Evaluate side-chains 308 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 291 time to evaluate : 1.343 ------------------------------------------------------------------------------- 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 117 LEU Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 188 MET Chi-restraints excluded: chain B residue 31 MET Chi-restraints excluded: chain B residue 105 MET Chi-restraints excluded: chain B residue 121 ARG Chi-restraints excluded: chain 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 104 MET Chi-restraints excluded: chain D residue 212 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 51 optimal weight: 0.8980 chunk 150 optimal weight: 4.9990 chunk 96 optimal weight: 1.9990 chunk 136 optimal weight: 0.6980 chunk 142 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 149 optimal weight: 0.7980 chunk 116 optimal weight: 0.0980 chunk 3 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 chunk 71 optimal weight: 0.0870 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 ASN C 199 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.130541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.103941 restraints weight = 26254.442| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 2.87 r_work: 0.3365 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12555 Z= 0.131 Angle : 0.665 14.529 17079 Z= 0.343 Chirality : 0.041 0.226 2067 Planarity : 0.005 0.054 2097 Dihedral : 4.890 30.539 1764 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.09 % Favored : 92.73 % Rotamer: Outliers : 1.82 % Allowed : 19.87 % Favored : 78.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.22), residues: 1623 helix: 0.87 (0.16), residues: 1131 sheet: None (None), residues: 0 loop : -2.55 (0.26), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP D 36 HIS 0.004 0.001 HIS B 298 PHE 0.020 0.001 PHE A 14 TYR 0.032 0.002 TYR Y 194 ARG 0.009 0.001 ARG A 127 Details of bonding type rmsd hydrogen bonds : bond 0.03615 ( 745) hydrogen bonds : angle 4.63671 ( 2235) covalent geometry : bond 0.00292 (12555) covalent geometry : angle 0.66462 (17079) *********************** 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 321 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 298 time to evaluate : 1.311 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Y 29 GLN cc_start: 0.8146 (mm-40) cc_final: 0.7821 (mm-40) REVERT: Y 146 CYS cc_start: 0.8597 (m) cc_final: 0.8184 (p) REVERT: Y 182 MET cc_start: 0.8535 (mmt) cc_final: 0.8287 (mmm) REVERT: Y 243 LYS cc_start: 0.8417 (tttt) cc_final: 0.7984 (mmmm) REVERT: A 29 GLN cc_start: 0.8035 (mm-40) cc_final: 0.7516 (mm-40) REVERT: A 133 ASN cc_start: 0.8065 (t0) cc_final: 0.6964 (t0) REVERT: A 135 ARG cc_start: 0.7917 (mpp-170) cc_final: 0.7471 (mtm-85) REVERT: B 54 ARG cc_start: 0.8077 (mmt180) cc_final: 0.7361 (mmt90) REVERT: B 59 LYS cc_start: 0.8606 (mmtm) cc_final: 0.8332 (mmtm) REVERT: B 121 ARG cc_start: 0.7808 (OUTLIER) cc_final: 0.7379 (mmm-85) REVERT: B 154 PHE cc_start: 0.8699 (t80) cc_final: 0.8418 (t80) REVERT: B 216 GLU cc_start: 0.8132 (tm-30) cc_final: 0.7657 (tm-30) REVERT: C 133 ASN cc_start: 0.7811 (t0) cc_final: 0.7248 (t0) REVERT: D 17 TRP cc_start: 0.8530 (t60) cc_final: 0.8288 (t-100) REVERT: D 29 GLU cc_start: 0.8232 (tm-30) cc_final: 0.7694 (tm-30) REVERT: D 31 MET cc_start: 0.7878 (OUTLIER) cc_final: 0.7596 (mtm) REVERT: D 54 ARG cc_start: 0.8150 (mmt180) cc_final: 0.7457 (mmt90) REVERT: D 83 GLU cc_start: 0.8549 (mt-10) cc_final: 0.8214 (mt-10) REVERT: D 104 MET cc_start: 0.7610 (OUTLIER) cc_final: 0.7238 (ptp) outliers start: 23 outliers final: 15 residues processed: 308 average time/residue: 0.2354 time to fit residues: 104.2171 Evaluate side-chains 311 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 293 time to evaluate : 1.397 ------------------------------------------------------------------------------- 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 261 ILE Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 188 MET Chi-restraints excluded: chain B residue 31 MET Chi-restraints excluded: chain B residue 105 MET Chi-restraints excluded: chain B residue 121 ARG Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 188 MET Chi-restraints excluded: chain C residue 199 ASN Chi-restraints excluded: chain D residue 31 MET Chi-restraints excluded: chain D residue 104 MET Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 290 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 136 optimal weight: 0.7980 chunk 123 optimal weight: 5.9990 chunk 131 optimal weight: 0.5980 chunk 156 optimal weight: 0.9980 chunk 27 optimal weight: 0.6980 chunk 75 optimal weight: 0.8980 chunk 138 optimal weight: 0.9990 chunk 34 optimal weight: 0.6980 chunk 59 optimal weight: 10.0000 chunk 95 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.129536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.102950 restraints weight = 26153.232| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 2.92 r_work: 0.3348 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12555 Z= 0.142 Angle : 0.670 10.584 17079 Z= 0.348 Chirality : 0.041 0.233 2067 Planarity : 0.005 0.060 2097 Dihedral : 4.942 31.326 1764 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.21 % Favored : 92.61 % Rotamer: Outliers : 1.58 % Allowed : 21.38 % Favored : 77.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.22), residues: 1623 helix: 0.89 (0.16), residues: 1125 sheet: None (None), residues: 0 loop : -2.57 (0.26), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 36 HIS 0.004 0.001 HIS B 298 PHE 0.019 0.001 PHE A 14 TYR 0.031 0.002 TYR Y 194 ARG 0.014 0.001 ARG A 127 Details of bonding type rmsd hydrogen bonds : bond 0.03630 ( 745) hydrogen bonds : angle 4.65620 ( 2235) covalent geometry : bond 0.00325 (12555) covalent geometry : angle 0.66994 (17079) *********************** 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 317 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 297 time to evaluate : 1.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 29 GLN cc_start: 0.8157 (mm-40) cc_final: 0.7858 (mm-40) REVERT: Y 146 CYS cc_start: 0.8629 (m) cc_final: 0.8207 (p) REVERT: Y 182 MET cc_start: 0.8578 (mmt) cc_final: 0.8337 (mmm) REVERT: Z 215 ASP cc_start: 0.8293 (p0) cc_final: 0.8079 (p0) REVERT: A 29 GLN cc_start: 0.8057 (mm-40) cc_final: 0.7524 (mm-40) REVERT: A 133 ASN cc_start: 0.8038 (t0) cc_final: 0.6929 (t0) REVERT: A 135 ARG cc_start: 0.7884 (mpp-170) cc_final: 0.7393 (mtm-85) REVERT: A 174 MET cc_start: 0.6888 (mmt) cc_final: 0.6620 (mmm) REVERT: B 36 TRP cc_start: 0.8109 (t60) cc_final: 0.7885 (t-100) REVERT: B 59 LYS cc_start: 0.8588 (mmtm) cc_final: 0.8311 (mmtm) REVERT: B 121 ARG cc_start: 0.7854 (OUTLIER) cc_final: 0.7402 (mmm-85) REVERT: B 154 PHE cc_start: 0.8718 (t80) cc_final: 0.8422 (t80) REVERT: B 216 GLU cc_start: 0.8129 (tm-30) cc_final: 0.7642 (tm-30) REVERT: C 133 ASN cc_start: 0.7936 (t0) cc_final: 0.7224 (t0) REVERT: C 199 ASN cc_start: 0.8867 (t0) cc_final: 0.8505 (t0) REVERT: D 17 TRP cc_start: 0.8539 (t60) cc_final: 0.8275 (t-100) REVERT: D 29 GLU cc_start: 0.8169 (tm-30) cc_final: 0.7630 (tm-30) REVERT: D 31 MET cc_start: 0.7914 (OUTLIER) cc_final: 0.7622 (mtm) REVERT: D 83 GLU cc_start: 0.8583 (mt-10) cc_final: 0.8252 (mt-10) outliers start: 20 outliers final: 14 residues processed: 307 average time/residue: 0.2419 time to fit residues: 105.8063 Evaluate side-chains 308 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 292 time to evaluate : 1.254 ------------------------------------------------------------------------------- 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 261 ILE Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 188 MET Chi-restraints excluded: chain B residue 31 MET Chi-restraints excluded: chain B residue 105 MET Chi-restraints excluded: chain B residue 121 ARG Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 188 MET Chi-restraints excluded: chain D residue 31 MET Chi-restraints excluded: chain D residue 212 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 88 optimal weight: 0.9990 chunk 128 optimal weight: 0.7980 chunk 60 optimal weight: 0.0770 chunk 86 optimal weight: 0.6980 chunk 131 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 94 optimal weight: 0.0870 chunk 93 optimal weight: 10.0000 chunk 102 optimal weight: 2.9990 chunk 114 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 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 = 0.3896 r_free = 0.3896 target = 0.130350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.103762 restraints weight = 25862.887| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 2.85 r_work: 0.3367 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.2578 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= 0.132 Angle : 0.666 9.626 17079 Z= 0.346 Chirality : 0.041 0.239 2067 Planarity : 0.005 0.054 2097 Dihedral : 4.893 30.641 1764 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.39 % Favored : 92.42 % Rotamer: Outliers : 1.50 % Allowed : 21.54 % Favored : 76.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.22), residues: 1623 helix: 0.90 (0.16), residues: 1125 sheet: None (None), residues: 0 loop : -2.56 (0.26), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 36 HIS 0.004 0.001 HIS B 298 PHE 0.019 0.001 PHE A 14 TYR 0.040 0.002 TYR Y 194 ARG 0.009 0.001 ARG C 127 Details of bonding type rmsd hydrogen bonds : bond 0.03598 ( 745) hydrogen bonds : angle 4.62943 ( 2235) covalent geometry : bond 0.00298 (12555) covalent geometry : angle 0.66590 (17079) ********************** 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 320 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 301 time to evaluate : 1.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 29 GLN cc_start: 0.8142 (mm-40) cc_final: 0.7820 (mm-40) REVERT: Y 182 MET cc_start: 0.8546 (mmt) cc_final: 0.8303 (mmm) REVERT: Z 215 ASP cc_start: 0.8256 (p0) cc_final: 0.8015 (p0) REVERT: Z 222 TRP cc_start: 0.8234 (m100) cc_final: 0.7960 (m100) REVERT: A 29 GLN cc_start: 0.8021 (mm-40) cc_final: 0.7501 (mm-40) REVERT: A 133 ASN cc_start: 0.7961 (t0) cc_final: 0.6863 (t0) REVERT: A 135 ARG cc_start: 0.7880 (mpp-170) cc_final: 0.7429 (mtm-85) REVERT: A 174 MET cc_start: 0.6823 (mmt) cc_final: 0.6557 (mmm) REVERT: B 36 TRP cc_start: 0.8050 (t60) cc_final: 0.7834 (t-100) REVERT: B 59 LYS cc_start: 0.8606 (mmtm) cc_final: 0.8313 (mmtm) REVERT: B 121 ARG cc_start: 0.7826 (OUTLIER) cc_final: 0.7455 (mmm-85) REVERT: B 154 PHE cc_start: 0.8700 (t80) cc_final: 0.8403 (t80) REVERT: B 159 GLN cc_start: 0.9073 (tm-30) cc_final: 0.8745 (tm-30) REVERT: B 216 GLU cc_start: 0.8173 (tm-30) cc_final: 0.7678 (tm-30) REVERT: B 246 SER cc_start: 0.8109 (t) cc_final: 0.7745 (m) REVERT: C 24 GLU cc_start: 0.7790 (mm-30) cc_final: 0.7460 (mm-30) REVERT: C 90 VAL cc_start: 0.8946 (t) cc_final: 0.8688 (m) REVERT: D 17 TRP cc_start: 0.8509 (t60) cc_final: 0.8297 (t-100) REVERT: D 29 GLU cc_start: 0.8236 (tm-30) cc_final: 0.7753 (tm-30) REVERT: D 31 MET cc_start: 0.7893 (OUTLIER) cc_final: 0.7596 (mtm) REVERT: D 54 ARG cc_start: 0.8124 (mmt180) cc_final: 0.6805 (mmt90) REVERT: D 83 GLU cc_start: 0.8576 (mt-10) cc_final: 0.8242 (mt-10) outliers start: 19 outliers final: 15 residues processed: 309 average time/residue: 0.2469 time to fit residues: 109.4748 Evaluate side-chains 315 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 298 time to evaluate : 1.401 ------------------------------------------------------------------------------- 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 261 ILE Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 188 MET Chi-restraints excluded: chain B residue 31 MET Chi-restraints excluded: chain B residue 105 MET Chi-restraints excluded: chain B residue 121 ARG Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 82 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 chunk 132 optimal weight: 0.6980 chunk 92 optimal weight: 0.9980 chunk 148 optimal weight: 2.9990 chunk 41 optimal weight: 0.1980 chunk 151 optimal weight: 1.9990 chunk 127 optimal weight: 0.6980 chunk 2 optimal weight: 0.0170 chunk 37 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 overall best weight: 0.5018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.130349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.103956 restraints weight = 26158.333| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 2.86 r_work: 0.3370 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12555 Z= 0.132 Angle : 0.670 9.347 17079 Z= 0.349 Chirality : 0.041 0.238 2067 Planarity : 0.005 0.054 2097 Dihedral : 4.870 30.236 1764 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.21 % Favored : 92.61 % Rotamer: Outliers : 1.27 % Allowed : 21.69 % Favored : 77.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.22), residues: 1623 helix: 0.92 (0.16), residues: 1122 sheet: None (None), residues: 0 loop : -2.58 (0.26), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 222 HIS 0.003 0.001 HIS B 298 PHE 0.018 0.001 PHE A 14 TYR 0.039 0.002 TYR Y 194 ARG 0.009 0.001 ARG C 127 Details of bonding type rmsd hydrogen bonds : bond 0.03549 ( 745) hydrogen bonds : angle 4.59732 ( 2235) covalent geometry : bond 0.00297 (12555) covalent geometry : angle 0.66996 (17079) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6761.39 seconds wall clock time: 118 minutes 21.02 seconds (7101.02 seconds total)