Starting phenix.real_space_refine on Mon Dec 30 05:17:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vlx_32030/12_2024/7vlx_32030.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vlx_32030/12_2024/7vlx_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_32030/12_2024/7vlx_32030.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vlx_32030/12_2024/7vlx_32030.map" model { file = "/net/cci-nas-00/data/ceres_data/7vlx_32030/12_2024/7vlx_32030.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vlx_32030/12_2024/7vlx_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-5532/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: 7.80, per 1000 atoms: 0.63 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: 3.25 Conformation dependent library (CDL) restraints added in 1.9 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: 1.14 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: 3.77 Time building geometry restraints manager: 3.71 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'Y' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'Z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.460 Check model and map are aligned: 0.090 Set scattering table: 0.170 Process input model: 30.250 Find NCS groups from input model: 0.450 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:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.590 ------------------------------------------------------------------------------- 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= 0.180 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 *********************** 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 : 1.424 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: 0.2407 time to fit residues: 113.8489 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 : 1.499 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 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= 0.270 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 *********************** 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 : 1.467 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Y 21 ILE cc_start: 0.8389 (pt) cc_final: 0.8174 (pt) REVERT: Y 127 ARG cc_start: 0.8112 (ttm110) cc_final: 0.7356 (ttm110) REVERT: Z 58 LEU cc_start: 0.8890 (mt) cc_final: 0.8580 (mt) REVERT: A 126 ASP cc_start: 0.7555 (t0) cc_final: 0.7213 (t0) REVERT: A 133 ASN cc_start: 0.7964 (t0) cc_final: 0.7757 (t0) REVERT: B 58 LEU cc_start: 0.8904 (mt) cc_final: 0.8604 (mt) REVERT: B 216 GLU cc_start: 0.7494 (tm-30) cc_final: 0.7157 (tm-30) REVERT: C 21 ILE cc_start: 0.8317 (pt) cc_final: 0.8071 (pt) REVERT: C 53 THR cc_start: 0.8710 (m) cc_final: 0.8450 (t) REVERT: C 127 ARG cc_start: 0.7896 (mtp-110) cc_final: 0.7245 (mtp-110) REVERT: C 131 LYS cc_start: 0.8914 (ptpp) cc_final: 0.8421 (tptp) REVERT: D 17 TRP cc_start: 0.8470 (t60) cc_final: 0.8233 (t-100) REVERT: D 86 ARG cc_start: 0.6809 (ttp80) cc_final: 0.6595 (ttp80) outliers start: 15 outliers final: 6 residues processed: 318 average time/residue: 0.2362 time to fit residues: 108.9431 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 : 1.424 ------------------------------------------------------------------------------- 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 80 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 120 optimal weight: 0.9990 chunk 98 optimal weight: 2.9990 chunk 39 optimal weight: 6.9990 chunk 144 optimal weight: 0.6980 chunk 156 optimal weight: 1.9990 chunk 128 optimal weight: 2.9990 chunk 143 optimal weight: 0.6980 chunk 49 optimal weight: 0.5980 chunk 116 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.1740 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= 0.205 Angle : 0.635 8.743 17079 Z= 0.330 Chirality : 0.041 0.188 2067 Planarity : 0.005 0.053 2097 Dihedral : 5.038 32.651 1764 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.96 % Favored : 92.98 % Rotamer: Outliers : 1.50 % Allowed : 13.70 % Favored : 84.80 % 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: -0.33 (0.22), residues: 1623 helix: 0.74 (0.16), residues: 1134 sheet: None (None), residues: 0 loop : -2.52 (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 0.018 0.001 PHE A 14 TYR 0.021 0.002 TYR Z 48 ARG 0.006 0.001 ARG A 127 *********************** 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: 19 poor density : 313 time to evaluate : 1.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 21 ILE cc_start: 0.8396 (pt) cc_final: 0.8194 (pt) REVERT: Y 29 GLN cc_start: 0.8006 (mm-40) cc_final: 0.7460 (mm-40) REVERT: Z 54 ARG cc_start: 0.8131 (mmt180) cc_final: 0.6914 (mmt90) REVERT: A 115 ARG cc_start: 0.8402 (mtp85) cc_final: 0.8178 (mtp85) REVERT: B 58 LEU cc_start: 0.8941 (mt) cc_final: 0.8637 (mt) REVERT: B 59 LYS cc_start: 0.8480 (mmtm) cc_final: 0.8041 (mmtm) REVERT: B 216 GLU cc_start: 0.7671 (tm-30) cc_final: 0.7232 (tm-30) REVERT: D 31 MET cc_start: 0.7986 (mtm) cc_final: 0.7741 (mtm) REVERT: D 83 GLU cc_start: 0.8253 (mt-10) cc_final: 0.7927 (mt-10) REVERT: D 141 ILE cc_start: 0.8623 (mm) cc_final: 0.8211 (mp) outliers start: 19 outliers final: 11 residues processed: 322 average time/residue: 0.2578 time to fit residues: 117.7948 Evaluate side-chains 306 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 295 time to evaluate : 1.281 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain C residue 188 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 142 optimal weight: 0.9990 chunk 108 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 16 optimal weight: 0.5980 chunk 69 optimal weight: 0.2980 chunk 97 optimal weight: 0.9990 chunk 145 optimal weight: 1.9990 chunk 153 optimal weight: 4.9990 chunk 137 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 127 optimal weight: 2.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 199 ASN C 133 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.2033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12555 Z= 0.205 Angle : 0.627 9.397 17079 Z= 0.327 Chirality : 0.041 0.186 2067 Planarity : 0.005 0.055 2097 Dihedral : 5.037 32.396 1764 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.33 % Favored : 92.61 % Rotamer: Outliers : 1.50 % Allowed : 15.91 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -0.29 (0.22), residues: 1623 helix: 0.78 (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 0.005 0.001 HIS B 298 PHE 0.021 0.001 PHE D 154 TYR 0.028 0.002 TYR Y 194 ARG 0.008 0.001 ARG Z 121 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3246 Ramachandran restraints generated. 1623 Oldfield, 0 Emsley, 1623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3246 Ramachandran restraints generated. 1623 Oldfield, 0 Emsley, 1623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 309 time to evaluate : 1.415 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Y 29 GLN cc_start: 0.8063 (mm-40) cc_final: 0.7738 (mm-40) REVERT: Z 52 GLU cc_start: 0.7961 (pm20) cc_final: 0.7500 (mp0) REVERT: Z 53 ASP cc_start: 0.8614 (p0) cc_final: 0.7633 (p0) REVERT: Z 54 ARG cc_start: 0.8063 (mmt180) cc_final: 0.7287 (mmt90) REVERT: Z 58 LEU cc_start: 0.8749 (mt) cc_final: 0.8522 (mt) REVERT: A 135 ARG cc_start: 0.7814 (mpp-170) cc_final: 0.7252 (mtm-85) REVERT: A 180 ASP cc_start: 0.7784 (p0) cc_final: 0.7507 (p0) REVERT: B 58 LEU cc_start: 0.8965 (mt) cc_final: 0.8685 (mt) REVERT: B 59 LYS cc_start: 0.8426 (mmtm) cc_final: 0.8182 (mmtm) REVERT: B 216 GLU cc_start: 0.7765 (tm-30) cc_final: 0.7265 (tm-30) REVERT: C 133 ASN cc_start: 0.8227 (t0) cc_final: 0.6590 (t0) REVERT: D 31 MET cc_start: 0.8004 (mtm) cc_final: 0.7690 (mtm) REVERT: D 104 MET cc_start: 0.7749 (OUTLIER) cc_final: 0.7319 (ptp) outliers start: 19 outliers final: 12 residues processed: 315 average time/residue: 0.2547 time to fit residues: 113.7417 Evaluate side-chains 305 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 292 time to evaluate : 1.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 143 SER Chi-restraints excluded: chain Y residue 148 GLN Chi-restraints excluded: chain Z residue 59 LYS Chi-restraints excluded: chain Z residue 219 TYR Chi-restraints excluded: chain Z residue 261 ILE Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 117 LEU 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 87 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 114 optimal weight: 2.9990 chunk 63 optimal weight: 0.0040 chunk 131 optimal weight: 1.9990 chunk 106 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 78 optimal weight: 0.6980 chunk 137 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 51 optimal weight: 0.0050 overall best weight: 0.5006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 148 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12555 Z= 0.183 Angle : 0.633 9.752 17079 Z= 0.328 Chirality : 0.041 0.197 2067 Planarity : 0.005 0.055 2097 Dihedral : 4.944 30.860 1764 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.96 % Favored : 92.98 % Rotamer: Outliers : 1.19 % Allowed : 17.42 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: 0.87 (0.16), residues: 1131 sheet: None (None), residues: 0 loop : -2.53 (0.26), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP Z 222 HIS 0.004 0.001 HIS B 298 PHE 0.012 0.001 PHE A 14 TYR 0.033 0.002 TYR Y 194 ARG 0.007 0.001 ARG A 127 *********************** 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 330 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 315 time to evaluate : 1.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 29 GLN cc_start: 0.7975 (mm-40) cc_final: 0.7614 (mm-40) REVERT: Y 243 LYS cc_start: 0.8317 (tttt) cc_final: 0.7996 (mmmm) REVERT: Z 58 LEU cc_start: 0.8759 (mt) cc_final: 0.8502 (mt) REVERT: A 133 ASN cc_start: 0.7923 (t0) cc_final: 0.7061 (t0) REVERT: A 135 ARG cc_start: 0.7823 (mpp-170) cc_final: 0.7270 (mtm-85) REVERT: B 54 ARG cc_start: 0.8012 (mmt180) cc_final: 0.7001 (mpt-90) REVERT: B 58 LEU cc_start: 0.8955 (mt) cc_final: 0.8674 (mt) REVERT: B 59 LYS cc_start: 0.8457 (mmtm) cc_final: 0.8203 (mmtm) REVERT: B 216 GLU cc_start: 0.7691 (tm-30) cc_final: 0.7306 (tm-30) REVERT: C 133 ASN cc_start: 0.7735 (t0) cc_final: 0.7333 (t0) REVERT: D 31 MET cc_start: 0.7941 (mtm) cc_final: 0.7618 (mtm) REVERT: D 83 GLU cc_start: 0.8256 (mt-10) cc_final: 0.8030 (mt-10) REVERT: D 104 MET cc_start: 0.7768 (OUTLIER) cc_final: 0.7064 (ptp) outliers start: 15 outliers final: 12 residues processed: 321 average time/residue: 0.2396 time to fit residues: 109.7505 Evaluate side-chains 302 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 289 time to evaluate : 1.460 ------------------------------------------------------------------------------- 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 D residue 104 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 138 optimal weight: 5.9990 chunk 30 optimal weight: 0.6980 chunk 90 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 153 optimal weight: 3.9990 chunk 127 optimal weight: 0.9980 chunk 71 optimal weight: 0.1980 chunk 12 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 chunk 80 optimal weight: 2.9990 chunk 148 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 199 ASN C 199 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12555 Z= 0.204 Angle : 0.653 10.295 17079 Z= 0.338 Chirality : 0.041 0.203 2067 Planarity : 0.005 0.055 2097 Dihedral : 4.956 31.708 1764 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.15 % Favored : 92.79 % Rotamer: Outliers : 1.98 % Allowed : 17.89 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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 : -2.53 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP Z 36 HIS 0.004 0.001 HIS B 298 PHE 0.020 0.001 PHE D 154 TYR 0.039 0.002 TYR Y 194 ARG 0.007 0.001 ARG C 115 *********************** 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: 25 poor density : 299 time to evaluate : 1.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 29 GLN cc_start: 0.8004 (mm-40) cc_final: 0.7639 (mm-40) REVERT: Y 243 LYS cc_start: 0.8284 (tttt) cc_final: 0.7974 (mmmm) REVERT: A 135 ARG cc_start: 0.7830 (mpp-170) cc_final: 0.7266 (mtm-85) REVERT: B 52 GLU cc_start: 0.7909 (pm20) cc_final: 0.7622 (mp0) REVERT: B 54 ARG cc_start: 0.7923 (mmt180) cc_final: 0.7130 (mmt90) REVERT: B 58 LEU cc_start: 0.8985 (mt) cc_final: 0.8726 (mt) REVERT: B 59 LYS cc_start: 0.8513 (mmtm) cc_final: 0.8248 (mmtm) REVERT: B 104 MET cc_start: 0.7507 (mtp) cc_final: 0.7191 (ptm) REVERT: B 216 GLU cc_start: 0.7736 (tm-30) cc_final: 0.7205 (tm-30) REVERT: D 29 GLU cc_start: 0.8071 (tm-30) cc_final: 0.7557 (tm-30) REVERT: D 31 MET cc_start: 0.7782 (mtm) cc_final: 0.7506 (mtm) REVERT: D 54 ARG cc_start: 0.8158 (mmt180) cc_final: 0.7824 (mmt90) REVERT: D 83 GLU cc_start: 0.8334 (mt-10) cc_final: 0.7983 (mt-10) REVERT: D 104 MET cc_start: 0.7733 (OUTLIER) cc_final: 0.7144 (ptp) outliers start: 25 outliers final: 17 residues processed: 310 average time/residue: 0.2448 time to fit residues: 108.5532 Evaluate side-chains 308 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 290 time to evaluate : 1.468 ------------------------------------------------------------------------------- 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 Z residue 285 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 17 optimal weight: 2.9990 chunk 87 optimal weight: 0.4980 chunk 112 optimal weight: 3.9990 chunk 129 optimal weight: 2.9990 chunk 85 optimal weight: 0.4980 chunk 153 optimal weight: 3.9990 chunk 95 optimal weight: 0.9980 chunk 93 optimal weight: 0.7980 chunk 70 optimal weight: 0.9990 chunk 94 optimal weight: 0.9990 chunk 61 optimal weight: 0.4980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12555 Z= 0.201 Angle : 0.662 13.839 17079 Z= 0.342 Chirality : 0.041 0.217 2067 Planarity : 0.005 0.054 2097 Dihedral : 4.955 31.500 1764 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.09 % Favored : 92.73 % Rotamer: Outliers : 1.74 % Allowed : 19.08 % Favored : 79.18 % 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: -0.20 (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 0.014 0.001 TRP D 200 HIS 0.004 0.001 HIS B 298 PHE 0.017 0.001 PHE A 14 TYR 0.033 0.002 TYR Y 194 ARG 0.008 0.001 ARG A 127 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3246 Ramachandran restraints generated. 1623 Oldfield, 0 Emsley, 1623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3246 Ramachandran restraints generated. 1623 Oldfield, 0 Emsley, 1623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 303 time to evaluate : 1.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 29 GLN cc_start: 0.7955 (mm-40) cc_final: 0.7597 (mm-40) REVERT: Y 146 CYS cc_start: 0.8191 (m) cc_final: 0.7886 (p) REVERT: Y 243 LYS cc_start: 0.8231 (tttt) cc_final: 0.7922 (mmmm) REVERT: B 54 ARG cc_start: 0.7873 (mmt180) cc_final: 0.6957 (mpt-90) REVERT: B 59 LYS cc_start: 0.8513 (mmtm) cc_final: 0.8238 (mmtm) REVERT: B 104 MET cc_start: 0.7553 (mtp) cc_final: 0.7251 (ptm) REVERT: B 216 GLU cc_start: 0.7690 (tm-30) cc_final: 0.7181 (tm-30) REVERT: C 133 ASN cc_start: 0.7469 (t0) cc_final: 0.6879 (t0) REVERT: D 31 MET cc_start: 0.7775 (mtm) cc_final: 0.7476 (mtm) REVERT: D 53 ASP cc_start: 0.8770 (p0) cc_final: 0.8416 (p0) REVERT: D 104 MET cc_start: 0.7720 (OUTLIER) cc_final: 0.7129 (ptp) REVERT: D 141 ILE cc_start: 0.8579 (mm) cc_final: 0.8220 (mp) outliers start: 22 outliers final: 15 residues processed: 312 average time/residue: 0.2469 time to fit residues: 109.9001 Evaluate side-chains 304 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 288 time to evaluate : 1.467 ------------------------------------------------------------------------------- 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 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 91 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 97 optimal weight: 5.9990 chunk 104 optimal weight: 0.9990 chunk 75 optimal weight: 0.5980 chunk 14 optimal weight: 0.9990 chunk 120 optimal weight: 0.6980 chunk 139 optimal weight: 0.4980 chunk 146 optimal weight: 0.2980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.2508 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= 0.200 Angle : 0.664 11.002 17079 Z= 0.343 Chirality : 0.041 0.222 2067 Planarity : 0.005 0.064 2097 Dihedral : 4.923 31.277 1764 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.27 % Favored : 92.54 % Rotamer: Outliers : 1.66 % Allowed : 19.95 % Favored : 78.38 % 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 : -2.57 (0.26), residues: 492 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 0.022 0.001 PHE D 154 TYR 0.031 0.002 TYR Y 194 ARG 0.013 0.001 ARG A 127 *********************** 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 312 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 291 time to evaluate : 1.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 29 GLN cc_start: 0.7971 (mm-40) cc_final: 0.7624 (mm-40) REVERT: Y 146 CYS cc_start: 0.8282 (m) cc_final: 0.7974 (p) REVERT: Z 216 GLU cc_start: 0.7674 (mm-30) cc_final: 0.7470 (mm-30) REVERT: A 133 ASN cc_start: 0.7882 (t0) cc_final: 0.6748 (t0) REVERT: A 135 ARG cc_start: 0.7715 (mpp-170) cc_final: 0.7368 (mtm-85) REVERT: B 54 ARG cc_start: 0.7980 (mmt180) cc_final: 0.7338 (mmt90) REVERT: B 59 LYS cc_start: 0.8547 (mmtm) cc_final: 0.8266 (mmtm) REVERT: B 104 MET cc_start: 0.7545 (mtp) cc_final: 0.7151 (ptm) REVERT: B 216 GLU cc_start: 0.7636 (tm-30) cc_final: 0.7133 (tm-30) REVERT: C 133 ASN cc_start: 0.7677 (t0) cc_final: 0.7106 (t0) REVERT: D 31 MET cc_start: 0.7758 (OUTLIER) cc_final: 0.7461 (mtm) REVERT: D 83 GLU cc_start: 0.8420 (mt-10) cc_final: 0.8109 (mt-10) REVERT: D 104 MET cc_start: 0.7584 (OUTLIER) cc_final: 0.7188 (ptp) REVERT: D 141 ILE cc_start: 0.8592 (mm) cc_final: 0.8213 (mp) outliers start: 21 outliers final: 13 residues processed: 300 average time/residue: 0.2359 time to fit residues: 101.7726 Evaluate side-chains 304 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 289 time to evaluate : 1.472 ------------------------------------------------------------------------------- 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 B residue 31 MET Chi-restraints excluded: chain B residue 105 MET Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 188 MET Chi-restraints excluded: chain D residue 31 MET Chi-restraints excluded: chain D residue 104 MET Chi-restraints excluded: chain D residue 212 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 133 optimal weight: 1.9990 chunk 142 optimal weight: 0.9980 chunk 146 optimal weight: 0.0470 chunk 85 optimal weight: 4.9990 chunk 62 optimal weight: 0.0770 chunk 112 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 129 optimal weight: 0.9980 chunk 135 optimal weight: 3.9990 chunk 93 optimal weight: 0.9990 chunk 151 optimal weight: 3.9990 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN C 199 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.2529 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= 0.198 Angle : 0.660 11.204 17079 Z= 0.342 Chirality : 0.041 0.229 2067 Planarity : 0.005 0.054 2097 Dihedral : 4.905 31.228 1764 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.21 % Favored : 92.61 % Rotamer: Outliers : 1.82 % Allowed : 19.95 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (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: 0.91 (0.16), residues: 1125 sheet: None (None), residues: 0 loop : -2.60 (0.26), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP Z 147 HIS 0.004 0.001 HIS B 298 PHE 0.016 0.001 PHE A 14 TYR 0.039 0.002 TYR Y 194 ARG 0.008 0.001 ARG A 127 *********************** 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 328 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 305 time to evaluate : 1.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 29 GLN cc_start: 0.7945 (mm-40) cc_final: 0.7594 (mm-40) REVERT: Y 90 VAL cc_start: 0.9072 (t) cc_final: 0.8851 (m) REVERT: Y 146 CYS cc_start: 0.8300 (m) cc_final: 0.7964 (p) REVERT: Y 182 MET cc_start: 0.8248 (mmt) cc_final: 0.7985 (mmm) REVERT: Z 222 TRP cc_start: 0.8172 (m100) cc_final: 0.7927 (m100) REVERT: A 133 ASN cc_start: 0.7882 (t0) cc_final: 0.6804 (t0) REVERT: A 135 ARG cc_start: 0.7687 (mpp-170) cc_final: 0.7280 (mtm-85) REVERT: B 59 LYS cc_start: 0.8542 (mmtm) cc_final: 0.8253 (mmtm) REVERT: B 104 MET cc_start: 0.7545 (mtp) cc_final: 0.7165 (ptm) REVERT: B 159 GLN cc_start: 0.8929 (tm-30) cc_final: 0.8604 (tm-30) REVERT: B 216 GLU cc_start: 0.7664 (tm-30) cc_final: 0.7155 (tm-30) REVERT: C 133 ASN cc_start: 0.7835 (t0) cc_final: 0.6976 (t0) REVERT: D 31 MET cc_start: 0.7752 (OUTLIER) cc_final: 0.7454 (mtm) REVERT: D 83 GLU cc_start: 0.8401 (mt-10) cc_final: 0.8096 (mt-10) REVERT: D 141 ILE cc_start: 0.8590 (mm) cc_final: 0.8216 (mp) outliers start: 23 outliers final: 15 residues processed: 313 average time/residue: 0.2411 time to fit residues: 108.9147 Evaluate side-chains 311 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 295 time to evaluate : 1.450 ------------------------------------------------------------------------------- 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 B residue 31 MET Chi-restraints excluded: chain B residue 105 MET Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 188 MET Chi-restraints excluded: chain C residue 199 ASN Chi-restraints excluded: chain D residue 31 MET Chi-restraints excluded: chain D residue 212 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 92 optimal weight: 0.6980 chunk 71 optimal weight: 0.5980 chunk 104 optimal weight: 0.6980 chunk 158 optimal weight: 0.7980 chunk 145 optimal weight: 3.9990 chunk 126 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 97 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 100 optimal weight: 0.9980 chunk 134 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 199 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12555 Z= 0.217 Angle : 0.689 11.771 17079 Z= 0.356 Chirality : 0.042 0.241 2067 Planarity : 0.005 0.054 2097 Dihedral : 5.014 31.655 1764 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.46 % Favored : 92.36 % Rotamer: Outliers : 1.27 % Allowed : 21.22 % Favored : 77.51 % 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: 0.88 (0.16), residues: 1131 sheet: None (None), residues: 0 loop : -2.58 (0.26), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 200 HIS 0.006 0.001 HIS Z 61 PHE 0.025 0.001 PHE A 27 TYR 0.040 0.002 TYR Y 194 ARG 0.011 0.001 ARG C 135 ********************** 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 313 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 297 time to evaluate : 1.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 29 GLN cc_start: 0.7969 (mm-40) cc_final: 0.7648 (mm-40) REVERT: Y 90 VAL cc_start: 0.9077 (t) cc_final: 0.8857 (m) REVERT: Y 182 MET cc_start: 0.8257 (mmt) cc_final: 0.7995 (mmm) REVERT: A 133 ASN cc_start: 0.7834 (t0) cc_final: 0.6937 (t0) REVERT: A 135 ARG cc_start: 0.7700 (mpp-170) cc_final: 0.7275 (mtm-85) REVERT: B 29 GLU cc_start: 0.8213 (tm-30) cc_final: 0.7792 (tm-30) REVERT: B 59 LYS cc_start: 0.8548 (mmtm) cc_final: 0.8248 (mmtm) REVERT: B 104 MET cc_start: 0.7557 (mtp) cc_final: 0.7168 (ptm) REVERT: B 154 PHE cc_start: 0.8601 (t80) cc_final: 0.8387 (t80) REVERT: B 216 GLU cc_start: 0.7680 (tm-30) cc_final: 0.7191 (tm-30) REVERT: B 246 SER cc_start: 0.7991 (t) cc_final: 0.7577 (m) REVERT: C 90 VAL cc_start: 0.8968 (t) cc_final: 0.8711 (m) REVERT: C 199 ASN cc_start: 0.8475 (OUTLIER) cc_final: 0.8152 (t0) REVERT: D 29 GLU cc_start: 0.7948 (tm-30) cc_final: 0.7476 (tm-30) REVERT: D 31 MET cc_start: 0.7768 (OUTLIER) cc_final: 0.7480 (mtm) REVERT: D 83 GLU cc_start: 0.8434 (mt-10) cc_final: 0.8152 (mt-10) REVERT: D 85 GLU cc_start: 0.7281 (pp20) cc_final: 0.6915 (mm-30) REVERT: D 104 MET cc_start: 0.6990 (ptm) cc_final: 0.6622 (ptp) REVERT: D 141 ILE cc_start: 0.8596 (mm) cc_final: 0.8220 (mp) outliers start: 16 outliers final: 13 residues processed: 303 average time/residue: 0.2475 time to fit residues: 107.5445 Evaluate side-chains 310 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 295 time to evaluate : 1.484 ------------------------------------------------------------------------------- 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 167 VAL Chi-restraints excluded: chain B residue 31 MET Chi-restraints excluded: chain B residue 105 MET Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 188 MET Chi-restraints excluded: chain 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 38 optimal weight: 0.9980 chunk 116 optimal weight: 0.0980 chunk 18 optimal weight: 0.2980 chunk 35 optimal weight: 0.9990 chunk 126 optimal weight: 0.5980 chunk 52 optimal weight: 0.6980 chunk 129 optimal weight: 0.9980 chunk 15 optimal weight: 5.9990 chunk 23 optimal weight: 0.6980 chunk 110 optimal weight: 0.6980 chunk 7 optimal weight: 0.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 224 HIS C 199 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.131011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.104740 restraints weight = 25772.129| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 2.83 r_work: 0.3371 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.2623 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= 0.194 Angle : 0.672 11.364 17079 Z= 0.347 Chirality : 0.041 0.240 2067 Planarity : 0.005 0.054 2097 Dihedral : 4.917 30.769 1764 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.09 % Favored : 92.73 % Rotamer: Outliers : 1.35 % Allowed : 21.06 % Favored : 77.59 % 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: 0.93 (0.16), residues: 1125 sheet: None (None), residues: 0 loop : -2.61 (0.26), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP Z 200 HIS 0.004 0.001 HIS Z 61 PHE 0.021 0.001 PHE A 14 TYR 0.038 0.002 TYR Y 194 ARG 0.009 0.001 ARG A 127 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3031.75 seconds wall clock time: 55 minutes 52.22 seconds (3352.22 seconds total)