Starting phenix.real_space_refine on Thu Mar 13 18:24:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ibn_35344/03_2025/8ibn_35344.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ibn_35344/03_2025/8ibn_35344.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ibn_35344/03_2025/8ibn_35344.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ibn_35344/03_2025/8ibn_35344.map" model { file = "/net/cci-nas-00/data/ceres_data/8ibn_35344/03_2025/8ibn_35344.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ibn_35344/03_2025/8ibn_35344.cif" } resolution = 3.03 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= 0.019 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: 6 Type Number sf(0) Gaussians K 4 8.98 5 P 12 5.49 5 S 44 5.16 5 C 5520 2.51 5 N 1552 2.21 5 O 1808 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8940 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2202 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 7, 'TRANS': 298} Chain: "B" Number of atoms: 2202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2202 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 7, 'TRANS': 298} Chain: "C" Number of atoms: 2202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2202 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 7, 'TRANS': 298} Chain: "D" Number of atoms: 2202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2202 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 7, 'TRANS': 298} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' K': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' K': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' K': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' K': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.90, per 1000 atoms: 0.66 Number of scatterers: 8940 At special positions: 0 Unit cell: (65.1672, 58.9608, 202.742, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) K 4 19.00 S 44 16.00 P 12 15.00 O 1808 8.00 N 1552 7.00 C 5520 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: 2.40 Conformation dependent library (CDL) restraints added in 1.1 seconds 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2120 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 12 sheets defined 44.2% alpha, 21.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.11 Creating SS restraints... Processing helix chain 'A' and resid 19 through 30 Processing helix chain 'A' and resid 46 through 51 removed outlier: 4.414A pdb=" N LYS A 51 " --> pdb=" O GLN A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 66 removed outlier: 3.525A pdb=" N LYS A 66 " --> pdb=" O SER A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 84 removed outlier: 4.368A pdb=" N GLY A 77 " --> pdb=" O ASN A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 92 removed outlier: 3.765A pdb=" N ALA A 90 " --> pdb=" O GLU A 86 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ALA A 91 " --> pdb=" O ALA A 87 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU A 92 " --> pdb=" O LEU A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 123 removed outlier: 3.549A pdb=" N GLY A 111 " --> pdb=" O GLY A 107 " (cutoff:3.500A) Proline residue: A 114 - end of helix Processing helix chain 'A' and resid 140 through 154 removed outlier: 3.669A pdb=" N PHE A 145 " --> pdb=" O LYS A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 168 removed outlier: 3.592A pdb=" N LYS A 167 " --> pdb=" O PRO A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 202 removed outlier: 3.756A pdb=" N ARG A 202 " --> pdb=" O GLU A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 217 removed outlier: 3.639A pdb=" N VAL A 213 " --> pdb=" O ASP A 209 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N MET A 217 " --> pdb=" O VAL A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 220 No H-bonds generated for 'chain 'A' and resid 218 through 220' Processing helix chain 'A' and resid 234 through 245 Processing helix chain 'A' and resid 271 through 283 removed outlier: 3.631A pdb=" N PHE A 275 " --> pdb=" O ARG A 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 30 removed outlier: 3.723A pdb=" N MET B 29 " --> pdb=" O ALA B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 84 removed outlier: 4.138A pdb=" N GLY B 77 " --> pdb=" O ASN B 73 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASP B 84 " --> pdb=" O ALA B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 92 removed outlier: 3.562A pdb=" N LEU B 88 " --> pdb=" O ASP B 84 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ALA B 90 " --> pdb=" O GLU B 86 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA B 91 " --> pdb=" O ALA B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 123 removed outlier: 3.918A pdb=" N ALA B 113 " --> pdb=" O GLY B 109 " (cutoff:3.500A) Proline residue: B 114 - end of helix Processing helix chain 'B' and resid 140 through 155 removed outlier: 3.928A pdb=" N PHE B 145 " --> pdb=" O LYS B 141 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N THR B 151 " --> pdb=" O GLU B 147 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LYS B 155 " --> pdb=" O THR B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 202 removed outlier: 4.151A pdb=" N ALA B 185 " --> pdb=" O ALA B 181 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ARG B 202 " --> pdb=" O GLU B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 215 removed outlier: 3.561A pdb=" N THR B 215 " --> pdb=" O ALA B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 220 removed outlier: 3.897A pdb=" N GLU B 219 " --> pdb=" O VAL B 216 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N MET B 220 " --> pdb=" O MET B 217 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 216 through 220' Processing helix chain 'B' and resid 234 through 245 Processing helix chain 'B' and resid 271 through 280 removed outlier: 4.016A pdb=" N THR B 277 " --> pdb=" O ASP B 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 19 through 30 removed outlier: 3.831A pdb=" N HIS C 28 " --> pdb=" O ASN C 24 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N MET C 29 " --> pdb=" O ALA C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 83 removed outlier: 4.169A pdb=" N GLY C 77 " --> pdb=" O ASN C 73 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA C 81 " --> pdb=" O GLY C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 92 removed outlier: 3.712A pdb=" N ALA C 90 " --> pdb=" O GLU C 86 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA C 91 " --> pdb=" O ALA C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 123 removed outlier: 3.543A pdb=" N GLY C 111 " --> pdb=" O GLY C 107 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ALA C 113 " --> pdb=" O GLY C 109 " (cutoff:3.500A) Proline residue: C 114 - end of helix Processing helix chain 'C' and resid 141 through 155 removed outlier: 3.971A pdb=" N PHE C 145 " --> pdb=" O LYS C 141 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N THR C 151 " --> pdb=" O GLU C 147 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LYS C 155 " --> pdb=" O THR C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 168 removed outlier: 3.577A pdb=" N LYS C 167 " --> pdb=" O PRO C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 202 removed outlier: 3.500A pdb=" N ALA C 185 " --> pdb=" O ALA C 181 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARG C 202 " --> pdb=" O GLU C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 215 removed outlier: 3.610A pdb=" N THR C 215 " --> pdb=" O ALA C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 220 removed outlier: 3.863A pdb=" N GLU C 219 " --> pdb=" O VAL C 216 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N MET C 220 " --> pdb=" O MET C 217 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 216 through 220' Processing helix chain 'C' and resid 234 through 245 Processing helix chain 'C' and resid 271 through 281 removed outlier: 3.885A pdb=" N THR C 281 " --> pdb=" O THR C 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 19 through 30 removed outlier: 3.736A pdb=" N MET D 29 " --> pdb=" O ALA D 25 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 66 Processing helix chain 'D' and resid 73 through 83 removed outlier: 4.219A pdb=" N GLY D 77 " --> pdb=" O ASN D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 92 removed outlier: 3.763A pdb=" N ALA D 90 " --> pdb=" O GLU D 86 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA D 91 " --> pdb=" O ALA D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 123 removed outlier: 3.911A pdb=" N ALA D 113 " --> pdb=" O GLY D 109 " (cutoff:3.500A) Proline residue: D 114 - end of helix Processing helix chain 'D' and resid 140 through 155 removed outlier: 3.531A pdb=" N ALA D 144 " --> pdb=" O LYS D 140 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N PHE D 145 " --> pdb=" O LYS D 141 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N THR D 151 " --> pdb=" O GLU D 147 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LYS D 155 " --> pdb=" O THR D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 168 removed outlier: 3.560A pdb=" N LYS D 167 " --> pdb=" O PRO D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 202 removed outlier: 4.026A pdb=" N ALA D 185 " --> pdb=" O ALA D 181 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ARG D 202 " --> pdb=" O GLU D 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 215 removed outlier: 3.541A pdb=" N VAL D 213 " --> pdb=" O ASP D 209 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N THR D 215 " --> pdb=" O ALA D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 216 through 220 removed outlier: 3.851A pdb=" N GLU D 219 " --> pdb=" O VAL D 216 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N MET D 220 " --> pdb=" O MET D 217 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 216 through 220' Processing helix chain 'D' and resid 234 through 245 Processing helix chain 'D' and resid 271 through 284 removed outlier: 3.613A pdb=" N VAL D 278 " --> pdb=" O GLU D 274 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE D 282 " --> pdb=" O VAL D 278 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA D 284 " --> pdb=" O ASN D 280 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 57 through 59 removed outlier: 8.036A pdb=" N ILE A 58 " --> pdb=" O PHE A 39 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N ALA A 41 " --> pdb=" O ILE A 58 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ILE A 13 " --> pdb=" O GLU A 38 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N PHE A 40 " --> pdb=" O ILE A 13 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N VAL A 15 " --> pdb=" O PHE A 40 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N VAL A 42 " --> pdb=" O VAL A 15 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N GLY A 17 " --> pdb=" O VAL A 42 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N VAL A 98 " --> pdb=" O VAL A 128 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N VAL A 130 " --> pdb=" O VAL A 98 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N ILE A 100 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N THR A 127 " --> pdb=" O SER A 159 " (cutoff:3.500A) removed outlier: 8.353A pdb=" N ILE A 161 " --> pdb=" O THR A 127 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N ALA A 129 " --> pdb=" O ILE A 161 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 225 through 230 removed outlier: 6.140A pdb=" N VAL A 260 " --> pdb=" O VAL A 293 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 225 through 230 removed outlier: 7.775A pdb=" N SER A 297 " --> pdb=" O VAL A 262 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N ILE A 264 " --> pdb=" O SER A 297 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 59 removed outlier: 7.910A pdb=" N ILE B 58 " --> pdb=" O PHE B 39 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ALA B 41 " --> pdb=" O ILE B 58 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ILE B 13 " --> pdb=" O GLU B 38 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N PHE B 40 " --> pdb=" O ILE B 13 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N VAL B 15 " --> pdb=" O PHE B 40 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N VAL B 42 " --> pdb=" O VAL B 15 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N GLY B 17 " --> pdb=" O VAL B 42 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N VAL B 98 " --> pdb=" O VAL B 128 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N VAL B 130 " --> pdb=" O VAL B 98 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N ILE B 100 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N SER B 159 " --> pdb=" O THR B 127 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 225 through 230 removed outlier: 3.540A pdb=" N GLY B 226 " --> pdb=" O VAL B 310 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 225 through 230 removed outlier: 3.540A pdb=" N GLY B 226 " --> pdb=" O VAL B 310 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N SER B 297 " --> pdb=" O VAL B 262 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ILE B 264 " --> pdb=" O SER B 297 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 57 through 59 removed outlier: 8.143A pdb=" N ILE C 58 " --> pdb=" O PHE C 39 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N ALA C 41 " --> pdb=" O ILE C 58 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ILE C 13 " --> pdb=" O GLU C 38 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N PHE C 40 " --> pdb=" O ILE C 13 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N VAL C 15 " --> pdb=" O PHE C 40 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N VAL C 42 " --> pdb=" O VAL C 15 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N GLY C 17 " --> pdb=" O VAL C 42 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N VAL C 98 " --> pdb=" O VAL C 128 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N VAL C 130 " --> pdb=" O VAL C 98 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N ILE C 100 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N THR C 127 " --> pdb=" O SER C 159 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N ILE C 161 " --> pdb=" O THR C 127 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N ALA C 129 " --> pdb=" O ILE C 161 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 225 through 230 removed outlier: 6.222A pdb=" N VAL C 260 " --> pdb=" O VAL C 293 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 225 through 230 removed outlier: 7.959A pdb=" N SER C 297 " --> pdb=" O VAL C 262 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ILE C 264 " --> pdb=" O SER C 297 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 57 through 59 removed outlier: 8.090A pdb=" N ILE D 58 " --> pdb=" O PHE D 39 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N ALA D 41 " --> pdb=" O ILE D 58 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ILE D 13 " --> pdb=" O GLU D 38 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N PHE D 40 " --> pdb=" O ILE D 13 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N VAL D 15 " --> pdb=" O PHE D 40 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N VAL D 42 " --> pdb=" O VAL D 15 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N GLY D 17 " --> pdb=" O VAL D 42 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N VAL D 98 " --> pdb=" O VAL D 128 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N VAL D 130 " --> pdb=" O VAL D 98 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N ILE D 100 " --> pdb=" O VAL D 130 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N SER D 159 " --> pdb=" O THR D 127 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 225 through 230 removed outlier: 3.608A pdb=" N GLY D 226 " --> pdb=" O VAL D 310 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N VAL D 260 " --> pdb=" O VAL D 293 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 225 through 230 removed outlier: 3.608A pdb=" N GLY D 226 " --> pdb=" O VAL D 310 " (cutoff:3.500A) 428 hydrogen bonds defined for protein. 1224 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: 2.65 Time building geometry restraints manager: 2.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3123 1.34 - 1.46: 1549 1.46 - 1.58: 4236 1.58 - 1.70: 20 1.70 - 1.81: 96 Bond restraints: 9024 Sorted by residual: bond pdb=" O3B G2P B 401 " pdb=" PG G2P B 401 " ideal model delta sigma weight residual 1.716 1.608 0.108 2.00e-02 2.50e+03 2.94e+01 bond pdb=" O3B G2P C 401 " pdb=" PG G2P C 401 " ideal model delta sigma weight residual 1.716 1.608 0.108 2.00e-02 2.50e+03 2.90e+01 bond pdb=" O3B G2P D 401 " pdb=" PG G2P D 401 " ideal model delta sigma weight residual 1.716 1.609 0.107 2.00e-02 2.50e+03 2.89e+01 bond pdb=" O3B G2P A 401 " pdb=" PG G2P A 401 " ideal model delta sigma weight residual 1.716 1.611 0.105 2.00e-02 2.50e+03 2.73e+01 bond pdb=" O1B G2P A 401 " pdb=" PB G2P A 401 " ideal model delta sigma weight residual 1.510 1.609 -0.099 2.00e-02 2.50e+03 2.43e+01 ... (remaining 9019 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.38: 11882 2.38 - 4.77: 249 4.77 - 7.15: 47 7.15 - 9.54: 37 9.54 - 11.92: 13 Bond angle restraints: 12228 Sorted by residual: angle pdb=" C VAL D 30 " pdb=" N ARG D 31 " pdb=" CA ARG D 31 " ideal model delta sigma weight residual 123.91 131.28 -7.37 1.66e+00 3.63e-01 1.97e+01 angle pdb=" C3A G2P D 401 " pdb=" PA G2P D 401 " pdb=" O5' G2P D 401 " ideal model delta sigma weight residual 99.14 111.06 -11.92 3.00e+00 1.11e-01 1.58e+01 angle pdb=" C3A G2P C 401 " pdb=" PA G2P C 401 " pdb=" O5' G2P C 401 " ideal model delta sigma weight residual 99.14 110.99 -11.85 3.00e+00 1.11e-01 1.56e+01 angle pdb=" C VAL A 30 " pdb=" N ARG A 31 " pdb=" CA ARG A 31 " ideal model delta sigma weight residual 125.66 132.92 -7.26 1.85e+00 2.92e-01 1.54e+01 angle pdb=" C3A G2P B 401 " pdb=" PA G2P B 401 " pdb=" O5' G2P B 401 " ideal model delta sigma weight residual 99.14 110.59 -11.45 3.00e+00 1.11e-01 1.46e+01 ... (remaining 12223 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 4908 17.90 - 35.80: 452 35.80 - 53.70: 71 53.70 - 71.60: 10 71.60 - 89.49: 15 Dihedral angle restraints: 5456 sinusoidal: 2112 harmonic: 3344 Sorted by residual: dihedral pdb=" CA LEU B 205 " pdb=" C LEU B 205 " pdb=" N MET B 206 " pdb=" CA MET B 206 " ideal model delta harmonic sigma weight residual 180.00 157.53 22.47 0 5.00e+00 4.00e-02 2.02e+01 dihedral pdb=" CA LEU A 205 " pdb=" C LEU A 205 " pdb=" N MET A 206 " pdb=" CA MET A 206 " ideal model delta harmonic sigma weight residual 180.00 157.99 22.01 0 5.00e+00 4.00e-02 1.94e+01 dihedral pdb=" CA LEU C 205 " pdb=" C LEU C 205 " pdb=" N MET C 206 " pdb=" CA MET C 206 " ideal model delta harmonic sigma weight residual 180.00 160.34 19.66 0 5.00e+00 4.00e-02 1.55e+01 ... (remaining 5453 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 1208 0.072 - 0.144: 238 0.144 - 0.215: 8 0.215 - 0.287: 0 0.287 - 0.359: 2 Chirality restraints: 1456 Sorted by residual: chirality pdb=" CB ILE A 16 " pdb=" CA ILE A 16 " pdb=" CG1 ILE A 16 " pdb=" CG2 ILE A 16 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.36 2.00e-01 2.50e+01 3.22e+00 chirality pdb=" CB ILE B 16 " pdb=" CA ILE B 16 " pdb=" CG1 ILE B 16 " pdb=" CG2 ILE B 16 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.32 2.00e-01 2.50e+01 2.52e+00 chirality pdb=" CB ILE A 60 " pdb=" CA ILE A 60 " pdb=" CG1 ILE A 60 " pdb=" CG2 ILE A 60 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.12e+00 ... (remaining 1453 not shown) Planarity restraints: 1604 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG B 202 " 0.059 5.00e-02 4.00e+02 8.97e-02 1.29e+01 pdb=" N PRO B 203 " -0.155 5.00e-02 4.00e+02 pdb=" CA PRO B 203 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO B 203 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 145 " 0.017 2.00e-02 2.50e+03 1.71e-02 5.09e+00 pdb=" CG PHE A 145 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 PHE A 145 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE A 145 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE A 145 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 145 " 0.009 2.00e-02 2.50e+03 pdb=" CZ PHE A 145 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 202 " 0.010 2.00e-02 2.50e+03 1.91e-02 3.64e+00 pdb=" C ARG A 202 " -0.033 2.00e-02 2.50e+03 pdb=" O ARG A 202 " 0.012 2.00e-02 2.50e+03 pdb=" N PRO A 203 " 0.011 2.00e-02 2.50e+03 ... (remaining 1601 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.86: 3157 2.86 - 3.43: 9494 3.43 - 4.00: 16264 4.00 - 4.57: 21988 4.57 - 5.14: 32286 Nonbonded interactions: 83189 Sorted by model distance: nonbonded pdb=" O1B G2P B 401 " pdb=" O2A G2P B 401 " model vdw 2.296 3.040 nonbonded pdb=" O1B G2P C 401 " pdb=" O2A G2P C 401 " model vdw 2.301 3.040 nonbonded pdb=" O ARG A 202 " pdb=" K K A 402 " model vdw 2.303 2.850 nonbonded pdb=" O ARG C 202 " pdb=" K K C 402 " model vdw 2.303 2.850 nonbonded pdb=" O ARG B 202 " pdb=" K K B 402 " model vdw 2.304 2.850 ... (remaining 83184 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 'B' selection = chain 'C' selection = chain 'D' } 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: 1.630 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: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 23.980 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5191 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 : 0.007 0.108 9024 Z= 0.430 Angle : 0.990 11.922 12228 Z= 0.458 Chirality : 0.055 0.359 1456 Planarity : 0.005 0.090 1604 Dihedral : 14.424 89.494 3336 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.21), residues: 1216 helix: -2.12 (0.18), residues: 432 sheet: 1.00 (0.36), residues: 248 loop : -1.68 (0.23), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 28 PHE 0.039 0.003 PHE A 145 TYR 0.006 0.001 TYR D 222 ARG 0.004 0.000 ARG C 283 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 0.848 Fit side-chains REVERT: B 104 MET cc_start: 0.5212 (mtp) cc_final: 0.4643 (mmm) REVERT: B 209 ASP cc_start: 0.6687 (m-30) cc_final: 0.6462 (m-30) REVERT: D 29 MET cc_start: 0.3931 (mtt) cc_final: 0.3643 (mtt) REVERT: D 242 MET cc_start: 0.7492 (tpp) cc_final: 0.7243 (tpp) outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 0.1473 time to fit residues: 29.4676 Evaluate side-chains 108 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 101 optimal weight: 4.9990 chunk 90 optimal weight: 5.9990 chunk 50 optimal weight: 0.0970 chunk 31 optimal weight: 0.7980 chunk 61 optimal weight: 0.9990 chunk 48 optimal weight: 0.5980 chunk 94 optimal weight: 0.0470 chunk 36 optimal weight: 0.2980 chunk 57 optimal weight: 2.9990 chunk 70 optimal weight: 0.4980 chunk 108 optimal weight: 0.9990 overall best weight: 0.3076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 186 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5122 r_free = 0.5122 target = 0.212138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4955 r_free = 0.4955 target = 0.197529 restraints weight = 16256.033| |-----------------------------------------------------------------------------| r_work (start): 0.4990 rms_B_bonded: 2.89 r_work: 0.4889 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.4889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5424 moved from start: 0.1316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9024 Z= 0.152 Angle : 0.514 5.334 12228 Z= 0.278 Chirality : 0.047 0.173 1456 Planarity : 0.004 0.058 1604 Dihedral : 8.712 80.629 1412 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 0.33 % Allowed : 9.26 % Favored : 90.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.22), residues: 1216 helix: -0.43 (0.24), residues: 420 sheet: 0.64 (0.31), residues: 288 loop : -1.50 (0.23), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 28 PHE 0.024 0.001 PHE B 145 TYR 0.001 0.000 TYR D 222 ARG 0.003 0.000 ARG D 142 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 106 time to evaluate : 0.870 Fit side-chains REVERT: A 186 ASN cc_start: 0.4712 (m-40) cc_final: 0.4328 (m-40) REVERT: B 104 MET cc_start: 0.5414 (mtp) cc_final: 0.5007 (mmm) REVERT: D 29 MET cc_start: 0.6332 (mtt) cc_final: 0.5536 (mtt) outliers start: 3 outliers final: 2 residues processed: 107 average time/residue: 0.1635 time to fit residues: 26.3715 Evaluate side-chains 96 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 94 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain D residue 294 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 69 optimal weight: 0.2980 chunk 2 optimal weight: 4.9990 chunk 72 optimal weight: 0.2980 chunk 114 optimal weight: 0.8980 chunk 21 optimal weight: 0.5980 chunk 91 optimal weight: 0.9990 chunk 94 optimal weight: 4.9990 chunk 80 optimal weight: 0.0980 chunk 100 optimal weight: 0.0170 chunk 71 optimal weight: 8.9990 chunk 86 optimal weight: 0.6980 overall best weight: 0.2618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 165 ASN B 165 ASN C 165 ASN D 165 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5150 r_free = 0.5150 target = 0.210569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4979 r_free = 0.4979 target = 0.196721 restraints weight = 16435.536| |-----------------------------------------------------------------------------| r_work (start): 0.4993 rms_B_bonded: 2.72 r_work: 0.4892 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.4892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5368 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9024 Z= 0.134 Angle : 0.456 5.510 12228 Z= 0.247 Chirality : 0.045 0.179 1456 Planarity : 0.003 0.050 1604 Dihedral : 7.586 87.453 1412 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.34 % Allowed : 12.39 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.23), residues: 1216 helix: 0.30 (0.24), residues: 456 sheet: 0.67 (0.31), residues: 280 loop : -1.41 (0.25), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS D 28 PHE 0.020 0.001 PHE A 145 TYR 0.003 0.001 TYR D 222 ARG 0.002 0.000 ARG C 142 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 107 time to evaluate : 0.871 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 104 MET cc_start: 0.5428 (mtp) cc_final: 0.5194 (mmm) REVERT: B 254 LEU cc_start: 0.5692 (tp) cc_final: 0.5465 (tp) REVERT: B 302 MET cc_start: 0.4029 (ppp) cc_final: 0.3455 (ptt) outliers start: 12 outliers final: 8 residues processed: 112 average time/residue: 0.1616 time to fit residues: 27.2278 Evaluate side-chains 105 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 97 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 GLU Chi-restraints excluded: chain B residue 206 MET Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain D residue 97 MET Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 206 MET Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain D residue 294 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 85 optimal weight: 4.9990 chunk 72 optimal weight: 0.7980 chunk 30 optimal weight: 7.9990 chunk 27 optimal weight: 0.0000 chunk 28 optimal weight: 6.9990 chunk 110 optimal weight: 0.4980 chunk 101 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 103 optimal weight: 0.5980 chunk 32 optimal weight: 0.9990 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 24 ASN C 186 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5143 r_free = 0.5143 target = 0.214092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4966 r_free = 0.4966 target = 0.198220 restraints weight = 16464.620| |-----------------------------------------------------------------------------| r_work (start): 0.4953 rms_B_bonded: 3.02 r_work: 0.4841 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.4841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5440 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 9024 Z= 0.148 Angle : 0.484 6.670 12228 Z= 0.255 Chirality : 0.046 0.166 1456 Planarity : 0.003 0.060 1604 Dihedral : 7.265 80.321 1412 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.34 % Allowed : 14.06 % Favored : 84.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.23), residues: 1216 helix: 0.57 (0.25), residues: 428 sheet: 0.67 (0.30), residues: 280 loop : -1.32 (0.24), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 28 PHE 0.020 0.001 PHE A 145 TYR 0.004 0.001 TYR D 222 ARG 0.003 0.000 ARG D 142 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 101 time to evaluate : 0.906 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 242 MET cc_start: 0.7814 (tpp) cc_final: 0.7515 (tpt) REVERT: A 254 LEU cc_start: 0.5703 (mt) cc_final: 0.5184 (mt) REVERT: B 104 MET cc_start: 0.5532 (mtp) cc_final: 0.5260 (mmm) REVERT: B 302 MET cc_start: 0.4286 (ppp) cc_final: 0.3721 (ptt) REVERT: D 220 MET cc_start: 0.3619 (mmt) cc_final: 0.2317 (ttm) outliers start: 12 outliers final: 10 residues processed: 106 average time/residue: 0.1568 time to fit residues: 25.6661 Evaluate side-chains 107 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 97 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 GLU Chi-restraints excluded: chain B residue 206 MET Chi-restraints excluded: chain C residue 29 MET Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 206 MET Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain D residue 294 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 11 optimal weight: 3.9990 chunk 52 optimal weight: 5.9990 chunk 81 optimal weight: 0.0270 chunk 13 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 51 optimal weight: 5.9990 chunk 70 optimal weight: 0.6980 chunk 3 optimal weight: 6.9990 chunk 86 optimal weight: 0.9990 chunk 57 optimal weight: 0.6980 overall best weight: 0.6838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5136 r_free = 0.5136 target = 0.213089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4964 r_free = 0.4964 target = 0.197107 restraints weight = 16611.472| |-----------------------------------------------------------------------------| r_work (start): 0.4958 rms_B_bonded: 3.04 r_work: 0.4845 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.4845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5473 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9024 Z= 0.160 Angle : 0.485 7.289 12228 Z= 0.256 Chirality : 0.046 0.171 1456 Planarity : 0.003 0.051 1604 Dihedral : 7.017 71.742 1412 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.56 % Allowed : 15.18 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.23), residues: 1216 helix: 0.74 (0.26), residues: 428 sheet: 0.53 (0.30), residues: 284 loop : -1.29 (0.24), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 28 PHE 0.020 0.002 PHE A 145 TYR 0.004 0.001 TYR D 222 ARG 0.003 0.000 ARG D 142 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 103 time to evaluate : 1.013 Fit side-chains revert: symmetry clash REVERT: A 242 MET cc_start: 0.7798 (tpp) cc_final: 0.7506 (tpt) REVERT: A 254 LEU cc_start: 0.5854 (mt) cc_final: 0.5351 (mt) REVERT: B 104 MET cc_start: 0.5625 (mtp) cc_final: 0.5376 (mmm) REVERT: B 302 MET cc_start: 0.4209 (ppp) cc_final: 0.3942 (ptt) outliers start: 14 outliers final: 11 residues processed: 111 average time/residue: 0.1732 time to fit residues: 28.9598 Evaluate side-chains 106 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 95 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 198 GLU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain C residue 29 MET Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 206 MET Chi-restraints excluded: chain D residue 294 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 104 optimal weight: 1.9990 chunk 103 optimal weight: 0.6980 chunk 113 optimal weight: 0.0980 chunk 44 optimal weight: 1.9990 chunk 51 optimal weight: 10.0000 chunk 20 optimal weight: 0.3980 chunk 95 optimal weight: 0.6980 chunk 17 optimal weight: 3.9990 chunk 98 optimal weight: 6.9990 chunk 82 optimal weight: 6.9990 chunk 84 optimal weight: 6.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5116 r_free = 0.5116 target = 0.206925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4947 r_free = 0.4947 target = 0.192735 restraints weight = 16525.451| |-----------------------------------------------------------------------------| r_work (start): 0.4961 rms_B_bonded: 2.74 r_work: 0.4854 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.4854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5499 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9024 Z= 0.170 Angle : 0.500 7.333 12228 Z= 0.264 Chirality : 0.046 0.172 1456 Planarity : 0.003 0.055 1604 Dihedral : 6.960 64.755 1412 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.67 % Allowed : 16.63 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.23), residues: 1216 helix: 0.59 (0.26), residues: 440 sheet: 0.61 (0.30), residues: 280 loop : -1.23 (0.24), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 28 PHE 0.020 0.002 PHE A 145 TYR 0.005 0.001 TYR D 222 ARG 0.003 0.000 ARG D 142 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 101 time to evaluate : 0.985 Fit side-chains revert: symmetry clash REVERT: A 242 MET cc_start: 0.7736 (tpp) cc_final: 0.7497 (tpt) REVERT: A 254 LEU cc_start: 0.5549 (mt) cc_final: 0.5011 (mt) REVERT: B 104 MET cc_start: 0.5715 (mtp) cc_final: 0.5474 (mmm) outliers start: 15 outliers final: 12 residues processed: 110 average time/residue: 0.1672 time to fit residues: 27.6782 Evaluate side-chains 109 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 97 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 198 GLU Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain C residue 29 MET Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 206 MET Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 294 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 74 optimal weight: 4.9990 chunk 106 optimal weight: 0.9990 chunk 115 optimal weight: 5.9990 chunk 112 optimal weight: 7.9990 chunk 5 optimal weight: 10.0000 chunk 65 optimal weight: 7.9990 chunk 97 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 79 optimal weight: 0.1980 chunk 98 optimal weight: 4.9990 chunk 111 optimal weight: 4.9990 overall best weight: 2.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5035 r_free = 0.5035 target = 0.198791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4857 r_free = 0.4857 target = 0.184118 restraints weight = 16737.202| |-----------------------------------------------------------------------------| r_work (start): 0.4876 rms_B_bonded: 2.79 r_work: 0.4774 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.4774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5743 moved from start: 0.3094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 9024 Z= 0.396 Angle : 0.739 8.020 12228 Z= 0.385 Chirality : 0.054 0.183 1456 Planarity : 0.005 0.057 1604 Dihedral : 8.224 86.164 1412 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 17.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 1.90 % Allowed : 18.42 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.23), residues: 1216 helix: -0.23 (0.24), residues: 444 sheet: -0.08 (0.29), residues: 292 loop : -1.50 (0.25), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS C 28 PHE 0.028 0.004 PHE C 145 TYR 0.014 0.003 TYR D 222 ARG 0.010 0.001 ARG A 142 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 100 time to evaluate : 0.889 Fit side-chains revert: symmetry clash REVERT: A 242 MET cc_start: 0.7755 (tpp) cc_final: 0.7534 (tpt) REVERT: B 104 MET cc_start: 0.6026 (mtp) cc_final: 0.5797 (mmm) REVERT: D 29 MET cc_start: 0.6357 (mtt) cc_final: 0.6124 (mtt) REVERT: D 254 LEU cc_start: 0.6126 (tp) cc_final: 0.5902 (tp) outliers start: 17 outliers final: 12 residues processed: 113 average time/residue: 0.1540 time to fit residues: 26.8274 Evaluate side-chains 107 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 95 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 198 GLU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain C residue 29 MET Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 206 MET Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 294 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 29 optimal weight: 0.3980 chunk 2 optimal weight: 0.5980 chunk 3 optimal weight: 0.9980 chunk 100 optimal weight: 0.1980 chunk 66 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 51 optimal weight: 7.9990 chunk 112 optimal weight: 7.9990 chunk 5 optimal weight: 0.4980 chunk 22 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 280 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5100 r_free = 0.5100 target = 0.205143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4928 r_free = 0.4928 target = 0.190839 restraints weight = 16712.160| |-----------------------------------------------------------------------------| r_work (start): 0.4952 rms_B_bonded: 2.77 r_work: 0.4850 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.4850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5545 moved from start: 0.3013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9024 Z= 0.168 Angle : 0.532 7.566 12228 Z= 0.280 Chirality : 0.047 0.191 1456 Planarity : 0.003 0.063 1604 Dihedral : 7.172 70.341 1412 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.67 % Allowed : 18.19 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.23), residues: 1216 helix: 0.33 (0.25), residues: 444 sheet: 0.25 (0.30), residues: 284 loop : -1.36 (0.24), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 28 PHE 0.020 0.002 PHE B 145 TYR 0.005 0.001 TYR A 222 ARG 0.003 0.000 ARG A 283 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 97 time to evaluate : 0.841 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.5113 (mmt) cc_final: 0.2749 (ttm) REVERT: A 242 MET cc_start: 0.7635 (tpp) cc_final: 0.7409 (tpt) REVERT: B 104 MET cc_start: 0.5701 (mtp) cc_final: 0.5457 (mmm) REVERT: D 29 MET cc_start: 0.6525 (mtt) cc_final: 0.6160 (mtt) outliers start: 15 outliers final: 11 residues processed: 108 average time/residue: 0.1587 time to fit residues: 26.4572 Evaluate side-chains 108 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 97 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 198 GLU Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain B residue 206 MET Chi-restraints excluded: chain C residue 29 MET Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 206 MET Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 294 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 116 optimal weight: 6.9990 chunk 84 optimal weight: 0.8980 chunk 91 optimal weight: 3.9990 chunk 62 optimal weight: 0.2980 chunk 118 optimal weight: 7.9990 chunk 63 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 89 optimal weight: 4.9990 chunk 7 optimal weight: 4.9990 chunk 47 optimal weight: 6.9990 chunk 109 optimal weight: 1.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5052 r_free = 0.5052 target = 0.200699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4875 r_free = 0.4875 target = 0.186332 restraints weight = 16724.209| |-----------------------------------------------------------------------------| r_work (start): 0.4898 rms_B_bonded: 2.74 r_work: 0.4792 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.4792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5694 moved from start: 0.3250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9024 Z= 0.291 Angle : 0.645 8.479 12228 Z= 0.334 Chirality : 0.050 0.188 1456 Planarity : 0.004 0.064 1604 Dihedral : 7.693 75.729 1412 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 15.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 1.90 % Allowed : 18.86 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.23), residues: 1216 helix: 0.06 (0.25), residues: 444 sheet: 0.01 (0.29), residues: 284 loop : -1.42 (0.25), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS C 28 PHE 0.026 0.003 PHE B 145 TYR 0.011 0.002 TYR D 222 ARG 0.004 0.000 ARG D 142 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 98 time to evaluate : 0.754 Fit side-chains revert: symmetry clash REVERT: A 242 MET cc_start: 0.7689 (tpp) cc_final: 0.7487 (tpt) REVERT: B 104 MET cc_start: 0.5927 (mtp) cc_final: 0.5674 (mmm) REVERT: C 225 MET cc_start: 0.6951 (tmm) cc_final: 0.6646 (ptm) REVERT: D 29 MET cc_start: 0.6516 (mtt) cc_final: 0.6237 (mtt) outliers start: 17 outliers final: 13 residues processed: 108 average time/residue: 0.1964 time to fit residues: 33.5201 Evaluate side-chains 110 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 97 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 198 GLU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain B residue 206 MET Chi-restraints excluded: chain B residue 225 MET Chi-restraints excluded: chain C residue 29 MET Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 206 MET Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 294 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 14 optimal weight: 0.5980 chunk 40 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 42 optimal weight: 0.2980 chunk 100 optimal weight: 0.7980 chunk 119 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 6 optimal weight: 0.7980 chunk 114 optimal weight: 9.9990 chunk 102 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5092 r_free = 0.5092 target = 0.204174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4918 r_free = 0.4918 target = 0.190030 restraints weight = 16634.724| |-----------------------------------------------------------------------------| r_work (start): 0.4945 rms_B_bonded: 2.74 r_work: 0.4848 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.4848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5562 moved from start: 0.3249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9024 Z= 0.178 Angle : 0.537 7.978 12228 Z= 0.281 Chirality : 0.047 0.187 1456 Planarity : 0.003 0.064 1604 Dihedral : 7.068 62.917 1412 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.34 % Allowed : 19.53 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.23), residues: 1216 helix: 0.36 (0.26), residues: 444 sheet: 0.25 (0.30), residues: 280 loop : -1.40 (0.24), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 28 PHE 0.021 0.002 PHE B 145 TYR 0.006 0.001 TYR D 222 ARG 0.003 0.000 ARG D 142 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 96 time to evaluate : 0.924 Fit side-chains revert: symmetry clash REVERT: A 242 MET cc_start: 0.7652 (tpp) cc_final: 0.7435 (tpt) REVERT: B 104 MET cc_start: 0.5719 (mtp) cc_final: 0.5391 (mmm) REVERT: B 303 ASN cc_start: 0.5195 (p0) cc_final: 0.4986 (m-40) REVERT: C 225 MET cc_start: 0.6557 (tmm) cc_final: 0.6308 (ptm) outliers start: 12 outliers final: 11 residues processed: 103 average time/residue: 0.2175 time to fit residues: 34.2754 Evaluate side-chains 104 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 93 time to evaluate : 1.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 198 GLU Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain B residue 206 MET Chi-restraints excluded: chain B residue 225 MET Chi-restraints excluded: chain C residue 29 MET Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 206 MET Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 294 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 35 optimal weight: 0.0060 chunk 81 optimal weight: 7.9990 chunk 102 optimal weight: 0.7980 chunk 61 optimal weight: 4.9990 chunk 34 optimal weight: 0.0270 chunk 112 optimal weight: 6.9990 chunk 45 optimal weight: 0.2980 chunk 84 optimal weight: 0.1980 chunk 53 optimal weight: 0.8980 chunk 2 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 overall best weight: 0.2654 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5139 r_free = 0.5139 target = 0.212215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4968 r_free = 0.4968 target = 0.197033 restraints weight = 16640.121| |-----------------------------------------------------------------------------| r_work (start): 0.4972 rms_B_bonded: 2.95 r_work: 0.4858 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.4858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5463 moved from start: 0.3320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9024 Z= 0.143 Angle : 0.495 7.758 12228 Z= 0.258 Chirality : 0.046 0.178 1456 Planarity : 0.003 0.061 1604 Dihedral : 6.154 49.921 1412 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.12 % Allowed : 19.64 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.24), residues: 1216 helix: 0.74 (0.26), residues: 444 sheet: 0.54 (0.30), residues: 280 loop : -1.27 (0.25), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 28 PHE 0.018 0.001 PHE B 145 TYR 0.004 0.001 TYR A 222 ARG 0.003 0.000 ARG D 142 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3955.42 seconds wall clock time: 72 minutes 7.68 seconds (4327.68 seconds total)