Starting phenix.real_space_refine on Thu Sep 18 07:34:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xx7_38748/09_2025/8xx7_38748.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xx7_38748/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/8xx7_38748/09_2025/8xx7_38748.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xx7_38748/09_2025/8xx7_38748.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xx7_38748/09_2025/8xx7_38748.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xx7_38748/09_2025/8xx7_38748.map" } resolution = 3.32 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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, 'TYR:plan': 1, 'ARG:plan': 2, 'GLN:plan1': 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, 'TYR:plan': 1, 'ARG:plan': 2} 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: 3.96, per 1000 atoms: 0.26 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: 1.21 Conformation dependent library (CDL) restraints added in 790.7 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.64 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: 2.76 Time building geometry restraints manager: 1.65 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: 9.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.330 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.780 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.040 ------------------------------------------------------------------------------- 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 : 7.05 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.004 0.000 ARG C 248 TYR 0.006 0.001 TYR R 86 PHE 0.014 0.001 PHE E 234 TRP 0.015 0.001 TRP H 211 HIS 0.003 0.001 HIS R 242 Details of bonding type rmsd covalent geometry : bond 0.00355 (15334) covalent geometry : angle 0.47613 (20783) SS BOND : bond 0.00287 ( 10) SS BOND : angle 1.79551 ( 20) hydrogen bonds : bond 0.19766 ( 774) hydrogen bonds : angle 6.21401 ( 2244) *********************** 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 : 0.640 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: 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: 0.8101 (m-30) REVERT: R 160 TYR cc_start: 0.7301 (m-80) cc_final: 0.7057 (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: 0.8560 (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: 0.8117 (m-30) REVERT: C 160 TYR cc_start: 0.7297 (m-80) cc_final: 0.7058 (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: 0.8556 (mp) outliers start: 0 outliers final: 0 residues processed: 419 average time/residue: 0.1628 time to fit residues: 93.7778 Evaluate side-chains 198 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 198 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 98 optimal weight: 8.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 2.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- 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 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 346 ASN E 9 GLN E 91 HIS E 176 GLN E 183 HIS E 266 HIS ** F 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 305 GLN F 346 ASN H 91 HIS H 176 GLN H 183 HIS H 266 HIS I 18 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.131918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.087544 restraints weight = 38859.021| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 3.61 r_work: 0.3123 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.4268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.072 15344 Z= 0.398 Angle : 0.840 8.012 20803 Z= 0.446 Chirality : 0.053 0.230 2440 Planarity : 0.006 0.076 2621 Dihedral : 4.728 27.650 2078 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.42 % Allowed : 11.86 % Favored : 84.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.05 (0.19), residues: 1914 helix: 1.15 (0.18), residues: 810 sheet: -0.25 (0.24), residues: 418 loop : -1.06 (0.23), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 197 TYR 0.021 0.003 TYR F 231 PHE 0.033 0.003 PHE B 62 TRP 0.018 0.003 TRP C 112 HIS 0.011 0.002 HIS R 247 Details of bonding type rmsd covalent geometry : bond 0.00931 (15334) covalent geometry : angle 0.83522 (20783) SS BOND : bond 0.01717 ( 10) SS BOND : angle 2.97888 ( 20) hydrogen bonds : bond 0.06533 ( 774) hydrogen bonds : angle 5.44954 ( 2244) *********************** 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 246 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 190 time to evaluate : 0.578 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: D 17 GLN cc_start: 0.8309 (tt0) cc_final: 0.7959 (tt0) REVERT: R 84 ASP cc_start: 0.9051 (m-30) cc_final: 0.8836 (m-30) REVERT: R 143 ASP cc_start: 0.9178 (t70) cc_final: 0.8970 (t0) REVERT: R 212 ARG cc_start: 0.9312 (OUTLIER) cc_final: 0.8179 (mtm180) REVERT: B 17 GLN cc_start: 0.8305 (tt0) cc_final: 0.7959 (tt0) REVERT: C 84 ASP cc_start: 0.9051 (m-30) cc_final: 0.8830 (m-30) REVERT: C 143 ASP cc_start: 0.9167 (t70) cc_final: 0.8966 (t0) REVERT: C 212 ARG cc_start: 0.9310 (OUTLIER) cc_final: 0.8178 (mtm180) REVERT: A 303 TYR cc_start: 0.8962 (t80) cc_final: 0.8691 (t80) REVERT: E 89 LYS cc_start: 0.8555 (mttp) cc_final: 0.8338 (mttp) REVERT: E 101 MET cc_start: 0.8844 (tpp) cc_final: 0.8613 (tpp) REVERT: E 124 TYR cc_start: 0.7849 (m-80) cc_final: 0.7240 (m-80) REVERT: E 339 TRP cc_start: 0.6273 (OUTLIER) cc_final: 0.4586 (m100) REVERT: F 303 TYR cc_start: 0.8950 (t80) cc_final: 0.8712 (t80) REVERT: H 89 LYS cc_start: 0.8528 (mttp) cc_final: 0.8312 (mttp) REVERT: H 124 TYR cc_start: 0.7862 (m-80) cc_final: 0.7249 (m-80) REVERT: H 339 TRP cc_start: 0.6182 (OUTLIER) cc_final: 0.4539 (m100) outliers start: 56 outliers final: 28 residues processed: 231 average time/residue: 0.1424 time to fit residues: 47.0267 Evaluate side-chains 192 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 160 time to evaluate : 0.619 ------------------------------------------------------------------------------- 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 191 ASN Chi-restraints excluded: chain R residue 212 ARG 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 B residue 65 LYS Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 191 ASN Chi-restraints excluded: chain C residue 212 ARG 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 A residue 245 HIS Chi-restraints excluded: chain A residue 313 ARG 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 246 ASP Chi-restraints excluded: chain E residue 339 TRP Chi-restraints excluded: chain F residue 49 ILE Chi-restraints excluded: chain F residue 245 HIS Chi-restraints excluded: chain F residue 313 ARG 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 246 ASP 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 5 optimal weight: 0.9980 chunk 96 optimal weight: 5.9990 chunk 127 optimal weight: 7.9990 chunk 185 optimal weight: 5.9990 chunk 106 optimal weight: 10.0000 chunk 141 optimal weight: 0.7980 chunk 81 optimal weight: 0.9990 chunk 149 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 51 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 GLN ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 305 GLN ** F 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 44 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 = 0.4240 r_free = 0.4240 target = 0.134058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.090405 restraints weight = 39112.567| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 3.51 r_work: 0.3186 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.4425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 15344 Z= 0.164 Angle : 0.600 8.620 20803 Z= 0.325 Chirality : 0.044 0.180 2440 Planarity : 0.004 0.046 2621 Dihedral : 4.514 31.704 2078 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.26 % Allowed : 13.39 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.69 (0.19), residues: 1914 helix: 1.79 (0.18), residues: 806 sheet: -0.05 (0.25), residues: 402 loop : -0.75 (0.23), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 209 TYR 0.009 0.001 TYR A 231 PHE 0.021 0.001 PHE E 235 TRP 0.013 0.001 TRP H 339 HIS 0.005 0.001 HIS G 44 Details of bonding type rmsd covalent geometry : bond 0.00384 (15334) covalent geometry : angle 0.59061 (20783) SS BOND : bond 0.00688 ( 10) SS BOND : angle 3.44937 ( 20) hydrogen bonds : bond 0.04953 ( 774) hydrogen bonds : angle 4.86585 ( 2244) *********************** 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 219 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 182 time to evaluate : 0.634 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: D 17 GLN cc_start: 0.8252 (tt0) cc_final: 0.7906 (tt0) REVERT: R 84 ASP cc_start: 0.9009 (m-30) cc_final: 0.8800 (m-30) REVERT: B 17 GLN cc_start: 0.8271 (tt0) cc_final: 0.7942 (tt0) REVERT: C 84 ASP cc_start: 0.8999 (m-30) cc_final: 0.8779 (m-30) REVERT: C 212 ARG cc_start: 0.9153 (OUTLIER) cc_final: 0.8904 (ttp-170) REVERT: A 211 LYS cc_start: 0.8187 (mmtm) cc_final: 0.7881 (mmtt) REVERT: A 297 TYR cc_start: 0.6815 (t80) cc_final: 0.6463 (t80) REVERT: E 235 PHE cc_start: 0.5399 (t80) cc_final: 0.4600 (t80) REVERT: E 256 ARG cc_start: 0.6249 (mtm180) cc_final: 0.5881 (mmm-85) REVERT: G 36 ASP cc_start: 0.8977 (t0) cc_final: 0.8451 (t0) REVERT: F 297 TYR cc_start: 0.6631 (t80) cc_final: 0.6276 (t80) REVERT: H 124 TYR cc_start: 0.7809 (m-80) cc_final: 0.7145 (m-80) REVERT: H 235 PHE cc_start: 0.5400 (t80) cc_final: 0.4591 (t80) REVERT: H 256 ARG cc_start: 0.6257 (mtm180) cc_final: 0.5877 (mmm-85) REVERT: H 339 TRP cc_start: 0.6396 (OUTLIER) cc_final: 0.4689 (m100) REVERT: I 36 ASP cc_start: 0.8977 (t0) cc_final: 0.8464 (t0) outliers start: 37 outliers final: 20 residues processed: 205 average time/residue: 0.1425 time to fit residues: 41.7920 Evaluate side-chains 181 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 159 time to evaluate : 0.580 ------------------------------------------------------------------------------- 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 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 212 ARG 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 A residue 313 ARG 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 F residue 49 ILE Chi-restraints excluded: chain F residue 313 ARG 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 25 optimal weight: 0.0980 chunk 134 optimal weight: 1.9990 chunk 97 optimal weight: 0.7980 chunk 139 optimal weight: 1.9990 chunk 82 optimal weight: 0.7980 chunk 135 optimal weight: 6.9990 chunk 85 optimal weight: 8.9990 chunk 146 optimal weight: 3.9990 chunk 118 optimal weight: 10.0000 chunk 172 optimal weight: 0.9980 chunk 86 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 HIS ** E 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.134014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.091473 restraints weight = 38473.937| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 3.17 r_work: 0.3245 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.4660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 15344 Z= 0.157 Angle : 0.558 7.680 20803 Z= 0.302 Chirality : 0.043 0.159 2440 Planarity : 0.004 0.057 2621 Dihedral : 4.395 32.256 2078 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.51 % Allowed : 14.55 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.96 (0.20), residues: 1914 helix: 2.02 (0.19), residues: 806 sheet: 0.22 (0.26), residues: 388 loop : -0.69 (0.24), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 212 TYR 0.023 0.001 TYR A 303 PHE 0.020 0.001 PHE B 62 TRP 0.013 0.001 TRP H 339 HIS 0.004 0.001 HIS G 44 Details of bonding type rmsd covalent geometry : bond 0.00369 (15334) covalent geometry : angle 0.55033 (20783) SS BOND : bond 0.00536 ( 10) SS BOND : angle 2.99103 ( 20) hydrogen bonds : bond 0.04617 ( 774) hydrogen bonds : angle 4.64504 ( 2244) *********************** 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 220 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 179 time to evaluate : 0.626 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: D 17 GLN cc_start: 0.8079 (tt0) cc_final: 0.7763 (tt0) REVERT: R 84 ASP cc_start: 0.8823 (m-30) cc_final: 0.8623 (m-30) REVERT: B 17 GLN cc_start: 0.8085 (tt0) cc_final: 0.7775 (tt0) REVERT: C 84 ASP cc_start: 0.8821 (m-30) cc_final: 0.8616 (m-30) REVERT: A 303 TYR cc_start: 0.8893 (t80) cc_final: 0.8589 (t80) REVERT: E 217 MET cc_start: 0.6094 (pmm) cc_final: 0.5754 (mpp) REVERT: E 235 PHE cc_start: 0.5602 (t80) cc_final: 0.4673 (t80) REVERT: E 256 ARG cc_start: 0.6276 (mtm180) cc_final: 0.5876 (mmm-85) REVERT: E 280 LYS cc_start: 0.7404 (mmmt) cc_final: 0.7071 (mmmt) REVERT: E 339 TRP cc_start: 0.6394 (OUTLIER) cc_final: 0.4585 (m100) REVERT: G 36 ASP cc_start: 0.8940 (t0) cc_final: 0.8442 (t0) REVERT: F 211 LYS cc_start: 0.8210 (mmtm) cc_final: 0.7946 (mmtt) REVERT: H 217 MET cc_start: 0.6060 (pmm) cc_final: 0.5558 (mpp) REVERT: H 235 PHE cc_start: 0.5609 (t80) cc_final: 0.4672 (t80) REVERT: H 256 ARG cc_start: 0.6234 (mtm180) cc_final: 0.5815 (mmm-85) REVERT: H 280 LYS cc_start: 0.7416 (mmmt) cc_final: 0.7006 (mmmt) REVERT: I 36 ASP cc_start: 0.8941 (t0) cc_final: 0.8449 (t0) REVERT: I 44 HIS cc_start: 0.6064 (t-170) cc_final: 0.5786 (t70) outliers start: 41 outliers final: 22 residues processed: 207 average time/residue: 0.1337 time to fit residues: 40.7026 Evaluate side-chains 185 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 162 time to evaluate : 0.633 ------------------------------------------------------------------------------- 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 203 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 203 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 E residue 339 TRP Chi-restraints excluded: chain F residue 49 ILE Chi-restraints excluded: chain F residue 313 ARG 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 34 optimal weight: 0.0870 chunk 79 optimal weight: 4.9990 chunk 154 optimal weight: 9.9990 chunk 6 optimal weight: 0.8980 chunk 124 optimal weight: 6.9990 chunk 133 optimal weight: 9.9990 chunk 167 optimal weight: 7.9990 chunk 38 optimal weight: 0.9990 chunk 78 optimal weight: 0.7980 chunk 168 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 overall best weight: 0.7160 ------------------------------------------------------------------------------- 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** G 44 HIS ** H 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.134232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.092579 restraints weight = 38382.842| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 3.20 r_work: 0.3254 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3136 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.4866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15344 Z= 0.136 Angle : 0.533 6.436 20803 Z= 0.290 Chirality : 0.042 0.163 2440 Planarity : 0.004 0.058 2621 Dihedral : 4.266 31.599 2078 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.08 % Allowed : 15.10 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.09 (0.20), residues: 1914 helix: 2.13 (0.19), residues: 808 sheet: 0.33 (0.26), residues: 382 loop : -0.66 (0.24), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 212 TYR 0.020 0.001 TYR F 303 PHE 0.019 0.001 PHE B 62 TRP 0.030 0.002 TRP E 211 HIS 0.004 0.001 HIS G 44 Details of bonding type rmsd covalent geometry : bond 0.00313 (15334) covalent geometry : angle 0.52709 (20783) SS BOND : bond 0.00512 ( 10) SS BOND : angle 2.52491 ( 20) hydrogen bonds : bond 0.04347 ( 774) hydrogen bonds : angle 4.53106 ( 2244) *********************** 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 207 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 173 time to evaluate : 0.675 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: D 17 GLN cc_start: 0.8134 (tt0) cc_final: 0.7824 (tt0) REVERT: B 17 GLN cc_start: 0.8107 (tt0) cc_final: 0.7816 (tt0) REVERT: A 211 LYS cc_start: 0.8125 (mmtm) cc_final: 0.7831 (mmtt) REVERT: A 303 TYR cc_start: 0.8820 (t80) cc_final: 0.8583 (t80) REVERT: A 307 GLN cc_start: 0.8798 (mm-40) cc_final: 0.8587 (mm-40) REVERT: E 211 TRP cc_start: 0.6263 (m100) cc_final: 0.5357 (m100) REVERT: E 235 PHE cc_start: 0.5915 (t80) cc_final: 0.4724 (t80) REVERT: E 256 ARG cc_start: 0.6290 (mtm180) cc_final: 0.5885 (mmm-85) REVERT: E 339 TRP cc_start: 0.6419 (OUTLIER) cc_final: 0.4591 (m100) REVERT: G 36 ASP cc_start: 0.8998 (t0) cc_final: 0.8573 (t0) REVERT: F 354 TYR cc_start: 0.7613 (t80) cc_final: 0.7318 (t80) REVERT: H 211 TRP cc_start: 0.6150 (m100) cc_final: 0.5371 (m100) REVERT: H 235 PHE cc_start: 0.5732 (t80) cc_final: 0.4570 (t80) REVERT: H 256 ARG cc_start: 0.6290 (mtm180) cc_final: 0.5905 (mmm-85) REVERT: H 339 TRP cc_start: 0.6392 (OUTLIER) cc_final: 0.4614 (m100) REVERT: I 36 ASP cc_start: 0.8993 (t0) cc_final: 0.8547 (t0) outliers start: 34 outliers final: 22 residues processed: 196 average time/residue: 0.1296 time to fit residues: 37.1159 Evaluate side-chains 182 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 158 time to evaluate : 0.591 ------------------------------------------------------------------------------- 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 203 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 203 ASN 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 52 optimal weight: 0.9990 chunk 164 optimal weight: 0.0570 chunk 166 optimal weight: 6.9990 chunk 159 optimal weight: 7.9990 chunk 72 optimal weight: 6.9990 chunk 18 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 chunk 45 optimal weight: 4.9990 chunk 17 optimal weight: 0.3980 chunk 73 optimal weight: 1.9990 chunk 128 optimal weight: 4.9990 overall best weight: 0.8102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.134009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.091705 restraints weight = 38303.862| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 3.21 r_work: 0.3251 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.5069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15344 Z= 0.141 Angle : 0.538 5.954 20803 Z= 0.292 Chirality : 0.042 0.157 2440 Planarity : 0.004 0.060 2621 Dihedral : 4.123 30.932 2078 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.14 % Allowed : 15.04 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.08 (0.20), residues: 1914 helix: 2.11 (0.19), residues: 810 sheet: 0.31 (0.27), residues: 358 loop : -0.62 (0.23), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 80 TYR 0.021 0.001 TYR A 297 PHE 0.020 0.001 PHE H 235 TRP 0.019 0.002 TRP H 211 HIS 0.003 0.001 HIS R 247 Details of bonding type rmsd covalent geometry : bond 0.00326 (15334) covalent geometry : angle 0.53383 (20783) SS BOND : bond 0.00519 ( 10) SS BOND : angle 2.09886 ( 20) hydrogen bonds : bond 0.04315 ( 774) hydrogen bonds : angle 4.44506 ( 2244) *********************** 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 205 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 170 time to evaluate : 0.595 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: B 17 GLN cc_start: 0.8154 (tt0) cc_final: 0.7776 (tt0) REVERT: A 211 LYS cc_start: 0.8148 (mmtm) cc_final: 0.7862 (mmtt) REVERT: A 303 TYR cc_start: 0.8823 (t80) cc_final: 0.8545 (t80) REVERT: A 354 TYR cc_start: 0.7562 (t80) cc_final: 0.7321 (t80) REVERT: E 211 TRP cc_start: 0.6327 (m100) cc_final: 0.5294 (m100) REVERT: E 235 PHE cc_start: 0.5992 (t80) cc_final: 0.4729 (t80) REVERT: E 256 ARG cc_start: 0.6259 (mtm180) cc_final: 0.5882 (mmm-85) REVERT: E 339 TRP cc_start: 0.6707 (OUTLIER) cc_final: 0.4611 (m100) REVERT: G 36 ASP cc_start: 0.8925 (t0) cc_final: 0.8542 (t0) REVERT: F 211 LYS cc_start: 0.8178 (mmtm) cc_final: 0.7894 (mmtt) REVERT: F 354 TYR cc_start: 0.7611 (t80) cc_final: 0.7377 (t80) REVERT: H 211 TRP cc_start: 0.6297 (m100) cc_final: 0.5255 (m100) REVERT: H 235 PHE cc_start: 0.5811 (t80) cc_final: 0.4597 (t80) REVERT: H 256 ARG cc_start: 0.6263 (mtm180) cc_final: 0.5862 (mmm-85) REVERT: H 339 TRP cc_start: 0.6524 (OUTLIER) cc_final: 0.4578 (m100) REVERT: I 27 ARG cc_start: 0.5973 (mtp180) cc_final: 0.5458 (mtt-85) REVERT: I 36 ASP cc_start: 0.8926 (t0) cc_final: 0.8548 (t0) outliers start: 35 outliers final: 23 residues processed: 196 average time/residue: 0.1277 time to fit residues: 37.0278 Evaluate side-chains 178 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 153 time to evaluate : 0.661 ------------------------------------------------------------------------------- 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 203 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 180 VAL Chi-restraints excluded: chain C residue 203 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 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 Chi-restraints excluded: chain H residue 339 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 0 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 128 optimal weight: 0.9980 chunk 169 optimal weight: 6.9990 chunk 99 optimal weight: 10.0000 chunk 187 optimal weight: 9.9990 chunk 126 optimal weight: 4.9990 chunk 142 optimal weight: 0.7980 chunk 113 optimal weight: 3.9990 chunk 137 optimal weight: 0.9980 chunk 78 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 91 HIS ** G 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 305 GLN H 91 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.133610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.091487 restraints weight = 38127.334| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 3.36 r_work: 0.3248 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.5232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15344 Z= 0.148 Angle : 0.550 7.620 20803 Z= 0.298 Chirality : 0.042 0.155 2440 Planarity : 0.004 0.060 2621 Dihedral : 4.148 30.733 2078 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.96 % Allowed : 15.65 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.05 (0.20), residues: 1914 helix: 2.05 (0.19), residues: 810 sheet: 0.29 (0.27), residues: 370 loop : -0.61 (0.24), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 212 TYR 0.019 0.001 TYR A 297 PHE 0.023 0.001 PHE E 235 TRP 0.018 0.002 TRP H 211 HIS 0.003 0.001 HIS C 247 Details of bonding type rmsd covalent geometry : bond 0.00346 (15334) covalent geometry : angle 0.54683 (20783) SS BOND : bond 0.00528 ( 10) SS BOND : angle 2.03747 ( 20) hydrogen bonds : bond 0.04365 ( 774) hydrogen bonds : angle 4.46913 ( 2244) *********************** 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 195 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 163 time to evaluate : 0.634 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: A 211 LYS cc_start: 0.8164 (mmtm) cc_final: 0.7892 (mmtt) REVERT: A 354 TYR cc_start: 0.7563 (t80) cc_final: 0.7354 (t80) REVERT: E 124 TYR cc_start: 0.7434 (m-10) cc_final: 0.7125 (m-10) REVERT: E 211 TRP cc_start: 0.6082 (m100) cc_final: 0.5105 (m100) REVERT: E 235 PHE cc_start: 0.6082 (t80) cc_final: 0.4963 (t80) REVERT: E 256 ARG cc_start: 0.6311 (mtm180) cc_final: 0.5903 (mmm-85) REVERT: E 339 TRP cc_start: 0.6683 (OUTLIER) cc_final: 0.4592 (m100) REVERT: G 36 ASP cc_start: 0.8946 (t0) cc_final: 0.8538 (t0) REVERT: F 211 LYS cc_start: 0.8190 (mmtm) cc_final: 0.7919 (mmtt) REVERT: H 217 MET cc_start: 0.5877 (pmm) cc_final: 0.5545 (mpp) REVERT: H 235 PHE cc_start: 0.6142 (t80) cc_final: 0.5038 (t80) REVERT: H 256 ARG cc_start: 0.6258 (mtm180) cc_final: 0.5799 (mmm-85) REVERT: H 339 TRP cc_start: 0.6672 (OUTLIER) cc_final: 0.4612 (m100) REVERT: I 27 ARG cc_start: 0.6136 (mtp180) cc_final: 0.5624 (mtt-85) REVERT: I 36 ASP cc_start: 0.8939 (t0) cc_final: 0.8553 (t0) outliers start: 32 outliers final: 27 residues processed: 188 average time/residue: 0.1314 time to fit residues: 36.5906 Evaluate side-chains 185 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 156 time to evaluate : 0.601 ------------------------------------------------------------------------------- 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 203 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 180 VAL Chi-restraints excluded: chain C residue 203 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 38 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 192 LEU 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 38 LEU 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 192 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 189 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 146 optimal weight: 9.9990 chunk 77 optimal weight: 3.9990 chunk 159 optimal weight: 6.9990 chunk 21 optimal weight: 0.9980 chunk 83 optimal weight: 0.9990 chunk 165 optimal weight: 10.0000 chunk 134 optimal weight: 0.8980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 ASN G 44 HIS F 256 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 = 0.4232 r_free = 0.4232 target = 0.132872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.090405 restraints weight = 38504.987| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 3.26 r_work: 0.3239 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.5455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15344 Z= 0.169 Angle : 0.563 7.597 20803 Z= 0.305 Chirality : 0.043 0.155 2440 Planarity : 0.004 0.059 2621 Dihedral : 4.192 32.590 2078 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.38 % Allowed : 15.71 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.02 (0.20), residues: 1914 helix: 2.02 (0.19), residues: 808 sheet: 0.37 (0.27), residues: 362 loop : -0.66 (0.23), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 212 TYR 0.017 0.001 TYR A 303 PHE 0.025 0.002 PHE H 235 TRP 0.026 0.002 TRP H 211 HIS 0.006 0.001 HIS R 247 Details of bonding type rmsd covalent geometry : bond 0.00399 (15334) covalent geometry : angle 0.55920 (20783) SS BOND : bond 0.00515 ( 10) SS BOND : angle 2.09566 ( 20) hydrogen bonds : bond 0.04544 ( 774) hydrogen bonds : angle 4.51269 ( 2244) *********************** 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 203 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 164 time to evaluate : 0.573 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: E 124 TYR cc_start: 0.7341 (m-10) cc_final: 0.7042 (m-10) REVERT: E 235 PHE cc_start: 0.6374 (t80) cc_final: 0.5085 (t80) REVERT: E 256 ARG cc_start: 0.6464 (mtm180) cc_final: 0.6008 (mmm-85) REVERT: E 339 TRP cc_start: 0.6765 (OUTLIER) cc_final: 0.4542 (m100) REVERT: G 27 ARG cc_start: 0.6121 (mtp180) cc_final: 0.5652 (mtp180) REVERT: G 36 ASP cc_start: 0.8926 (t0) cc_final: 0.8539 (t0) REVERT: F 211 LYS cc_start: 0.8212 (mmtm) cc_final: 0.7949 (mmtt) REVERT: F 297 TYR cc_start: 0.6225 (t80) cc_final: 0.5959 (t80) REVERT: H 211 TRP cc_start: 0.6330 (m100) cc_final: 0.4863 (m100) REVERT: H 217 MET cc_start: 0.5853 (pmm) cc_final: 0.5598 (mpp) REVERT: H 235 PHE cc_start: 0.6340 (t80) cc_final: 0.5188 (t80) REVERT: H 256 ARG cc_start: 0.6393 (mtm180) cc_final: 0.5875 (mmm-85) REVERT: H 339 TRP cc_start: 0.6735 (OUTLIER) cc_final: 0.4544 (m100) REVERT: I 27 ARG cc_start: 0.6155 (mtp180) cc_final: 0.5758 (mtp180) REVERT: I 36 ASP cc_start: 0.8926 (t0) cc_final: 0.8557 (t0) outliers start: 39 outliers final: 28 residues processed: 195 average time/residue: 0.1246 time to fit residues: 35.9855 Evaluate side-chains 183 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 153 time to evaluate : 0.644 ------------------------------------------------------------------------------- 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 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 323 HIS Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain A residue 38 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 192 LEU 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 38 LEU Chi-restraints excluded: chain F residue 49 ILE Chi-restraints excluded: chain H residue 7 LEU Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 103 CYS Chi-restraints excluded: chain H residue 192 LEU Chi-restraints excluded: chain H residue 262 MET 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 72 optimal weight: 2.9990 chunk 144 optimal weight: 2.9990 chunk 151 optimal weight: 0.5980 chunk 186 optimal weight: 0.7980 chunk 137 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 106 optimal weight: 9.9990 chunk 20 optimal weight: 0.5980 chunk 146 optimal weight: 8.9990 chunk 130 optimal weight: 3.9990 chunk 111 optimal weight: 4.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 305 GLN H 91 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.133091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.091462 restraints weight = 38472.003| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 3.22 r_work: 0.3243 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.5561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15344 Z= 0.149 Angle : 0.566 10.808 20803 Z= 0.304 Chirality : 0.043 0.207 2440 Planarity : 0.004 0.060 2621 Dihedral : 4.145 32.415 2078 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.08 % Allowed : 16.63 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.08 (0.20), residues: 1914 helix: 2.06 (0.19), residues: 810 sheet: 0.48 (0.27), residues: 360 loop : -0.66 (0.23), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 212 TYR 0.022 0.001 TYR A 303 PHE 0.022 0.002 PHE H 235 TRP 0.028 0.002 TRP E 211 HIS 0.004 0.001 HIS C 247 Details of bonding type rmsd covalent geometry : bond 0.00351 (15334) covalent geometry : angle 0.56328 (20783) SS BOND : bond 0.00514 ( 10) SS BOND : angle 1.95322 ( 20) hydrogen bonds : bond 0.04380 ( 774) hydrogen bonds : angle 4.45684 ( 2244) *********************** 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 196 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 162 time to evaluate : 0.604 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: A 297 TYR cc_start: 0.6288 (t80) cc_final: 0.5947 (t80) REVERT: E 57 LYS cc_start: 0.9251 (mttt) cc_final: 0.9018 (mtmm) REVERT: E 124 TYR cc_start: 0.7422 (m-10) cc_final: 0.7133 (m-10) REVERT: E 211 TRP cc_start: 0.6274 (m100) cc_final: 0.4705 (m100) REVERT: E 235 PHE cc_start: 0.6375 (t80) cc_final: 0.5084 (t80) REVERT: E 256 ARG cc_start: 0.6470 (mtm180) cc_final: 0.6018 (mmm-85) REVERT: E 339 TRP cc_start: 0.6915 (OUTLIER) cc_final: 0.4627 (m100) REVERT: G 27 ARG cc_start: 0.6140 (mtp180) cc_final: 0.5660 (mtp180) REVERT: G 36 ASP cc_start: 0.8900 (t0) cc_final: 0.8512 (t0) REVERT: F 211 LYS cc_start: 0.8220 (mmtm) cc_final: 0.7980 (mmtt) REVERT: F 297 TYR cc_start: 0.6197 (t80) cc_final: 0.5873 (t80) REVERT: H 57 LYS cc_start: 0.9223 (mttt) cc_final: 0.9015 (mtmm) REVERT: H 211 TRP cc_start: 0.6242 (m100) cc_final: 0.4844 (m100) REVERT: H 235 PHE cc_start: 0.6286 (t80) cc_final: 0.5115 (t80) REVERT: H 256 ARG cc_start: 0.6422 (mtm180) cc_final: 0.5927 (mmm-85) REVERT: H 339 TRP cc_start: 0.6912 (OUTLIER) cc_final: 0.4654 (m100) REVERT: I 27 ARG cc_start: 0.6133 (mtp180) cc_final: 0.5738 (mtp180) REVERT: I 36 ASP cc_start: 0.8904 (t0) cc_final: 0.8523 (t0) outliers start: 34 outliers final: 25 residues processed: 189 average time/residue: 0.1359 time to fit residues: 37.6138 Evaluate side-chains 179 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 152 time to evaluate : 0.633 ------------------------------------------------------------------------------- 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 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 323 HIS Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain A residue 38 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 192 LEU Chi-restraints excluded: chain E residue 262 MET Chi-restraints excluded: chain E residue 339 TRP Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 49 ILE Chi-restraints excluded: chain H residue 7 LEU Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 103 CYS Chi-restraints excluded: chain H residue 192 LEU 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 83 optimal weight: 0.6980 chunk 170 optimal weight: 0.7980 chunk 63 optimal weight: 1.9990 chunk 87 optimal weight: 7.9990 chunk 136 optimal weight: 4.9990 chunk 1 optimal weight: 0.1980 chunk 105 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 123 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 chunk 2 optimal weight: 0.0670 overall best weight: 0.5520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 6 GLN G 18 GLN H 91 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.133806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.092592 restraints weight = 38682.225| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 3.47 r_work: 0.3252 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.5641 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= 0.121 Angle : 0.558 10.106 20803 Z= 0.300 Chirality : 0.042 0.196 2440 Planarity : 0.003 0.060 2621 Dihedral : 3.993 28.965 2078 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 1.71 % Allowed : 17.42 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.16 (0.20), residues: 1914 helix: 2.12 (0.19), residues: 812 sheet: 0.65 (0.28), residues: 338 loop : -0.65 (0.23), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 209 TYR 0.017 0.001 TYR A 303 PHE 0.025 0.001 PHE H 235 TRP 0.022 0.001 TRP E 211 HIS 0.004 0.001 HIS H 183 Details of bonding type rmsd covalent geometry : bond 0.00275 (15334) covalent geometry : angle 0.55564 (20783) SS BOND : bond 0.00514 ( 10) SS BOND : angle 1.78235 ( 20) hydrogen bonds : bond 0.04092 ( 774) hydrogen bonds : angle 4.36006 ( 2244) ********************** 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 189 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 161 time to evaluate : 0.676 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: E 124 TYR cc_start: 0.7371 (m-10) cc_final: 0.7106 (m-10) REVERT: E 211 TRP cc_start: 0.6280 (m100) cc_final: 0.4780 (m100) REVERT: E 235 PHE cc_start: 0.6415 (t80) cc_final: 0.5305 (t80) REVERT: E 256 ARG cc_start: 0.6478 (mtm180) cc_final: 0.6023 (mmm-85) REVERT: E 339 TRP cc_start: 0.6918 (OUTLIER) cc_final: 0.4612 (m100) REVERT: G 27 ARG cc_start: 0.6096 (mtp180) cc_final: 0.5606 (mtp180) REVERT: G 36 ASP cc_start: 0.8875 (t0) cc_final: 0.8474 (t0) REVERT: F 297 TYR cc_start: 0.6385 (t80) cc_final: 0.5942 (t80) REVERT: H 211 TRP cc_start: 0.6128 (m100) cc_final: 0.4729 (m100) REVERT: H 235 PHE cc_start: 0.6348 (t80) cc_final: 0.5288 (t80) REVERT: H 256 ARG cc_start: 0.6476 (mtm180) cc_final: 0.6020 (mmm-85) REVERT: H 339 TRP cc_start: 0.6917 (OUTLIER) cc_final: 0.4641 (m100) REVERT: I 36 ASP cc_start: 0.8874 (t0) cc_final: 0.8478 (t0) outliers start: 28 outliers final: 25 residues processed: 180 average time/residue: 0.1352 time to fit residues: 35.8830 Evaluate side-chains 179 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 152 time to evaluate : 0.628 ------------------------------------------------------------------------------- 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 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 323 HIS Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain E residue 30 LEU 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 38 LEU Chi-restraints excluded: chain F residue 49 ILE Chi-restraints excluded: chain H residue 7 LEU 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 192 LEU 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 41 optimal weight: 0.9990 chunk 86 optimal weight: 0.0070 chunk 171 optimal weight: 0.7980 chunk 134 optimal weight: 0.7980 chunk 106 optimal weight: 9.9990 chunk 5 optimal weight: 0.2980 chunk 170 optimal weight: 5.9990 chunk 149 optimal weight: 4.9990 chunk 78 optimal weight: 0.0870 chunk 121 optimal weight: 6.9990 chunk 120 optimal weight: 1.9990 overall best weight: 0.3976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 91 HIS F 305 GLN H 91 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.134307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.092809 restraints weight = 38624.996| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 3.34 r_work: 0.3278 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.5691 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= 0.114 Angle : 0.563 11.576 20803 Z= 0.301 Chirality : 0.042 0.214 2440 Planarity : 0.003 0.060 2621 Dihedral : 3.887 21.515 2078 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.83 % Allowed : 16.99 % Favored : 81.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.20 (0.20), residues: 1914 helix: 2.13 (0.19), residues: 812 sheet: 0.88 (0.29), residues: 328 loop : -0.69 (0.22), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 209 TYR 0.015 0.001 TYR A 303 PHE 0.025 0.001 PHE H 235 TRP 0.020 0.002 TRP E 211 HIS 0.004 0.001 HIS H 183 Details of bonding type rmsd covalent geometry : bond 0.00253 (15334) covalent geometry : angle 0.56109 (20783) SS BOND : bond 0.00505 ( 10) SS BOND : angle 1.65549 ( 20) hydrogen bonds : bond 0.03947 ( 774) hydrogen bonds : angle 4.33214 ( 2244) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6124.84 seconds wall clock time: 105 minutes 13.85 seconds (6313.85 seconds total)