Starting phenix.real_space_refine on Sat May 17 00:52:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xx7_38748/05_2025/8xx7_38748.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xx7_38748/05_2025/8xx7_38748.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xx7_38748/05_2025/8xx7_38748.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xx7_38748/05_2025/8xx7_38748.map" model { file = "/net/cci-nas-00/data/ceres_data/8xx7_38748/05_2025/8xx7_38748.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xx7_38748/05_2025/8xx7_38748.cif" } resolution = 3.32 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= 1.000 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 112 5.16 5 C 9607 2.51 5 N 2586 2.21 5 O 2749 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 15054 Number of models: 1 Model: "" Number of chains: 10 Chain: "D" Number of atoms: 483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 483 Classifications: {'peptide': 65} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 60} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "R" Number of atoms: 2337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2337 Classifications: {'peptide': 300} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 9, 'TRANS': 290} Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 2, 'GLN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 49 Chain: "B" Number of atoms: 483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 483 Classifications: {'peptide': 65} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 60} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 2353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2353 Classifications: {'peptide': 300} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 9, 'TRANS': 290} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 45 Chain: "A" Number of atoms: 1711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1711 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 210} Chain breaks: 1 Chain: "E" Number of atoms: 2581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2581 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 330} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "G" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 407 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 4, 'TRANS': 48} Chain: "F" Number of atoms: 1711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1711 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 210} Chain breaks: 1 Chain: "H" Number of atoms: 2581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2581 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 330} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "I" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 407 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 4, 'TRANS': 48} Time building chain proxies: 9.60, per 1000 atoms: 0.64 Number of scatterers: 15054 At special positions: 0 Unit cell: (220.788, 123.599, 116.204, 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 112 16.00 O 2749 8.00 N 2586 7.00 C 9607 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS D 13 " - pdb=" SG CYS D 39 " distance=2.03 Simple disulfide: pdb=" SG CYS D 15 " - pdb=" SG CYS D 55 " distance=2.03 Simple disulfide: pdb=" SG CYS R 39 " - pdb=" SG CYS R 286 " distance=2.03 Simple disulfide: pdb=" SG CYS R 119 " - pdb=" SG CYS R 196 " distance=2.03 Simple disulfide: pdb=" SG CYS B 13 " - pdb=" SG CYS B 39 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 55 " distance=2.03 Simple disulfide: pdb=" SG CYS C 39 " - pdb=" SG CYS C 286 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 103 " - pdb=" SG CYS E 114 " distance=2.04 Simple disulfide: pdb=" SG CYS H 103 " - pdb=" SG CYS H 114 " distance=2.04 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: 3.65 Conformation dependent library (CDL) restraints added in 1.9 seconds 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3656 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 21 sheets defined 44.0% alpha, 19.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.66 Creating SS restraints... Processing helix chain 'D' and resid 23 through 25 No H-bonds generated for 'chain 'D' and resid 23 through 25' Processing helix chain 'D' and resid 60 through 71 removed outlier: 4.417A pdb=" N LYS D 64 " --> pdb=" O ALA D 60 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS D 65 " --> pdb=" O PRO D 61 " (cutoff:3.500A) Processing helix chain 'R' and resid 31 through 36 removed outlier: 3.813A pdb=" N LEU R 34 " --> pdb=" O PRO R 31 " (cutoff:3.500A) Processing helix chain 'R' and resid 44 through 76 removed outlier: 4.184A pdb=" N SER R 76 " --> pdb=" O VAL R 72 " (cutoff:3.500A) Processing helix chain 'R' and resid 81 through 111 Proline residue: R 102 - end of helix Processing helix chain 'R' and resid 115 through 149 Processing helix chain 'R' and resid 154 through 160 removed outlier: 3.550A pdb=" N GLN R 157 " --> pdb=" O THR R 154 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N TYR R 160 " --> pdb=" O GLN R 157 " (cutoff:3.500A) Processing helix chain 'R' and resid 161 through 177 Processing helix chain 'R' and resid 177 through 183 removed outlier: 3.507A pdb=" N LEU R 181 " --> pdb=" O ALA R 177 " (cutoff:3.500A) Processing helix chain 'R' and resid 203 through 212 Processing helix chain 'R' and resid 212 through 218 removed outlier: 3.571A pdb=" N GLN R 216 " --> pdb=" O ARG R 212 " (cutoff:3.500A) Processing helix chain 'R' and resid 220 through 240 removed outlier: 3.608A pdb=" N LYS R 240 " --> pdb=" O ARG R 236 " (cutoff:3.500A) Processing helix chain 'R' and resid 245 through 279 removed outlier: 3.547A pdb=" N ALA R 249 " --> pdb=" O GLN R 245 " (cutoff:3.500A) Proline residue: R 266 - end of helix Processing helix chain 'R' and resid 285 through 304 Processing helix chain 'R' and resid 305 through 315 Proline residue: R 311 - end of helix Processing helix chain 'R' and resid 318 through 329 Processing helix chain 'B' and resid 23 through 25 No H-bonds generated for 'chain 'B' and resid 23 through 25' Processing helix chain 'B' and resid 60 through 71 removed outlier: 4.417A pdb=" N LYS B 64 " --> pdb=" O ALA B 60 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS B 65 " --> pdb=" O PRO B 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 36 removed outlier: 3.813A pdb=" N LEU C 34 " --> pdb=" O PRO C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 76 removed outlier: 4.184A pdb=" N SER C 76 " --> pdb=" O VAL C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 111 Proline residue: C 102 - end of helix Processing helix chain 'C' and resid 115 through 149 Processing helix chain 'C' and resid 154 through 160 removed outlier: 3.550A pdb=" N GLN C 157 " --> pdb=" O THR C 154 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N TYR C 160 " --> pdb=" O GLN C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 161 through 177 Processing helix chain 'C' and resid 177 through 183 removed outlier: 3.507A pdb=" N LEU C 181 " --> pdb=" O ALA C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 212 Processing helix chain 'C' and resid 212 through 218 removed outlier: 3.570A pdb=" N GLN C 216 " --> pdb=" O ARG C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 240 removed outlier: 3.609A pdb=" N LYS C 240 " --> pdb=" O ARG C 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 279 removed outlier: 3.547A pdb=" N ALA C 249 " --> pdb=" O GLN C 245 " (cutoff:3.500A) Proline residue: C 266 - end of helix Processing helix chain 'C' and resid 285 through 304 Processing helix chain 'C' and resid 305 through 315 Proline residue: C 311 - end of helix Processing helix chain 'C' and resid 318 through 329 Processing helix chain 'A' and resid 6 through 30 Processing helix chain 'A' and resid 208 through 217 removed outlier: 4.786A pdb=" N ILE A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N HIS A 214 " --> pdb=" O LYS A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 256 Processing helix chain 'A' and resid 271 through 282 removed outlier: 4.112A pdb=" N LYS A 280 " --> pdb=" O GLY A 276 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LYS A 281 " --> pdb=" O GLU A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 310 Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'E' and resid 6 through 26 removed outlier: 3.706A pdb=" N ALA E 26 " --> pdb=" O ARG E 22 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 34 Processing helix chain 'G' and resid 12 through 24 removed outlier: 3.607A pdb=" N GLU G 17 " --> pdb=" O ARG G 13 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 55 through 59 removed outlier: 3.646A pdb=" N ASN G 59 " --> pdb=" O ALA G 56 " (cutoff:3.500A) Processing helix chain 'F' and resid 6 through 30 Processing helix chain 'F' and resid 208 through 217 removed outlier: 4.786A pdb=" N ILE F 213 " --> pdb=" O LYS F 210 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N HIS F 214 " --> pdb=" O LYS F 211 " (cutoff:3.500A) Processing helix chain 'F' and resid 243 through 256 Processing helix chain 'F' and resid 271 through 282 removed outlier: 4.113A pdb=" N LYS F 280 " --> pdb=" O GLY F 276 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYS F 281 " --> pdb=" O GLU F 277 " (cutoff:3.500A) Processing helix chain 'F' and resid 296 through 310 Processing helix chain 'F' and resid 330 through 351 Processing helix chain 'H' and resid 6 through 26 removed outlier: 3.705A pdb=" N ALA H 26 " --> pdb=" O ARG H 22 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 34 Processing helix chain 'I' and resid 12 through 24 removed outlier: 3.608A pdb=" N GLU I 17 " --> pdb=" O ARG I 13 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASN I 24 " --> pdb=" O LYS I 20 " (cutoff:3.500A) Processing helix chain 'I' and resid 29 through 44 Processing helix chain 'I' and resid 55 through 59 removed outlier: 3.646A pdb=" N ASN I 59 " --> pdb=" O ALA I 56 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 53 through 56 removed outlier: 4.516A pdb=" N VAL D 44 " --> pdb=" O LEU D 56 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N VAL B 44 " --> pdb=" O LEU B 56 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'R' and resid 184 through 187 Processing sheet with id=AA3, first strand: chain 'C' and resid 184 through 187 Processing sheet with id=AA4, first strand: chain 'A' and resid 186 through 188 Processing sheet with id=AA5, first strand: chain 'A' and resid 186 through 188 removed outlier: 9.585A pdb=" N ALA A 221 " --> pdb=" O ASP A 33 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N LYS A 35 " --> pdb=" O ALA A 221 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N ILE A 223 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N LEU A 37 " --> pdb=" O ILE A 223 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N CYS A 225 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N LEU A 39 " --> pdb=" O CYS A 225 " (cutoff:3.500A) removed outlier: 8.745A pdb=" N ASP A 227 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ILE A 222 " --> pdb=" O ILE A 266 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N PHE A 268 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N PHE A 224 " --> pdb=" O PHE A 268 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N ASN A 270 " --> pdb=" O PHE A 224 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N VAL A 226 " --> pdb=" O ASN A 270 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 47 through 52 removed outlier: 4.402A pdb=" N PHE E 335 " --> pdb=" O SER E 331 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER E 331 " --> pdb=" O PHE E 335 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 58 through 63 removed outlier: 6.963A pdb=" N ALA E 73 " --> pdb=" O TYR E 59 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N MET E 61 " --> pdb=" O VAL E 71 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N VAL E 71 " --> pdb=" O MET E 61 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N TRP E 63 " --> pdb=" O LEU E 69 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N LEU E 69 " --> pdb=" O TRP E 63 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N SER E 74 " --> pdb=" O LYS E 78 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N LYS E 78 " --> pdb=" O SER E 74 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N HIS E 91 " --> pdb=" O ILE E 81 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ASP E 83 " --> pdb=" O LYS E 89 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N LYS E 89 " --> pdb=" O ASP E 83 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 100 through 103 removed outlier: 4.210A pdb=" N SER E 122 " --> pdb=" O CYS E 114 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ASN E 125 " --> pdb=" O VAL E 135 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N VAL E 135 " --> pdb=" O ASN E 125 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 146 through 153 removed outlier: 4.600A pdb=" N CYS E 149 " --> pdb=" O VAL E 158 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N VAL E 158 " --> pdb=" O CYS E 149 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N PHE E 151 " --> pdb=" O GLN E 156 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N GLN E 156 " --> pdb=" O PHE E 151 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE E 157 " --> pdb=" O TRP E 169 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER E 161 " --> pdb=" O THR E 165 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N THR E 165 " --> pdb=" O SER E 161 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 187 through 192 removed outlier: 3.567A pdb=" N SER E 201 " --> pdb=" O LYS E 209 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N SER E 207 " --> pdb=" O ALA E 203 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN E 220 " --> pdb=" O LEU E 210 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N ASP E 212 " --> pdb=" O CYS E 218 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N CYS E 218 " --> pdb=" O ASP E 212 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 229 through 234 removed outlier: 6.406A pdb=" N GLY E 244 " --> pdb=" O ASN E 230 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ILE E 232 " --> pdb=" O ALA E 242 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ALA E 242 " --> pdb=" O ILE E 232 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N PHE E 234 " --> pdb=" O ALA E 240 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ALA E 240 " --> pdb=" O PHE E 234 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N CYS E 250 " --> pdb=" O THR E 263 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N THR E 263 " --> pdb=" O CYS E 250 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N LEU E 252 " --> pdb=" O LEU E 261 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 273 through 278 removed outlier: 6.395A pdb=" N GLY E 288 " --> pdb=" O THR E 274 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N VAL E 276 " --> pdb=" O LEU E 286 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N LEU E 286 " --> pdb=" O VAL E 276 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N PHE E 278 " --> pdb=" O LEU E 284 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N LEU E 284 " --> pdb=" O PHE E 278 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N CYS E 294 " --> pdb=" O VAL E 307 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N VAL E 307 " --> pdb=" O CYS E 294 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N VAL E 296 " --> pdb=" O ALA E 305 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 186 through 188 Processing sheet with id=AB5, first strand: chain 'F' and resid 186 through 188 removed outlier: 9.585A pdb=" N ALA F 221 " --> pdb=" O ASP F 33 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N LYS F 35 " --> pdb=" O ALA F 221 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N ILE F 223 " --> pdb=" O LYS F 35 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N LEU F 37 " --> pdb=" O ILE F 223 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N CYS F 225 " --> pdb=" O LEU F 37 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N LEU F 39 " --> pdb=" O CYS F 225 " (cutoff:3.500A) removed outlier: 8.746A pdb=" N ASP F 227 " --> pdb=" O LEU F 39 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ILE F 222 " --> pdb=" O ILE F 266 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N PHE F 268 " --> pdb=" O ILE F 222 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N PHE F 224 " --> pdb=" O PHE F 268 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N ASN F 270 " --> pdb=" O PHE F 224 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N VAL F 226 " --> pdb=" O ASN F 270 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 47 through 52 removed outlier: 4.402A pdb=" N PHE H 335 " --> pdb=" O SER H 331 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER H 331 " --> pdb=" O PHE H 335 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 58 through 63 removed outlier: 6.964A pdb=" N ALA H 73 " --> pdb=" O TYR H 59 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N MET H 61 " --> pdb=" O VAL H 71 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N VAL H 71 " --> pdb=" O MET H 61 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N TRP H 63 " --> pdb=" O LEU H 69 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N LEU H 69 " --> pdb=" O TRP H 63 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N SER H 74 " --> pdb=" O LYS H 78 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N LYS H 78 " --> pdb=" O SER H 74 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N HIS H 91 " --> pdb=" O ILE H 81 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ASP H 83 " --> pdb=" O LYS H 89 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N LYS H 89 " --> pdb=" O ASP H 83 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 100 through 103 removed outlier: 4.210A pdb=" N SER H 122 " --> pdb=" O CYS H 114 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ASN H 125 " --> pdb=" O VAL H 135 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N VAL H 135 " --> pdb=" O ASN H 125 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 146 through 153 removed outlier: 4.600A pdb=" N CYS H 149 " --> pdb=" O VAL H 158 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N VAL H 158 " --> pdb=" O CYS H 149 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N PHE H 151 " --> pdb=" O GLN H 156 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N GLN H 156 " --> pdb=" O PHE H 151 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE H 157 " --> pdb=" O TRP H 169 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER H 161 " --> pdb=" O THR H 165 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N THR H 165 " --> pdb=" O SER H 161 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 187 through 192 removed outlier: 3.567A pdb=" N SER H 201 " --> pdb=" O LYS H 209 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N SER H 207 " --> pdb=" O ALA H 203 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN H 220 " --> pdb=" O LEU H 210 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N ASP H 212 " --> pdb=" O CYS H 218 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N CYS H 218 " --> pdb=" O ASP H 212 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 229 through 234 removed outlier: 6.406A pdb=" N GLY H 244 " --> pdb=" O ASN H 230 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ILE H 232 " --> pdb=" O ALA H 242 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ALA H 242 " --> pdb=" O ILE H 232 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N PHE H 234 " --> pdb=" O ALA H 240 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ALA H 240 " --> pdb=" O PHE H 234 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N CYS H 250 " --> pdb=" O THR H 263 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N THR H 263 " --> pdb=" O CYS H 250 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N LEU H 252 " --> pdb=" O LEU H 261 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 273 through 278 removed outlier: 6.396A pdb=" N GLY H 288 " --> pdb=" O THR H 274 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N VAL H 276 " --> pdb=" O LEU H 286 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N LEU H 286 " --> pdb=" O VAL H 276 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N PHE H 278 " --> pdb=" O LEU H 284 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N LEU H 284 " --> pdb=" O PHE H 278 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N CYS H 294 " --> pdb=" O VAL H 307 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N VAL H 307 " --> pdb=" O CYS H 294 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N VAL H 296 " --> pdb=" O ALA H 305 " (cutoff:3.500A) 782 hydrogen bonds defined for protein. 2244 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: 4.61 Time building geometry restraints manager: 4.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 4906 1.35 - 1.46: 3514 1.46 - 1.58: 6760 1.58 - 1.70: 0 1.70 - 1.82: 154 Bond restraints: 15334 Sorted by residual: bond pdb=" CA ILE R 46 " pdb=" CB ILE R 46 " ideal model delta sigma weight residual 1.540 1.521 0.020 1.25e-02 6.40e+03 2.44e+00 bond pdb=" CA ILE C 46 " pdb=" CB ILE C 46 " ideal model delta sigma weight residual 1.540 1.521 0.019 1.25e-02 6.40e+03 2.37e+00 bond pdb=" CA CYS C 196 " pdb=" CB CYS C 196 " ideal model delta sigma weight residual 1.523 1.540 -0.017 1.27e-02 6.20e+03 1.83e+00 bond pdb=" CB CYS E 103 " pdb=" SG CYS E 103 " ideal model delta sigma weight residual 1.808 1.763 0.045 3.30e-02 9.18e+02 1.82e+00 bond pdb=" CB CYS H 103 " pdb=" SG CYS H 103 " ideal model delta sigma weight residual 1.808 1.764 0.044 3.30e-02 9.18e+02 1.81e+00 ... (remaining 15329 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.08: 20029 1.08 - 2.17: 639 2.17 - 3.25: 80 3.25 - 4.34: 26 4.34 - 5.42: 9 Bond angle restraints: 20783 Sorted by residual: angle pdb=" C ALA E 309 " pdb=" CA ALA E 309 " pdb=" CB ALA E 309 " ideal model delta sigma weight residual 115.89 110.47 5.42 1.32e+00 5.74e-01 1.69e+01 angle pdb=" C ALA H 309 " pdb=" CA ALA H 309 " pdb=" CB ALA H 309 " ideal model delta sigma weight residual 115.89 110.47 5.42 1.32e+00 5.74e-01 1.69e+01 angle pdb=" N ILE R 317 " pdb=" CA ILE R 317 " pdb=" C ILE R 317 " ideal model delta sigma weight residual 112.80 109.34 3.46 1.15e+00 7.56e-01 9.06e+00 angle pdb=" N ILE C 317 " pdb=" CA ILE C 317 " pdb=" C ILE C 317 " ideal model delta sigma weight residual 112.80 109.35 3.45 1.15e+00 7.56e-01 8.99e+00 angle pdb=" CA VAL R 222 " pdb=" C VAL R 222 " pdb=" N PRO R 223 " ideal model delta sigma weight residual 120.83 119.03 1.80 6.10e-01 2.69e+00 8.69e+00 ... (remaining 20778 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.33: 8413 17.33 - 34.65: 685 34.65 - 51.98: 93 51.98 - 69.31: 18 69.31 - 86.63: 8 Dihedral angle restraints: 9217 sinusoidal: 3583 harmonic: 5634 Sorted by residual: dihedral pdb=" CA PHE H 234 " pdb=" C PHE H 234 " pdb=" N PHE H 235 " pdb=" CA PHE H 235 " ideal model delta harmonic sigma weight residual 180.00 162.33 17.67 0 5.00e+00 4.00e-02 1.25e+01 dihedral pdb=" CA PHE E 234 " pdb=" C PHE E 234 " pdb=" N PHE E 235 " pdb=" CA PHE E 235 " ideal model delta harmonic sigma weight residual 180.00 162.36 17.64 0 5.00e+00 4.00e-02 1.24e+01 dihedral pdb=" CB GLU H 172 " pdb=" CG GLU H 172 " pdb=" CD GLU H 172 " pdb=" OE1 GLU H 172 " ideal model delta sinusoidal sigma weight residual 0.00 86.63 -86.63 1 3.00e+01 1.11e-03 1.00e+01 ... (remaining 9214 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1523 0.030 - 0.061: 618 0.061 - 0.091: 184 0.091 - 0.121: 108 0.121 - 0.151: 7 Chirality restraints: 2440 Sorted by residual: chirality pdb=" CB ILE F 55 " pdb=" CA ILE F 55 " pdb=" CG1 ILE F 55 " pdb=" CG2 ILE F 55 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.15 2.00e-01 2.50e+01 5.74e-01 chirality pdb=" CB ILE A 55 " pdb=" CA ILE A 55 " pdb=" CG1 ILE A 55 " pdb=" CG2 ILE A 55 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.15 2.00e-01 2.50e+01 5.73e-01 chirality pdb=" CA ILE F 222 " pdb=" N ILE F 222 " pdb=" C ILE F 222 " pdb=" CB ILE F 222 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.18e-01 ... (remaining 2437 not shown) Planarity restraints: 2621 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL G 54 " 0.026 5.00e-02 4.00e+02 4.00e-02 2.56e+00 pdb=" N PRO G 55 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO G 55 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO G 55 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL I 54 " -0.026 5.00e-02 4.00e+02 3.99e-02 2.54e+00 pdb=" N PRO I 55 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO I 55 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO I 55 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE E 235 " 0.025 5.00e-02 4.00e+02 3.77e-02 2.27e+00 pdb=" N PRO E 236 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO E 236 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO E 236 " 0.021 5.00e-02 4.00e+02 ... (remaining 2618 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2375 2.76 - 3.30: 14466 3.30 - 3.83: 24147 3.83 - 4.37: 27897 4.37 - 4.90: 50246 Nonbonded interactions: 119131 Sorted by model distance: nonbonded pdb=" O ILE H 58 " pdb=" OG SER H 316 " model vdw 2.229 3.040 nonbonded pdb=" O ILE E 58 " pdb=" OG SER E 316 " model vdw 2.230 3.040 nonbonded pdb=" O GLY R 201 " pdb=" OG1 THR R 204 " model vdw 2.240 3.040 nonbonded pdb=" O GLY C 201 " pdb=" OG1 THR C 204 " model vdw 2.240 3.040 nonbonded pdb=" O ILE F 343 " pdb=" ND2 ASN F 347 " model vdw 2.244 3.120 ... (remaining 119126 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 'F' } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = (chain 'C' and (resid 31 through 47 or (resid 48 through 50 and (name N or name \ CA or name C or name O or name CB )) or resid 51 through 239 or (resid 240 throu \ gh 241 and (name N or name CA or name C or name O or name CB )) or resid 242 thr \ ough 318 or (resid 319 through 320 and (name N or name CA or name C or name O or \ name CB )) or resid 321 through 330)) selection = chain 'R' } ncs_group { reference = chain 'E' selection = chain 'H' } ncs_group { reference = chain 'G' selection = chain 'I' } 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: 3.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.590 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 35.070 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.080 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5522 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 : 0.004 0.045 15344 Z= 0.157 Angle : 0.479 5.423 20803 Z= 0.282 Chirality : 0.040 0.151 2440 Planarity : 0.003 0.040 2621 Dihedral : 12.689 86.631 5531 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % 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: 0.54 (0.19), residues: 1914 helix: 1.88 (0.19), residues: 800 sheet: -0.44 (0.25), residues: 424 loop : -0.88 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 211 HIS 0.003 0.001 HIS R 242 PHE 0.014 0.001 PHE E 234 TYR 0.006 0.001 TYR R 86 ARG 0.004 0.000 ARG C 248 Details of bonding type rmsd hydrogen bonds : bond 0.19766 ( 774) hydrogen bonds : angle 6.21401 ( 2244) SS BOND : bond 0.00287 ( 10) SS BOND : angle 1.79551 ( 20) covalent geometry : bond 0.00355 (15334) covalent geometry : angle 0.47613 (20783) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 419 time to evaluate : 1.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 17 GLN cc_start: 0.7539 (tt0) cc_final: 0.7206 (tt0) REVERT: R 84 ASP cc_start: 0.8350 (m-30) cc_final: 0.8097 (m-30) REVERT: R 160 TYR cc_start: 0.7301 (m-80) cc_final: 0.7060 (m-80) REVERT: R 213 ILE cc_start: 0.8730 (tt) cc_final: 0.8472 (mt) REVERT: R 305 LEU cc_start: 0.8779 (mt) cc_final: 0.8561 (mp) REVERT: B 17 GLN cc_start: 0.7536 (tt0) cc_final: 0.7196 (tt0) REVERT: C 84 ASP cc_start: 0.8376 (m-30) cc_final: 0.8112 (m-30) REVERT: C 160 TYR cc_start: 0.7297 (m-80) cc_final: 0.7061 (m-80) REVERT: C 213 ILE cc_start: 0.8726 (tt) cc_final: 0.8471 (mt) REVERT: C 305 LEU cc_start: 0.8776 (mt) cc_final: 0.8557 (mp) outliers start: 0 outliers final: 0 residues processed: 419 average time/residue: 0.3289 time to fit residues: 188.0764 Evaluate side-chains 196 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 196 time to evaluate : 1.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 160 optimal weight: 6.9990 chunk 144 optimal weight: 5.9990 chunk 79 optimal weight: 0.0870 chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 20.0000 chunk 76 optimal weight: 2.9990 chunk 148 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 chunk 90 optimal weight: 4.9990 chunk 110 optimal weight: 0.9990 chunk 172 optimal weight: 6.9990 overall best weight: 1.1964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 17 GLN D 29 ASN R 47 ASN R 89 ASN B 17 GLN B 29 ASN C 47 ASN C 89 ASN ** A 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 256 ASN E 176 GLN E 183 HIS E 266 HIS ** F 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 256 ASN F 305 GLN H 176 GLN H 183 HIS H 266 HIS I 18 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.136327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.092132 restraints weight = 38993.806| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 3.57 r_work: 0.3249 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.3523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 15344 Z= 0.204 Angle : 0.680 11.319 20803 Z= 0.363 Chirality : 0.046 0.168 2440 Planarity : 0.005 0.071 2621 Dihedral : 4.239 24.185 2078 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.26 % Allowed : 11.19 % Favored : 86.55 % 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: 0.53 (0.19), residues: 1914 helix: 1.72 (0.18), residues: 820 sheet: -0.18 (0.25), residues: 396 loop : -0.95 (0.23), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP H 339 HIS 0.005 0.001 HIS R 247 PHE 0.025 0.002 PHE B 62 TYR 0.019 0.002 TYR F 231 ARG 0.006 0.001 ARG F 209 Details of bonding type rmsd hydrogen bonds : bond 0.05179 ( 774) hydrogen bonds : angle 4.98393 ( 2244) SS BOND : bond 0.01028 ( 10) SS BOND : angle 2.68770 ( 20) covalent geometry : bond 0.00470 (15334) covalent geometry : angle 0.67522 (20783) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 217 time to evaluate : 2.076 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 17 GLN cc_start: 0.8138 (tt0) cc_final: 0.7826 (tt0) REVERT: R 84 ASP cc_start: 0.8970 (m-30) cc_final: 0.8743 (m-30) REVERT: R 213 ILE cc_start: 0.9268 (tt) cc_final: 0.8917 (mt) REVERT: B 17 GLN cc_start: 0.8137 (tt0) cc_final: 0.7824 (tt0) REVERT: C 84 ASP cc_start: 0.8966 (m-30) cc_final: 0.8732 (m-30) REVERT: C 213 ILE cc_start: 0.9258 (tt) cc_final: 0.8909 (mt) REVERT: A 303 TYR cc_start: 0.8926 (t80) cc_final: 0.8721 (t80) REVERT: A 307 GLN cc_start: 0.8616 (mm110) cc_final: 0.7869 (tp-100) REVERT: E 91 HIS cc_start: 0.6590 (m-70) cc_final: 0.6318 (m170) REVERT: E 101 MET cc_start: 0.8831 (tpp) cc_final: 0.8587 (tpp) REVERT: E 339 TRP cc_start: 0.6398 (OUTLIER) cc_final: 0.4617 (m100) REVERT: G 22 GLU cc_start: 0.8947 (tt0) cc_final: 0.8098 (tp30) REVERT: F 303 TYR cc_start: 0.8946 (t80) cc_final: 0.8741 (t80) REVERT: F 307 GLN cc_start: 0.8624 (mm110) cc_final: 0.7851 (tp-100) REVERT: H 91 HIS cc_start: 0.6588 (m-70) cc_final: 0.6326 (m170) REVERT: H 101 MET cc_start: 0.8786 (tpp) cc_final: 0.8533 (tpp) REVERT: H 124 TYR cc_start: 0.7719 (m-80) cc_final: 0.7517 (m-10) REVERT: H 339 TRP cc_start: 0.6158 (OUTLIER) cc_final: 0.4513 (m100) REVERT: I 22 GLU cc_start: 0.8910 (tt0) cc_final: 0.8072 (tp30) outliers start: 37 outliers final: 19 residues processed: 245 average time/residue: 0.2703 time to fit residues: 96.9718 Evaluate side-chains 202 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 181 time to evaluate : 1.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 50 ASN Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 191 ASN Chi-restraints excluded: chain R residue 304 ILE Chi-restraints excluded: chain R residue 308 CYS Chi-restraints excluded: chain R residue 325 LEU Chi-restraints excluded: chain B residue 50 ASN Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 191 ASN Chi-restraints excluded: chain C residue 304 ILE Chi-restraints excluded: chain C residue 308 CYS Chi-restraints excluded: chain C residue 323 HIS Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 103 CYS Chi-restraints excluded: chain E residue 339 TRP Chi-restraints excluded: chain F residue 49 ILE Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 103 CYS Chi-restraints excluded: chain H residue 339 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 108 optimal weight: 5.9990 chunk 140 optimal weight: 0.6980 chunk 129 optimal weight: 2.9990 chunk 176 optimal weight: 10.0000 chunk 9 optimal weight: 2.9990 chunk 96 optimal weight: 0.0000 chunk 180 optimal weight: 10.0000 chunk 172 optimal weight: 7.9990 chunk 97 optimal weight: 6.9990 chunk 35 optimal weight: 0.0670 chunk 62 optimal weight: 0.8980 overall best weight: 0.9324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 GLN A 346 ASN E 91 HIS ** G 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 305 GLN F 346 ASN H 91 HIS ** I 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.135677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.092019 restraints weight = 38913.280| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 3.20 r_work: 0.3253 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.4011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 15344 Z= 0.163 Angle : 0.586 8.030 20803 Z= 0.316 Chirality : 0.043 0.175 2440 Planarity : 0.004 0.063 2621 Dihedral : 4.281 28.885 2078 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.08 % Allowed : 13.08 % Favored : 84.84 % 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: 0.85 (0.19), residues: 1914 helix: 2.04 (0.19), residues: 798 sheet: 0.11 (0.26), residues: 382 loop : -0.84 (0.22), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP E 211 HIS 0.005 0.001 HIS G 44 PHE 0.020 0.001 PHE B 62 TYR 0.008 0.001 TYR A 354 ARG 0.004 0.001 ARG G 27 Details of bonding type rmsd hydrogen bonds : bond 0.04739 ( 774) hydrogen bonds : angle 4.71313 ( 2244) SS BOND : bond 0.00602 ( 10) SS BOND : angle 3.17365 ( 20) covalent geometry : bond 0.00378 (15334) covalent geometry : angle 0.57780 (20783) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 194 time to evaluate : 1.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 17 GLN cc_start: 0.8174 (tt0) cc_final: 0.7851 (tt0) REVERT: R 84 ASP cc_start: 0.8903 (m-30) cc_final: 0.8695 (m-30) REVERT: R 213 ILE cc_start: 0.9216 (tt) cc_final: 0.8950 (mt) REVERT: B 17 GLN cc_start: 0.8169 (tt0) cc_final: 0.7851 (tt0) REVERT: C 84 ASP cc_start: 0.8903 (m-30) cc_final: 0.8689 (m-30) REVERT: C 213 ILE cc_start: 0.9199 (tt) cc_final: 0.8928 (mt) REVERT: A 211 LYS cc_start: 0.8128 (mmtm) cc_final: 0.7781 (mmtt) REVERT: A 297 TYR cc_start: 0.6787 (t80) cc_final: 0.6383 (t80) REVERT: A 303 TYR cc_start: 0.8986 (t80) cc_final: 0.8717 (t80) REVERT: E 211 TRP cc_start: 0.5963 (m100) cc_final: 0.5351 (m100) REVERT: E 235 PHE cc_start: 0.5151 (t80) cc_final: 0.4410 (t80) REVERT: E 256 ARG cc_start: 0.6244 (mtm180) cc_final: 0.5938 (mmm-85) REVERT: G 22 GLU cc_start: 0.9027 (tt0) cc_final: 0.8531 (tp30) REVERT: G 36 ASP cc_start: 0.8930 (t0) cc_final: 0.8402 (t0) REVERT: F 211 LYS cc_start: 0.8195 (mmtm) cc_final: 0.7856 (mmtt) REVERT: F 297 TYR cc_start: 0.6859 (t80) cc_final: 0.6470 (t80) REVERT: F 303 TYR cc_start: 0.8983 (t80) cc_final: 0.8763 (t80) REVERT: H 211 TRP cc_start: 0.6057 (m100) cc_final: 0.5471 (m100) REVERT: H 235 PHE cc_start: 0.5144 (t80) cc_final: 0.4405 (t80) REVERT: H 256 ARG cc_start: 0.6252 (mtm180) cc_final: 0.5932 (mmm-85) REVERT: H 339 TRP cc_start: 0.6310 (OUTLIER) cc_final: 0.4575 (m100) REVERT: I 36 ASP cc_start: 0.8930 (t0) cc_final: 0.8404 (t0) outliers start: 34 outliers final: 24 residues processed: 215 average time/residue: 0.2830 time to fit residues: 87.6504 Evaluate side-chains 197 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 172 time to evaluate : 1.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 50 ASN Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 191 ASN Chi-restraints excluded: chain R residue 304 ILE Chi-restraints excluded: chain R residue 325 LEU Chi-restraints excluded: chain B residue 50 ASN Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 191 ASN Chi-restraints excluded: chain C residue 304 ILE Chi-restraints excluded: chain C residue 323 HIS Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 103 CYS Chi-restraints excluded: chain E residue 234 PHE Chi-restraints excluded: chain E residue 262 MET Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain F residue 49 ILE Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 103 CYS Chi-restraints excluded: chain H residue 234 PHE Chi-restraints excluded: chain H residue 262 MET Chi-restraints excluded: chain H residue 339 TRP Chi-restraints excluded: chain I residue 31 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 52 optimal weight: 0.4980 chunk 130 optimal weight: 6.9990 chunk 55 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 chunk 138 optimal weight: 6.9990 chunk 153 optimal weight: 7.9990 chunk 133 optimal weight: 9.9990 chunk 73 optimal weight: 0.9980 chunk 63 optimal weight: 3.9990 chunk 103 optimal weight: 10.0000 chunk 25 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 ASN E 91 HIS H 91 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.135180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.091416 restraints weight = 38433.475| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 3.38 r_work: 0.3232 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.4370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15344 Z= 0.143 Angle : 0.546 7.565 20803 Z= 0.295 Chirality : 0.042 0.154 2440 Planarity : 0.004 0.063 2621 Dihedral : 4.186 30.711 2078 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.20 % Allowed : 13.26 % Favored : 84.54 % 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: 1.04 (0.20), residues: 1914 helix: 2.16 (0.19), residues: 806 sheet: 0.21 (0.26), residues: 382 loop : -0.71 (0.23), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 211 HIS 0.004 0.001 HIS G 44 PHE 0.019 0.001 PHE B 62 TYR 0.006 0.001 TYR H 124 ARG 0.003 0.000 ARG A 209 Details of bonding type rmsd hydrogen bonds : bond 0.04391 ( 774) hydrogen bonds : angle 4.51096 ( 2244) SS BOND : bond 0.00569 ( 10) SS BOND : angle 3.07347 ( 20) covalent geometry : bond 0.00333 (15334) covalent geometry : angle 0.53831 (20783) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 183 time to evaluate : 1.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 17 GLN cc_start: 0.8128 (tt0) cc_final: 0.7743 (tt0) REVERT: R 84 ASP cc_start: 0.8934 (m-30) cc_final: 0.8733 (m-30) REVERT: R 213 ILE cc_start: 0.9255 (tt) cc_final: 0.8994 (mt) REVERT: B 17 GLN cc_start: 0.8154 (tt0) cc_final: 0.7774 (tt0) REVERT: C 84 ASP cc_start: 0.8924 (m-30) cc_final: 0.8719 (m-30) REVERT: C 213 ILE cc_start: 0.9254 (tt) cc_final: 0.8996 (mt) REVERT: A 211 LYS cc_start: 0.8187 (mmtm) cc_final: 0.7849 (mmtt) REVERT: A 297 TYR cc_start: 0.6776 (t80) cc_final: 0.6516 (t80) REVERT: E 235 PHE cc_start: 0.5460 (t80) cc_final: 0.4633 (t80) REVERT: E 256 ARG cc_start: 0.6215 (mtm180) cc_final: 0.5947 (mmm-85) REVERT: E 280 LYS cc_start: 0.7474 (mmmt) cc_final: 0.7261 (mmmt) REVERT: E 339 TRP cc_start: 0.6406 (OUTLIER) cc_final: 0.4578 (m100) REVERT: G 36 ASP cc_start: 0.8938 (t0) cc_final: 0.8426 (t0) REVERT: F 297 TYR cc_start: 0.6776 (t80) cc_final: 0.6550 (t80) REVERT: H 235 PHE cc_start: 0.5385 (t80) cc_final: 0.4547 (t80) REVERT: H 256 ARG cc_start: 0.6219 (mtm180) cc_final: 0.5940 (mmm-85) REVERT: H 280 LYS cc_start: 0.7486 (mmmt) cc_final: 0.7278 (mmmt) REVERT: I 36 ASP cc_start: 0.8928 (t0) cc_final: 0.8430 (t0) outliers start: 36 outliers final: 17 residues processed: 208 average time/residue: 0.2857 time to fit residues: 86.2357 Evaluate side-chains 181 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 163 time to evaluate : 1.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 50 ASN Chi-restraints excluded: chain R residue 304 ILE Chi-restraints excluded: chain R residue 325 LEU Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 50 ASN Chi-restraints excluded: chain C residue 304 ILE Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 103 CYS Chi-restraints excluded: chain E residue 234 PHE Chi-restraints excluded: chain E residue 339 TRP Chi-restraints excluded: chain F residue 49 ILE Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 103 CYS Chi-restraints excluded: chain H residue 234 PHE Chi-restraints excluded: chain H residue 262 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 13 optimal weight: 0.9980 chunk 119 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 145 optimal weight: 8.9990 chunk 11 optimal weight: 2.9990 chunk 110 optimal weight: 10.0000 chunk 139 optimal weight: 0.1980 chunk 23 optimal weight: 0.8980 chunk 133 optimal weight: 9.9990 chunk 158 optimal weight: 9.9990 chunk 186 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 ASN A 305 GLN ** E 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.133791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.090965 restraints weight = 39077.276| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 3.69 r_work: 0.3188 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.4779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15344 Z= 0.183 Angle : 0.570 7.004 20803 Z= 0.308 Chirality : 0.043 0.157 2440 Planarity : 0.004 0.062 2621 Dihedral : 4.273 33.764 2078 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.81 % Allowed : 13.45 % Favored : 83.74 % 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 (0.20), residues: 1914 helix: 2.04 (0.18), residues: 808 sheet: 0.18 (0.26), residues: 358 loop : -0.68 (0.23), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP E 211 HIS 0.006 0.001 HIS G 44 PHE 0.020 0.002 PHE D 62 TYR 0.015 0.001 TYR F 303 ARG 0.005 0.001 ARG A 243 Details of bonding type rmsd hydrogen bonds : bond 0.04658 ( 774) hydrogen bonds : angle 4.54478 ( 2244) SS BOND : bond 0.00564 ( 10) SS BOND : angle 3.15238 ( 20) covalent geometry : bond 0.00433 (15334) covalent geometry : angle 0.56227 (20783) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 171 time to evaluate : 1.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 17 GLN cc_start: 0.8294 (tt0) cc_final: 0.7804 (tt0) REVERT: R 213 ILE cc_start: 0.9292 (OUTLIER) cc_final: 0.9018 (mt) REVERT: B 17 GLN cc_start: 0.8294 (tt0) cc_final: 0.7807 (tt0) REVERT: C 213 ILE cc_start: 0.9282 (OUTLIER) cc_final: 0.9012 (mt) REVERT: A 211 LYS cc_start: 0.8239 (mmtm) cc_final: 0.7936 (mmtt) REVERT: A 354 TYR cc_start: 0.7767 (t80) cc_final: 0.7448 (t80) REVERT: E 235 PHE cc_start: 0.5535 (t80) cc_final: 0.4655 (t80) REVERT: E 256 ARG cc_start: 0.6332 (mtm180) cc_final: 0.6039 (mmm-85) REVERT: E 339 TRP cc_start: 0.6546 (OUTLIER) cc_final: 0.4523 (m100) REVERT: G 21 MET cc_start: 0.7949 (ppp) cc_final: 0.7689 (ppp) REVERT: G 36 ASP cc_start: 0.8942 (t0) cc_final: 0.8464 (t0) REVERT: G 44 HIS cc_start: 0.6107 (t-170) cc_final: 0.5708 (t70) REVERT: F 341 ASP cc_start: 0.8820 (OUTLIER) cc_final: 0.8561 (m-30) REVERT: F 354 TYR cc_start: 0.7779 (t80) cc_final: 0.7492 (t80) REVERT: H 211 TRP cc_start: 0.6127 (m100) cc_final: 0.4989 (m100) REVERT: H 235 PHE cc_start: 0.5507 (t80) cc_final: 0.4623 (t80) REVERT: H 256 ARG cc_start: 0.6340 (mtm180) cc_final: 0.6032 (mmm-85) REVERT: H 339 TRP cc_start: 0.6408 (OUTLIER) cc_final: 0.4628 (m100) REVERT: I 36 ASP cc_start: 0.8941 (t0) cc_final: 0.8468 (t0) REVERT: I 44 HIS cc_start: 0.6091 (t-170) cc_final: 0.5696 (t70) outliers start: 46 outliers final: 22 residues processed: 202 average time/residue: 0.2938 time to fit residues: 86.4913 Evaluate side-chains 182 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 155 time to evaluate : 1.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 50 ASN Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 213 ILE Chi-restraints excluded: chain R residue 304 ILE Chi-restraints excluded: chain R residue 316 PHE Chi-restraints excluded: chain R residue 325 LEU Chi-restraints excluded: chain B residue 50 ASN Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 304 ILE Chi-restraints excluded: chain C residue 316 PHE Chi-restraints excluded: chain C residue 323 HIS Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 103 CYS Chi-restraints excluded: chain E residue 234 PHE Chi-restraints excluded: chain E residue 262 MET Chi-restraints excluded: chain E residue 339 TRP Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain F residue 49 ILE Chi-restraints excluded: chain F residue 341 ASP Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 103 CYS Chi-restraints excluded: chain H residue 234 PHE Chi-restraints excluded: chain H residue 339 TRP Chi-restraints excluded: chain I residue 31 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 122 optimal weight: 6.9990 chunk 183 optimal weight: 9.9990 chunk 168 optimal weight: 0.9990 chunk 184 optimal weight: 6.9990 chunk 10 optimal weight: 5.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 5.9990 chunk 186 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 chunk 74 optimal weight: 9.9990 chunk 102 optimal weight: 3.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 43 ASN F 305 GLN ** H 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.130740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.088383 restraints weight = 38379.310| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 3.30 r_work: 0.3178 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.5450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.065 15344 Z= 0.363 Angle : 0.740 8.007 20803 Z= 0.397 Chirality : 0.050 0.191 2440 Planarity : 0.005 0.062 2621 Dihedral : 4.832 43.343 2078 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.75 % Allowed : 15.34 % Favored : 81.91 % 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: 0.44 (0.19), residues: 1914 helix: 1.46 (0.18), residues: 800 sheet: 0.05 (0.26), residues: 380 loop : -0.83 (0.24), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP E 211 HIS 0.009 0.002 HIS C 247 PHE 0.027 0.003 PHE D 33 TYR 0.021 0.002 TYR F 303 ARG 0.006 0.001 ARG R 80 Details of bonding type rmsd hydrogen bonds : bond 0.05972 ( 774) hydrogen bonds : angle 5.05892 ( 2244) SS BOND : bond 0.00597 ( 10) SS BOND : angle 3.54396 ( 20) covalent geometry : bond 0.00861 (15334) covalent geometry : angle 0.73209 (20783) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 158 time to evaluate : 1.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 LYS cc_start: 0.8255 (mmtm) cc_final: 0.7984 (mmtt) REVERT: A 297 TYR cc_start: 0.6844 (t80) cc_final: 0.6502 (t80) REVERT: A 341 ASP cc_start: 0.8807 (OUTLIER) cc_final: 0.8571 (m-30) REVERT: E 124 TYR cc_start: 0.7577 (m-10) cc_final: 0.7314 (m-10) REVERT: E 235 PHE cc_start: 0.5817 (t80) cc_final: 0.4633 (t80) REVERT: E 256 ARG cc_start: 0.6407 (mtm180) cc_final: 0.6103 (mmm-85) REVERT: E 339 TRP cc_start: 0.6525 (OUTLIER) cc_final: 0.4620 (m100) REVERT: G 36 ASP cc_start: 0.8892 (t0) cc_final: 0.8469 (t0) REVERT: F 211 LYS cc_start: 0.8310 (mmtm) cc_final: 0.8069 (mmtt) REVERT: F 297 TYR cc_start: 0.6970 (t80) cc_final: 0.6564 (t80) REVERT: H 124 TYR cc_start: 0.7463 (m-10) cc_final: 0.7239 (m-10) REVERT: H 235 PHE cc_start: 0.5766 (t80) cc_final: 0.4564 (t80) REVERT: H 256 ARG cc_start: 0.6340 (mtm180) cc_final: 0.6028 (mmm-85) REVERT: H 339 TRP cc_start: 0.6456 (OUTLIER) cc_final: 0.4568 (m100) REVERT: I 36 ASP cc_start: 0.8887 (t0) cc_final: 0.8486 (t0) outliers start: 45 outliers final: 23 residues processed: 192 average time/residue: 0.2730 time to fit residues: 77.7862 Evaluate side-chains 166 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 140 time to evaluate : 1.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 50 ASN Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 304 ILE Chi-restraints excluded: chain R residue 316 PHE Chi-restraints excluded: chain R residue 325 LEU Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 50 ASN Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 304 ILE Chi-restraints excluded: chain C residue 316 PHE Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 103 CYS Chi-restraints excluded: chain E residue 220 GLN Chi-restraints excluded: chain E residue 234 PHE Chi-restraints excluded: chain E residue 339 TRP Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain F residue 49 ILE Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 103 CYS Chi-restraints excluded: chain H residue 234 PHE Chi-restraints excluded: chain H residue 339 TRP Chi-restraints excluded: chain I residue 31 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 135 optimal weight: 6.9990 chunk 33 optimal weight: 0.7980 chunk 95 optimal weight: 10.0000 chunk 92 optimal weight: 0.6980 chunk 167 optimal weight: 0.8980 chunk 26 optimal weight: 0.6980 chunk 189 optimal weight: 0.4980 chunk 173 optimal weight: 0.8980 chunk 50 optimal weight: 0.0470 chunk 105 optimal weight: 0.9980 chunk 61 optimal weight: 0.4980 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 ASN E 91 HIS F 43 ASN H 6 GLN H 91 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.133736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 91)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.093118 restraints weight = 38622.641| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 3.78 r_work: 0.3231 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.5424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15344 Z= 0.123 Angle : 0.572 8.002 20803 Z= 0.307 Chirality : 0.042 0.157 2440 Planarity : 0.004 0.062 2621 Dihedral : 4.445 40.453 2078 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.83 % Allowed : 16.75 % Favored : 81.42 % 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: 0.92 (0.20), residues: 1914 helix: 1.95 (0.18), residues: 802 sheet: 0.44 (0.27), residues: 374 loop : -0.80 (0.24), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 211 HIS 0.004 0.001 HIS H 183 PHE 0.018 0.001 PHE B 62 TYR 0.026 0.001 TYR A 303 ARG 0.004 0.000 ARG H 219 Details of bonding type rmsd hydrogen bonds : bond 0.04371 ( 774) hydrogen bonds : angle 4.54365 ( 2244) SS BOND : bond 0.00502 ( 10) SS BOND : angle 2.57135 ( 20) covalent geometry : bond 0.00276 (15334) covalent geometry : angle 0.56651 (20783) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 173 time to evaluate : 1.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 297 TYR cc_start: 0.6643 (t80) cc_final: 0.6437 (t80) REVERT: E 124 TYR cc_start: 0.7526 (m-10) cc_final: 0.7264 (m-10) REVERT: E 217 MET cc_start: 0.5919 (pmm) cc_final: 0.5470 (mpp) REVERT: E 235 PHE cc_start: 0.5924 (t80) cc_final: 0.4532 (t80) REVERT: E 256 ARG cc_start: 0.6337 (mtm180) cc_final: 0.6108 (mmm-85) REVERT: E 339 TRP cc_start: 0.6798 (OUTLIER) cc_final: 0.4592 (m100) REVERT: G 36 ASP cc_start: 0.8934 (t0) cc_final: 0.8531 (t0) REVERT: F 211 LYS cc_start: 0.8236 (mmtm) cc_final: 0.7955 (mmtt) REVERT: F 297 TYR cc_start: 0.6662 (t80) cc_final: 0.6391 (t80) REVERT: F 341 ASP cc_start: 0.8750 (OUTLIER) cc_final: 0.8538 (m-30) REVERT: H 124 TYR cc_start: 0.7618 (m-10) cc_final: 0.7347 (m-10) REVERT: H 235 PHE cc_start: 0.5942 (t80) cc_final: 0.4630 (t80) REVERT: H 256 ARG cc_start: 0.6285 (mtm180) cc_final: 0.6020 (mmm-85) REVERT: H 339 TRP cc_start: 0.6708 (OUTLIER) cc_final: 0.4696 (m100) REVERT: I 36 ASP cc_start: 0.8933 (t0) cc_final: 0.8536 (t0) outliers start: 30 outliers final: 17 residues processed: 196 average time/residue: 0.2662 time to fit residues: 77.3389 Evaluate side-chains 171 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 151 time to evaluate : 1.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 304 ILE Chi-restraints excluded: chain R residue 316 PHE Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 304 ILE Chi-restraints excluded: chain C residue 316 PHE Chi-restraints excluded: chain C residue 323 HIS Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain E residue 7 LEU Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 103 CYS Chi-restraints excluded: chain E residue 339 TRP Chi-restraints excluded: chain F residue 49 ILE Chi-restraints excluded: chain F residue 341 ASP Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 103 CYS Chi-restraints excluded: chain H residue 339 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 58 optimal weight: 0.7980 chunk 128 optimal weight: 3.9990 chunk 171 optimal weight: 0.8980 chunk 123 optimal weight: 20.0000 chunk 68 optimal weight: 0.7980 chunk 163 optimal weight: 0.6980 chunk 183 optimal weight: 6.9990 chunk 6 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 134 optimal weight: 3.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 91 HIS F 316 ASN H 91 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.132703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.092209 restraints weight = 38414.408| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 3.54 r_work: 0.3219 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.5568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15344 Z= 0.166 Angle : 0.601 8.807 20803 Z= 0.322 Chirality : 0.043 0.158 2440 Planarity : 0.004 0.064 2621 Dihedral : 4.435 45.916 2078 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.08 % Allowed : 17.18 % Favored : 80.75 % 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: 1.00 (0.20), residues: 1914 helix: 1.99 (0.19), residues: 808 sheet: 0.31 (0.26), residues: 406 loop : -0.67 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP H 211 HIS 0.004 0.001 HIS R 247 PHE 0.019 0.002 PHE D 62 TYR 0.020 0.001 TYR A 303 ARG 0.003 0.000 ARG H 219 Details of bonding type rmsd hydrogen bonds : bond 0.04561 ( 774) hydrogen bonds : angle 4.60997 ( 2244) SS BOND : bond 0.00516 ( 10) SS BOND : angle 2.78920 ( 20) covalent geometry : bond 0.00393 (15334) covalent geometry : angle 0.59463 (20783) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 148 time to evaluate : 1.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 217 MET cc_start: 0.6009 (pmm) cc_final: 0.5491 (mpp) REVERT: E 235 PHE cc_start: 0.5955 (t80) cc_final: 0.4845 (t80) REVERT: E 256 ARG cc_start: 0.6341 (mtm180) cc_final: 0.6077 (mmm-85) REVERT: E 339 TRP cc_start: 0.6821 (OUTLIER) cc_final: 0.4636 (m100) REVERT: G 36 ASP cc_start: 0.8905 (t0) cc_final: 0.8495 (t0) REVERT: F 211 LYS cc_start: 0.8231 (mmtm) cc_final: 0.7996 (mmtt) REVERT: F 341 ASP cc_start: 0.8773 (OUTLIER) cc_final: 0.8552 (m-30) REVERT: H 124 TYR cc_start: 0.7530 (m-10) cc_final: 0.7266 (m-10) REVERT: H 235 PHE cc_start: 0.5958 (t80) cc_final: 0.4688 (t80) REVERT: H 256 ARG cc_start: 0.6338 (mtm180) cc_final: 0.6029 (mmm-85) REVERT: H 339 TRP cc_start: 0.6831 (OUTLIER) cc_final: 0.4661 (m100) REVERT: I 36 ASP cc_start: 0.8902 (t0) cc_final: 0.8501 (t0) outliers start: 34 outliers final: 24 residues processed: 174 average time/residue: 0.2772 time to fit residues: 71.1222 Evaluate side-chains 171 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 144 time to evaluate : 1.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 50 ASN Chi-restraints excluded: chain R residue 60 LEU Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 304 ILE Chi-restraints excluded: chain R residue 316 PHE Chi-restraints excluded: chain R residue 325 LEU Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 50 ASN Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 304 ILE Chi-restraints excluded: chain C residue 316 PHE Chi-restraints excluded: chain C residue 323 HIS Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain E residue 7 LEU Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 103 CYS Chi-restraints excluded: chain E residue 137 ARG Chi-restraints excluded: chain E residue 262 MET Chi-restraints excluded: chain E residue 339 TRP Chi-restraints excluded: chain F residue 49 ILE Chi-restraints excluded: chain F residue 341 ASP Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 103 CYS Chi-restraints excluded: chain H residue 339 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 52 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 chunk 187 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 0 optimal weight: 0.9990 chunk 100 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 102 optimal weight: 7.9990 chunk 85 optimal weight: 0.5980 chunk 104 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 6 GLN E 91 HIS ** F 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 91 HIS I 18 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.133036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.092283 restraints weight = 38721.381| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 3.40 r_work: 0.3236 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.5664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15344 Z= 0.145 Angle : 0.601 9.857 20803 Z= 0.324 Chirality : 0.043 0.211 2440 Planarity : 0.004 0.115 2621 Dihedral : 4.413 48.727 2078 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.96 % Allowed : 17.60 % Favored : 80.44 % 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: 1.02 (0.20), residues: 1914 helix: 2.02 (0.18), residues: 806 sheet: 0.40 (0.27), residues: 370 loop : -0.68 (0.23), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP H 211 HIS 0.003 0.001 HIS R 247 PHE 0.018 0.001 PHE E 235 TYR 0.016 0.001 TYR A 303 ARG 0.007 0.000 ARG F 313 Details of bonding type rmsd hydrogen bonds : bond 0.04383 ( 774) hydrogen bonds : angle 4.55345 ( 2244) SS BOND : bond 0.00510 ( 10) SS BOND : angle 2.65713 ( 20) covalent geometry : bond 0.00339 (15334) covalent geometry : angle 0.59609 (20783) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 152 time to evaluate : 1.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 211 TRP cc_start: 0.6234 (m100) cc_final: 0.4766 (m100) REVERT: E 217 MET cc_start: 0.6023 (pmm) cc_final: 0.5471 (mpp) REVERT: E 235 PHE cc_start: 0.6035 (t80) cc_final: 0.4929 (t80) REVERT: E 256 ARG cc_start: 0.6342 (mtm180) cc_final: 0.6064 (mmm-85) REVERT: E 339 TRP cc_start: 0.6910 (OUTLIER) cc_final: 0.4611 (m100) REVERT: G 36 ASP cc_start: 0.8860 (t0) cc_final: 0.8460 (t0) REVERT: F 211 LYS cc_start: 0.8215 (mmtm) cc_final: 0.7965 (mmtt) REVERT: F 297 TYR cc_start: 0.6645 (t80) cc_final: 0.6443 (t80) REVERT: F 341 ASP cc_start: 0.8728 (OUTLIER) cc_final: 0.8514 (m-30) REVERT: H 217 MET cc_start: 0.5689 (pmm) cc_final: 0.5342 (mpp) REVERT: H 235 PHE cc_start: 0.6016 (t80) cc_final: 0.4894 (t80) REVERT: H 256 ARG cc_start: 0.6332 (mtm180) cc_final: 0.6007 (mmm-85) REVERT: H 339 TRP cc_start: 0.6900 (OUTLIER) cc_final: 0.4639 (m100) REVERT: I 27 ARG cc_start: 0.6391 (mtp180) cc_final: 0.6034 (mtp180) REVERT: I 36 ASP cc_start: 0.8873 (t0) cc_final: 0.8481 (t0) outliers start: 32 outliers final: 26 residues processed: 174 average time/residue: 0.2857 time to fit residues: 73.3535 Evaluate side-chains 175 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 146 time to evaluate : 1.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 50 ASN Chi-restraints excluded: chain R residue 60 LEU Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 304 ILE Chi-restraints excluded: chain R residue 316 PHE Chi-restraints excluded: chain R residue 325 LEU Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 50 ASN Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 304 ILE Chi-restraints excluded: chain C residue 316 PHE Chi-restraints excluded: chain C residue 323 HIS Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 103 CYS Chi-restraints excluded: chain E residue 137 ARG Chi-restraints excluded: chain E residue 234 PHE Chi-restraints excluded: chain E residue 262 MET Chi-restraints excluded: chain E residue 339 TRP Chi-restraints excluded: chain F residue 49 ILE Chi-restraints excluded: chain F residue 341 ASP Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 103 CYS Chi-restraints excluded: chain H residue 234 PHE Chi-restraints excluded: chain H residue 262 MET Chi-restraints excluded: chain H residue 339 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 142 optimal weight: 0.3980 chunk 117 optimal weight: 10.0000 chunk 45 optimal weight: 3.9990 chunk 46 optimal weight: 0.0070 chunk 150 optimal weight: 0.9980 chunk 103 optimal weight: 7.9990 chunk 186 optimal weight: 3.9990 chunk 170 optimal weight: 6.9990 chunk 54 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 137 optimal weight: 0.8980 overall best weight: 0.6600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 91 HIS H 91 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.133557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 92)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.093178 restraints weight = 38797.555| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 3.55 r_work: 0.3244 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.5751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15344 Z= 0.131 Angle : 0.580 10.608 20803 Z= 0.312 Chirality : 0.042 0.196 2440 Planarity : 0.004 0.066 2621 Dihedral : 4.358 51.728 2078 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.83 % Allowed : 17.42 % Favored : 80.75 % 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: 1.10 (0.20), residues: 1914 helix: 2.09 (0.18), residues: 806 sheet: 0.47 (0.27), residues: 368 loop : -0.65 (0.23), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP E 211 HIS 0.004 0.001 HIS H 183 PHE 0.019 0.001 PHE E 235 TYR 0.014 0.001 TYR F 303 ARG 0.003 0.000 ARG F 313 Details of bonding type rmsd hydrogen bonds : bond 0.04230 ( 774) hydrogen bonds : angle 4.48823 ( 2244) SS BOND : bond 0.00528 ( 10) SS BOND : angle 2.56457 ( 20) covalent geometry : bond 0.00305 (15334) covalent geometry : angle 0.57506 (20783) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 161 time to evaluate : 1.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 211 TRP cc_start: 0.6076 (m100) cc_final: 0.4551 (m100) REVERT: E 217 MET cc_start: 0.6049 (pmm) cc_final: 0.5445 (mpp) REVERT: E 235 PHE cc_start: 0.6149 (t80) cc_final: 0.5030 (t80) REVERT: E 256 ARG cc_start: 0.6318 (mtm180) cc_final: 0.6037 (mmm-85) REVERT: E 339 TRP cc_start: 0.6905 (OUTLIER) cc_final: 0.4620 (m100) REVERT: G 36 ASP cc_start: 0.8842 (t0) cc_final: 0.8490 (t0) REVERT: F 211 LYS cc_start: 0.8243 (mmtm) cc_final: 0.7991 (mmtt) REVERT: F 257 ASN cc_start: 0.7966 (t0) cc_final: 0.7686 (t0) REVERT: F 297 TYR cc_start: 0.6806 (t80) cc_final: 0.5913 (t80) REVERT: F 298 GLU cc_start: 0.6577 (mp0) cc_final: 0.6354 (pm20) REVERT: H 211 TRP cc_start: 0.6087 (m100) cc_final: 0.4581 (m100) REVERT: H 235 PHE cc_start: 0.6187 (t80) cc_final: 0.5115 (t80) REVERT: H 256 ARG cc_start: 0.6306 (mtm180) cc_final: 0.5965 (mmm-85) REVERT: H 339 TRP cc_start: 0.6907 (OUTLIER) cc_final: 0.4648 (m100) REVERT: I 36 ASP cc_start: 0.8843 (t0) cc_final: 0.8493 (t0) outliers start: 30 outliers final: 23 residues processed: 182 average time/residue: 0.2551 time to fit residues: 68.9955 Evaluate side-chains 173 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 148 time to evaluate : 1.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 304 ILE Chi-restraints excluded: chain R residue 316 PHE Chi-restraints excluded: chain R residue 325 LEU Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 304 ILE Chi-restraints excluded: chain C residue 316 PHE Chi-restraints excluded: chain C residue 323 HIS Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain E residue 103 CYS Chi-restraints excluded: chain E residue 137 ARG Chi-restraints excluded: chain E residue 262 MET Chi-restraints excluded: chain E residue 339 TRP Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain F residue 49 ILE Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 103 CYS Chi-restraints excluded: chain H residue 137 ARG Chi-restraints excluded: chain H residue 262 MET Chi-restraints excluded: chain H residue 339 TRP Chi-restraints excluded: chain I residue 31 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 149 optimal weight: 4.9990 chunk 128 optimal weight: 5.9990 chunk 98 optimal weight: 10.0000 chunk 52 optimal weight: 0.9980 chunk 110 optimal weight: 2.9990 chunk 150 optimal weight: 0.9980 chunk 131 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 158 optimal weight: 9.9990 chunk 163 optimal weight: 7.9990 chunk 146 optimal weight: 0.4980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 245 GLN E 91 HIS F 43 ASN F 305 GLN H 91 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.132619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 103)---------------| | r_work = 0.3602 r_free = 0.3602 target = 0.092698 restraints weight = 38666.523| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 2.96 r_work: 0.3234 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.5892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15344 Z= 0.170 Angle : 0.620 12.628 20803 Z= 0.331 Chirality : 0.044 0.216 2440 Planarity : 0.004 0.091 2621 Dihedral : 4.494 60.901 2078 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.71 % Allowed : 17.97 % Favored : 80.32 % 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: 1.01 (0.20), residues: 1914 helix: 1.97 (0.18), residues: 806 sheet: 0.44 (0.27), residues: 370 loop : -0.65 (0.23), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP H 211 HIS 0.005 0.001 HIS R 247 PHE 0.020 0.002 PHE D 62 TYR 0.017 0.001 TYR A 303 ARG 0.003 0.000 ARG F 313 Details of bonding type rmsd hydrogen bonds : bond 0.04560 ( 774) hydrogen bonds : angle 4.60422 ( 2244) SS BOND : bond 0.00508 ( 10) SS BOND : angle 2.71000 ( 20) covalent geometry : bond 0.00404 (15334) covalent geometry : angle 0.61504 (20783) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12046.20 seconds wall clock time: 207 minutes 58.37 seconds (12478.37 seconds total)