Starting phenix.real_space_refine on Fri Jun 13 13:41:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xx7_38748/06_2025/8xx7_38748.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xx7_38748/06_2025/8xx7_38748.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xx7_38748/06_2025/8xx7_38748.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xx7_38748/06_2025/8xx7_38748.map" model { file = "/net/cci-nas-00/data/ceres_data/8xx7_38748/06_2025/8xx7_38748.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xx7_38748/06_2025/8xx7_38748.cif" } resolution = 3.32 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 112 5.16 5 C 9607 2.51 5 N 2586 2.21 5 O 2749 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 15054 Number of models: 1 Model: "" Number of chains: 10 Chain: "D" Number of atoms: 483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 483 Classifications: {'peptide': 65} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 60} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "R" Number of atoms: 2337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2337 Classifications: {'peptide': 300} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 9, 'TRANS': 290} Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 2, 'GLN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 49 Chain: "B" Number of atoms: 483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 483 Classifications: {'peptide': 65} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 60} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 2353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2353 Classifications: {'peptide': 300} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 9, 'TRANS': 290} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 45 Chain: "A" Number of atoms: 1711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1711 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 210} Chain breaks: 1 Chain: "E" Number of atoms: 2581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2581 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 330} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "G" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 407 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 4, 'TRANS': 48} Chain: "F" Number of atoms: 1711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1711 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 210} Chain breaks: 1 Chain: "H" Number of atoms: 2581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2581 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 330} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "I" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 407 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 4, 'TRANS': 48} Time building chain proxies: 10.51, per 1000 atoms: 0.70 Number of scatterers: 15054 At special positions: 0 Unit cell: (220.788, 123.599, 116.204, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 112 16.00 O 2749 8.00 N 2586 7.00 C 9607 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS D 13 " - pdb=" SG CYS D 39 " distance=2.03 Simple disulfide: pdb=" SG CYS D 15 " - pdb=" SG CYS D 55 " distance=2.03 Simple disulfide: pdb=" SG CYS R 39 " - pdb=" SG CYS R 286 " distance=2.03 Simple disulfide: pdb=" SG CYS R 119 " - pdb=" SG CYS R 196 " distance=2.03 Simple disulfide: pdb=" SG CYS B 13 " - pdb=" SG CYS B 39 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 55 " distance=2.03 Simple disulfide: pdb=" SG CYS C 39 " - pdb=" SG CYS C 286 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 103 " - pdb=" SG CYS E 114 " distance=2.04 Simple disulfide: pdb=" SG CYS H 103 " - pdb=" SG CYS H 114 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.72 Conformation dependent library (CDL) restraints added in 2.0 seconds 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3656 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 21 sheets defined 44.0% alpha, 19.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.72 Creating SS restraints... Processing helix chain 'D' and resid 23 through 25 No H-bonds generated for 'chain 'D' and resid 23 through 25' Processing helix chain 'D' and resid 60 through 71 removed outlier: 4.417A pdb=" N LYS D 64 " --> pdb=" O ALA D 60 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS D 65 " --> pdb=" O PRO D 61 " (cutoff:3.500A) Processing helix chain 'R' and resid 31 through 36 removed outlier: 3.813A pdb=" N LEU R 34 " --> pdb=" O PRO R 31 " (cutoff:3.500A) Processing helix chain 'R' and resid 44 through 76 removed outlier: 4.184A pdb=" N SER R 76 " --> pdb=" O VAL R 72 " (cutoff:3.500A) Processing helix chain 'R' and resid 81 through 111 Proline residue: R 102 - end of helix Processing helix chain 'R' and resid 115 through 149 Processing helix chain 'R' and resid 154 through 160 removed outlier: 3.550A pdb=" N GLN R 157 " --> pdb=" O THR R 154 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N TYR R 160 " --> pdb=" O GLN R 157 " (cutoff:3.500A) Processing helix chain 'R' and resid 161 through 177 Processing helix chain 'R' and resid 177 through 183 removed outlier: 3.507A pdb=" N LEU R 181 " --> pdb=" O ALA R 177 " (cutoff:3.500A) Processing helix chain 'R' and resid 203 through 212 Processing helix chain 'R' and resid 212 through 218 removed outlier: 3.571A pdb=" N GLN R 216 " --> pdb=" O ARG R 212 " (cutoff:3.500A) Processing helix chain 'R' and resid 220 through 240 removed outlier: 3.608A pdb=" N LYS R 240 " --> pdb=" O ARG R 236 " (cutoff:3.500A) Processing helix chain 'R' and resid 245 through 279 removed outlier: 3.547A pdb=" N ALA R 249 " --> pdb=" O GLN R 245 " (cutoff:3.500A) Proline residue: R 266 - end of helix Processing helix chain 'R' and resid 285 through 304 Processing helix chain 'R' and resid 305 through 315 Proline residue: R 311 - end of helix Processing helix chain 'R' and resid 318 through 329 Processing helix chain 'B' and resid 23 through 25 No H-bonds generated for 'chain 'B' and resid 23 through 25' Processing helix chain 'B' and resid 60 through 71 removed outlier: 4.417A pdb=" N LYS B 64 " --> pdb=" O ALA B 60 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS B 65 " --> pdb=" O PRO B 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 36 removed outlier: 3.813A pdb=" N LEU C 34 " --> pdb=" O PRO C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 76 removed outlier: 4.184A pdb=" N SER C 76 " --> pdb=" O VAL C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 111 Proline residue: C 102 - end of helix Processing helix chain 'C' and resid 115 through 149 Processing helix chain 'C' and resid 154 through 160 removed outlier: 3.550A pdb=" N GLN C 157 " --> pdb=" O THR C 154 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N TYR C 160 " --> pdb=" O GLN C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 161 through 177 Processing helix chain 'C' and resid 177 through 183 removed outlier: 3.507A pdb=" N LEU C 181 " --> pdb=" O ALA C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 212 Processing helix chain 'C' and resid 212 through 218 removed outlier: 3.570A pdb=" N GLN C 216 " --> pdb=" O ARG C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 240 removed outlier: 3.609A pdb=" N LYS C 240 " --> pdb=" O ARG C 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 279 removed outlier: 3.547A pdb=" N ALA C 249 " --> pdb=" O GLN C 245 " (cutoff:3.500A) Proline residue: C 266 - end of helix Processing helix chain 'C' and resid 285 through 304 Processing helix chain 'C' and resid 305 through 315 Proline residue: C 311 - end of helix Processing helix chain 'C' and resid 318 through 329 Processing helix chain 'A' and resid 6 through 30 Processing helix chain 'A' and resid 208 through 217 removed outlier: 4.786A pdb=" N ILE A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N HIS A 214 " --> pdb=" O LYS A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 256 Processing helix chain 'A' and resid 271 through 282 removed outlier: 4.112A pdb=" N LYS A 280 " --> pdb=" O GLY A 276 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LYS A 281 " --> pdb=" O GLU A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 310 Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'E' and resid 6 through 26 removed outlier: 3.706A pdb=" N ALA E 26 " --> pdb=" O ARG E 22 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 34 Processing helix chain 'G' and resid 12 through 24 removed outlier: 3.607A pdb=" N GLU G 17 " --> pdb=" O ARG G 13 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 55 through 59 removed outlier: 3.646A pdb=" N ASN G 59 " --> pdb=" O ALA G 56 " (cutoff:3.500A) Processing helix chain 'F' and resid 6 through 30 Processing helix chain 'F' and resid 208 through 217 removed outlier: 4.786A pdb=" N ILE F 213 " --> pdb=" O LYS F 210 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N HIS F 214 " --> pdb=" O LYS F 211 " (cutoff:3.500A) Processing helix chain 'F' and resid 243 through 256 Processing helix chain 'F' and resid 271 through 282 removed outlier: 4.113A pdb=" N LYS F 280 " --> pdb=" O GLY F 276 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYS F 281 " --> pdb=" O GLU F 277 " (cutoff:3.500A) Processing helix chain 'F' and resid 296 through 310 Processing helix chain 'F' and resid 330 through 351 Processing helix chain 'H' and resid 6 through 26 removed outlier: 3.705A pdb=" N ALA H 26 " --> pdb=" O ARG H 22 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 34 Processing helix chain 'I' and resid 12 through 24 removed outlier: 3.608A pdb=" N GLU I 17 " --> pdb=" O ARG I 13 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASN I 24 " --> pdb=" O LYS I 20 " (cutoff:3.500A) Processing helix chain 'I' and resid 29 through 44 Processing helix chain 'I' and resid 55 through 59 removed outlier: 3.646A pdb=" N ASN I 59 " --> pdb=" O ALA I 56 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 53 through 56 removed outlier: 4.516A pdb=" N VAL D 44 " --> pdb=" O LEU D 56 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N VAL B 44 " --> pdb=" O LEU B 56 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'R' and resid 184 through 187 Processing sheet with id=AA3, first strand: chain 'C' and resid 184 through 187 Processing sheet with id=AA4, first strand: chain 'A' and resid 186 through 188 Processing sheet with id=AA5, first strand: chain 'A' and resid 186 through 188 removed outlier: 9.585A pdb=" N ALA A 221 " --> pdb=" O ASP A 33 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N LYS A 35 " --> pdb=" O ALA A 221 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N ILE A 223 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N LEU A 37 " --> pdb=" O ILE A 223 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N CYS A 225 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N LEU A 39 " --> pdb=" O CYS A 225 " (cutoff:3.500A) removed outlier: 8.745A pdb=" N ASP A 227 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ILE A 222 " --> pdb=" O ILE A 266 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N PHE A 268 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N PHE A 224 " --> pdb=" O PHE A 268 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N ASN A 270 " --> pdb=" O PHE A 224 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N VAL A 226 " --> pdb=" O ASN A 270 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 47 through 52 removed outlier: 4.402A pdb=" N PHE E 335 " --> pdb=" O SER E 331 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER E 331 " --> pdb=" O PHE E 335 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 58 through 63 removed outlier: 6.963A pdb=" N ALA E 73 " --> pdb=" O TYR E 59 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N MET E 61 " --> pdb=" O VAL E 71 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N VAL E 71 " --> pdb=" O MET E 61 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N TRP E 63 " --> pdb=" O LEU E 69 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N LEU E 69 " --> pdb=" O TRP E 63 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N SER E 74 " --> pdb=" O LYS E 78 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N LYS E 78 " --> pdb=" O SER E 74 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N HIS E 91 " --> pdb=" O ILE E 81 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ASP E 83 " --> pdb=" O LYS E 89 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N LYS E 89 " --> pdb=" O ASP E 83 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 100 through 103 removed outlier: 4.210A pdb=" N SER E 122 " --> pdb=" O CYS E 114 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ASN E 125 " --> pdb=" O VAL E 135 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N VAL E 135 " --> pdb=" O ASN E 125 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 146 through 153 removed outlier: 4.600A pdb=" N CYS E 149 " --> pdb=" O VAL E 158 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N VAL E 158 " --> pdb=" O CYS E 149 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N PHE E 151 " --> pdb=" O GLN E 156 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N GLN E 156 " --> pdb=" O PHE E 151 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE E 157 " --> pdb=" O TRP E 169 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER E 161 " --> pdb=" O THR E 165 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N THR E 165 " --> pdb=" O SER E 161 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 187 through 192 removed outlier: 3.567A pdb=" N SER E 201 " --> pdb=" O LYS E 209 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N SER E 207 " --> pdb=" O ALA E 203 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN E 220 " --> pdb=" O LEU E 210 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N ASP E 212 " --> pdb=" O CYS E 218 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N CYS E 218 " --> pdb=" O ASP E 212 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 229 through 234 removed outlier: 6.406A pdb=" N GLY E 244 " --> pdb=" O ASN E 230 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ILE E 232 " --> pdb=" O ALA E 242 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ALA E 242 " --> pdb=" O ILE E 232 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N PHE E 234 " --> pdb=" O ALA E 240 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ALA E 240 " --> pdb=" O PHE E 234 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N CYS E 250 " --> pdb=" O THR E 263 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N THR E 263 " --> pdb=" O CYS E 250 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N LEU E 252 " --> pdb=" O LEU E 261 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 273 through 278 removed outlier: 6.395A pdb=" N GLY E 288 " --> pdb=" O THR E 274 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N VAL E 276 " --> pdb=" O LEU E 286 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N LEU E 286 " --> pdb=" O VAL E 276 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N PHE E 278 " --> pdb=" O LEU E 284 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N LEU E 284 " --> pdb=" O PHE E 278 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N CYS E 294 " --> pdb=" O VAL E 307 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N VAL E 307 " --> pdb=" O CYS E 294 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N VAL E 296 " --> pdb=" O ALA E 305 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 186 through 188 Processing sheet with id=AB5, first strand: chain 'F' and resid 186 through 188 removed outlier: 9.585A pdb=" N ALA F 221 " --> pdb=" O ASP F 33 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N LYS F 35 " --> pdb=" O ALA F 221 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N ILE F 223 " --> pdb=" O LYS F 35 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N LEU F 37 " --> pdb=" O ILE F 223 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N CYS F 225 " --> pdb=" O LEU F 37 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N LEU F 39 " --> pdb=" O CYS F 225 " (cutoff:3.500A) removed outlier: 8.746A pdb=" N ASP F 227 " --> pdb=" O LEU F 39 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ILE F 222 " --> pdb=" O ILE F 266 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N PHE F 268 " --> pdb=" O ILE F 222 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N PHE F 224 " --> pdb=" O PHE F 268 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N ASN F 270 " --> pdb=" O PHE F 224 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N VAL F 226 " --> pdb=" O ASN F 270 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 47 through 52 removed outlier: 4.402A pdb=" N PHE H 335 " --> pdb=" O SER H 331 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER H 331 " --> pdb=" O PHE H 335 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 58 through 63 removed outlier: 6.964A pdb=" N ALA H 73 " --> pdb=" O TYR H 59 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N MET H 61 " --> pdb=" O VAL H 71 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N VAL H 71 " --> pdb=" O MET H 61 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N TRP H 63 " --> pdb=" O LEU H 69 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N LEU H 69 " --> pdb=" O TRP H 63 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N SER H 74 " --> pdb=" O LYS H 78 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N LYS H 78 " --> pdb=" O SER H 74 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N HIS H 91 " --> pdb=" O ILE H 81 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ASP H 83 " --> pdb=" O LYS H 89 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N LYS H 89 " --> pdb=" O ASP H 83 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 100 through 103 removed outlier: 4.210A pdb=" N SER H 122 " --> pdb=" O CYS H 114 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ASN H 125 " --> pdb=" O VAL H 135 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N VAL H 135 " --> pdb=" O ASN H 125 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 146 through 153 removed outlier: 4.600A pdb=" N CYS H 149 " --> pdb=" O VAL H 158 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N VAL H 158 " --> pdb=" O CYS H 149 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N PHE H 151 " --> pdb=" O GLN H 156 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N GLN H 156 " --> pdb=" O PHE H 151 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE H 157 " --> pdb=" O TRP H 169 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER H 161 " --> pdb=" O THR H 165 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N THR H 165 " --> pdb=" O SER H 161 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 187 through 192 removed outlier: 3.567A pdb=" N SER H 201 " --> pdb=" O LYS H 209 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N SER H 207 " --> pdb=" O ALA H 203 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN H 220 " --> pdb=" O LEU H 210 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N ASP H 212 " --> pdb=" O CYS H 218 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N CYS H 218 " --> pdb=" O ASP H 212 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 229 through 234 removed outlier: 6.406A pdb=" N GLY H 244 " --> pdb=" O ASN H 230 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ILE H 232 " --> pdb=" O ALA H 242 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ALA H 242 " --> pdb=" O ILE H 232 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N PHE H 234 " --> pdb=" O ALA H 240 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ALA H 240 " --> pdb=" O PHE H 234 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N CYS H 250 " --> pdb=" O THR H 263 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N THR H 263 " --> pdb=" O CYS H 250 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N LEU H 252 " --> pdb=" O LEU H 261 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 273 through 278 removed outlier: 6.396A pdb=" N GLY H 288 " --> pdb=" O THR H 274 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N VAL H 276 " --> pdb=" O LEU H 286 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N LEU H 286 " --> pdb=" O VAL H 276 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N PHE H 278 " --> pdb=" O LEU H 284 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N LEU H 284 " --> pdb=" O PHE H 278 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N CYS H 294 " --> pdb=" O VAL H 307 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N VAL H 307 " --> pdb=" O CYS H 294 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N VAL H 296 " --> pdb=" O ALA H 305 " (cutoff:3.500A) 782 hydrogen bonds defined for protein. 2244 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.87 Time building geometry restraints manager: 4.42 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: 6.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.660 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 37.330 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5522 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 15344 Z= 0.157 Angle : 0.479 5.423 20803 Z= 0.282 Chirality : 0.040 0.151 2440 Planarity : 0.003 0.040 2621 Dihedral : 12.689 86.631 5531 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.19), residues: 1914 helix: 1.88 (0.19), residues: 800 sheet: -0.44 (0.25), residues: 424 loop : -0.88 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 211 HIS 0.003 0.001 HIS R 242 PHE 0.014 0.001 PHE E 234 TYR 0.006 0.001 TYR R 86 ARG 0.004 0.000 ARG C 248 Details of bonding type rmsd hydrogen bonds : bond 0.19766 ( 774) hydrogen bonds : angle 6.21401 ( 2244) SS BOND : bond 0.00287 ( 10) SS BOND : angle 1.79551 ( 20) covalent geometry : bond 0.00355 (15334) covalent geometry : angle 0.47613 (20783) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 419 time to evaluate : 1.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 17 GLN cc_start: 0.7539 (tt0) cc_final: 0.7206 (tt0) REVERT: R 84 ASP cc_start: 0.8350 (m-30) cc_final: 0.8097 (m-30) REVERT: R 160 TYR cc_start: 0.7301 (m-80) cc_final: 0.7060 (m-80) REVERT: R 213 ILE cc_start: 0.8730 (tt) cc_final: 0.8472 (mt) REVERT: R 305 LEU cc_start: 0.8779 (mt) cc_final: 0.8561 (mp) REVERT: B 17 GLN cc_start: 0.7536 (tt0) cc_final: 0.7196 (tt0) REVERT: C 84 ASP cc_start: 0.8376 (m-30) cc_final: 0.8112 (m-30) REVERT: C 160 TYR cc_start: 0.7297 (m-80) cc_final: 0.7061 (m-80) REVERT: C 213 ILE cc_start: 0.8726 (tt) cc_final: 0.8471 (mt) REVERT: C 305 LEU cc_start: 0.8776 (mt) cc_final: 0.8557 (mp) outliers start: 0 outliers final: 0 residues processed: 419 average time/residue: 0.3395 time to fit residues: 193.8640 Evaluate side-chains 196 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 196 time to evaluate : 1.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 160 optimal weight: 6.9990 chunk 144 optimal weight: 5.9990 chunk 79 optimal weight: 0.0870 chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 20.0000 chunk 76 optimal weight: 2.9990 chunk 148 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 chunk 90 optimal weight: 4.9990 chunk 110 optimal weight: 0.9990 chunk 172 optimal weight: 6.9990 overall best weight: 1.1964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 17 GLN D 29 ASN R 47 ASN R 89 ASN B 17 GLN B 29 ASN C 47 ASN C 89 ASN ** A 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 256 ASN E 176 GLN E 183 HIS E 266 HIS ** F 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 256 ASN F 305 GLN H 176 GLN H 183 HIS H 266 HIS I 18 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.136326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.092136 restraints weight = 38993.285| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 3.57 r_work: 0.3249 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.3523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 15344 Z= 0.204 Angle : 0.680 11.319 20803 Z= 0.363 Chirality : 0.046 0.168 2440 Planarity : 0.005 0.071 2621 Dihedral : 4.239 24.185 2078 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.26 % Allowed : 11.19 % Favored : 86.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.19), residues: 1914 helix: 1.72 (0.18), residues: 820 sheet: -0.18 (0.25), residues: 396 loop : -0.95 (0.23), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP H 339 HIS 0.005 0.001 HIS R 247 PHE 0.025 0.002 PHE B 62 TYR 0.019 0.002 TYR F 231 ARG 0.006 0.001 ARG F 209 Details of bonding type rmsd hydrogen bonds : bond 0.05179 ( 774) hydrogen bonds : angle 4.98395 ( 2244) SS BOND : bond 0.01029 ( 10) SS BOND : angle 2.68776 ( 20) covalent geometry : bond 0.00470 (15334) covalent geometry : angle 0.67523 (20783) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 217 time to evaluate : 1.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 17 GLN cc_start: 0.8163 (tt0) cc_final: 0.7845 (tt0) REVERT: R 84 ASP cc_start: 0.8960 (m-30) cc_final: 0.8734 (m-30) REVERT: R 213 ILE cc_start: 0.9270 (tt) cc_final: 0.8918 (mt) REVERT: B 17 GLN cc_start: 0.8162 (tt0) cc_final: 0.7843 (tt0) REVERT: C 84 ASP cc_start: 0.8956 (m-30) cc_final: 0.8722 (m-30) REVERT: C 213 ILE cc_start: 0.9261 (tt) cc_final: 0.8911 (mt) REVERT: A 303 TYR cc_start: 0.8936 (t80) cc_final: 0.8734 (t80) REVERT: A 307 GLN cc_start: 0.8626 (mm110) cc_final: 0.7875 (tp-100) REVERT: E 91 HIS cc_start: 0.6570 (m-70) cc_final: 0.6307 (m170) REVERT: E 101 MET cc_start: 0.8827 (tpp) cc_final: 0.8585 (tpp) REVERT: E 339 TRP cc_start: 0.6392 (OUTLIER) cc_final: 0.4621 (m100) REVERT: G 22 GLU cc_start: 0.8942 (tt0) cc_final: 0.8090 (tp30) REVERT: F 262 ASP cc_start: 0.7699 (m-30) cc_final: 0.7496 (p0) REVERT: F 303 TYR cc_start: 0.8957 (t80) cc_final: 0.8753 (t80) REVERT: F 307 GLN cc_start: 0.8629 (mm110) cc_final: 0.7855 (tp-100) REVERT: H 91 HIS cc_start: 0.6558 (m-70) cc_final: 0.6305 (m170) REVERT: H 101 MET cc_start: 0.8777 (tpp) cc_final: 0.8527 (tpp) REVERT: H 124 TYR cc_start: 0.7720 (m-80) cc_final: 0.7519 (m-10) REVERT: H 339 TRP cc_start: 0.6156 (OUTLIER) cc_final: 0.4519 (m100) REVERT: I 22 GLU cc_start: 0.8904 (tt0) cc_final: 0.8063 (tp30) outliers start: 37 outliers final: 19 residues processed: 245 average time/residue: 0.2694 time to fit residues: 96.8006 Evaluate side-chains 203 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 182 time to evaluate : 2.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 50 ASN Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 191 ASN Chi-restraints excluded: chain R residue 304 ILE Chi-restraints excluded: chain R residue 308 CYS Chi-restraints excluded: chain R residue 325 LEU Chi-restraints excluded: chain B residue 50 ASN Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 191 ASN Chi-restraints excluded: chain C residue 304 ILE Chi-restraints excluded: chain C residue 308 CYS Chi-restraints excluded: chain C residue 323 HIS Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 103 CYS Chi-restraints excluded: chain E residue 339 TRP Chi-restraints excluded: chain F residue 49 ILE Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 103 CYS Chi-restraints excluded: chain H residue 339 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 108 optimal weight: 5.9990 chunk 140 optimal weight: 0.9980 chunk 129 optimal weight: 1.9990 chunk 176 optimal weight: 10.0000 chunk 9 optimal weight: 2.9990 chunk 96 optimal weight: 0.0050 chunk 180 optimal weight: 9.9990 chunk 172 optimal weight: 6.9990 chunk 97 optimal weight: 4.9990 chunk 35 optimal weight: 0.0770 chunk 62 optimal weight: 0.9980 overall best weight: 0.8154 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 GLN A 346 ASN E 91 HIS F 256 ASN H 91 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.136003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.092346 restraints weight = 38990.510| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 3.49 r_work: 0.3238 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.3979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 15344 Z= 0.152 Angle : 0.576 8.190 20803 Z= 0.311 Chirality : 0.043 0.175 2440 Planarity : 0.004 0.063 2621 Dihedral : 4.260 28.584 2078 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.96 % Allowed : 13.08 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.19), residues: 1914 helix: 2.08 (0.19), residues: 798 sheet: 0.12 (0.26), residues: 382 loop : -0.85 (0.22), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP E 211 HIS 0.006 0.001 HIS G 44 PHE 0.019 0.001 PHE B 62 TYR 0.008 0.001 TYR A 354 ARG 0.004 0.001 ARG A 209 Details of bonding type rmsd hydrogen bonds : bond 0.04645 ( 774) hydrogen bonds : angle 4.68250 ( 2244) SS BOND : bond 0.00738 ( 10) SS BOND : angle 3.30095 ( 20) covalent geometry : bond 0.00352 (15334) covalent geometry : angle 0.56710 (20783) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 203 time to evaluate : 2.049 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: 0.8190 (tt0) cc_final: 0.7858 (tt0) REVERT: R 84 ASP cc_start: 0.8960 (m-30) cc_final: 0.8750 (m-30) REVERT: R 213 ILE cc_start: 0.9221 (tt) cc_final: 0.8957 (mt) REVERT: B 17 GLN cc_start: 0.8190 (tt0) cc_final: 0.7861 (tt0) REVERT: C 84 ASP cc_start: 0.8952 (m-30) cc_final: 0.8735 (m-30) REVERT: C 213 ILE cc_start: 0.9216 (tt) cc_final: 0.8943 (mt) REVERT: A 211 LYS cc_start: 0.8143 (mmtm) cc_final: 0.7807 (mmtt) REVERT: A 297 TYR cc_start: 0.6761 (t80) cc_final: 0.6364 (t80) REVERT: A 303 TYR cc_start: 0.9001 (t80) cc_final: 0.8749 (t80) REVERT: E 211 TRP cc_start: 0.5946 (m100) cc_final: 0.5223 (m100) REVERT: E 235 PHE cc_start: 0.5172 (t80) cc_final: 0.4422 (t80) REVERT: E 256 ARG cc_start: 0.6248 (mtm180) cc_final: 0.5942 (mmm-85) REVERT: G 22 GLU cc_start: 0.9019 (tt0) cc_final: 0.8493 (tp30) REVERT: G 36 ASP cc_start: 0.8934 (t0) cc_final: 0.8396 (t0) REVERT: F 211 LYS cc_start: 0.8214 (mmtm) cc_final: 0.7880 (mmtt) REVERT: F 297 TYR cc_start: 0.6847 (t80) cc_final: 0.6440 (t80) REVERT: F 303 TYR cc_start: 0.9002 (t80) cc_final: 0.8785 (t80) REVERT: H 91 HIS cc_start: 0.6762 (m90) cc_final: 0.6459 (m-70) REVERT: H 211 TRP cc_start: 0.5928 (m100) cc_final: 0.5170 (m100) REVERT: H 235 PHE cc_start: 0.5151 (t80) cc_final: 0.4404 (t80) REVERT: H 256 ARG cc_start: 0.6258 (mtm180) cc_final: 0.5935 (mmm-85) REVERT: H 339 TRP cc_start: 0.6328 (OUTLIER) cc_final: 0.4582 (m100) REVERT: I 22 GLU cc_start: 0.8986 (tt0) cc_final: 0.8292 (tp30) REVERT: I 36 ASP cc_start: 0.8934 (t0) cc_final: 0.8399 (t0) outliers start: 32 outliers final: 22 residues processed: 222 average time/residue: 0.3059 time to fit residues: 97.4749 Evaluate side-chains 197 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 174 time to evaluate : 1.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 50 ASN Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain R residue 191 ASN Chi-restraints excluded: chain R residue 304 ILE Chi-restraints excluded: chain R residue 325 LEU Chi-restraints excluded: chain B residue 50 ASN Chi-restraints excluded: chain C residue 191 ASN Chi-restraints excluded: chain C residue 304 ILE Chi-restraints excluded: chain C residue 323 HIS Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 103 CYS Chi-restraints excluded: chain E residue 234 PHE Chi-restraints excluded: chain E residue 262 MET Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain F residue 49 ILE Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 103 CYS Chi-restraints excluded: chain H residue 234 PHE Chi-restraints excluded: chain H residue 262 MET Chi-restraints excluded: chain H residue 339 TRP Chi-restraints excluded: chain I residue 31 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 52 optimal weight: 0.6980 chunk 130 optimal weight: 5.9990 chunk 55 optimal weight: 0.5980 chunk 40 optimal weight: 0.5980 chunk 138 optimal weight: 4.9990 chunk 153 optimal weight: 7.9990 chunk 133 optimal weight: 9.9990 chunk 73 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 103 optimal weight: 0.2980 chunk 25 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 ASN E 91 HIS F 346 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.135731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.092024 restraints weight = 38521.882| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 3.23 r_work: 0.3263 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.4334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15344 Z= 0.130 Angle : 0.537 7.575 20803 Z= 0.290 Chirality : 0.042 0.160 2440 Planarity : 0.004 0.063 2621 Dihedral : 4.146 29.858 2078 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.26 % Allowed : 13.33 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.20), residues: 1914 helix: 2.21 (0.19), residues: 806 sheet: 0.23 (0.26), residues: 382 loop : -0.73 (0.23), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 211 HIS 0.006 0.001 HIS G 44 PHE 0.018 0.001 PHE B 62 TYR 0.006 0.001 TYR A 303 ARG 0.003 0.000 ARG F 313 Details of bonding type rmsd hydrogen bonds : bond 0.04229 ( 774) hydrogen bonds : angle 4.46072 ( 2244) SS BOND : bond 0.00575 ( 10) SS BOND : angle 2.96717 ( 20) covalent geometry : bond 0.00294 (15334) covalent geometry : angle 0.52929 (20783) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 184 time to evaluate : 1.689 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: D 17 GLN cc_start: 0.8073 (tt0) cc_final: 0.7713 (tt0) REVERT: R 84 ASP cc_start: 0.8895 (m-30) cc_final: 0.8681 (m-30) REVERT: R 213 ILE cc_start: 0.9228 (tt) cc_final: 0.8976 (mt) REVERT: B 17 GLN cc_start: 0.8107 (tt0) cc_final: 0.7746 (tt0) REVERT: C 84 ASP cc_start: 0.8888 (m-30) cc_final: 0.8670 (m-30) REVERT: C 213 ILE cc_start: 0.9221 (tt) cc_final: 0.8957 (mt) REVERT: A 211 LYS cc_start: 0.8207 (mmtm) cc_final: 0.7875 (mmtt) REVERT: A 297 TYR cc_start: 0.6645 (t80) cc_final: 0.6440 (t80) REVERT: A 303 TYR cc_start: 0.8982 (t80) cc_final: 0.8766 (t80) REVERT: E 235 PHE cc_start: 0.5412 (t80) cc_final: 0.4607 (t80) REVERT: E 256 ARG cc_start: 0.6245 (mtm180) cc_final: 0.5974 (mmm-85) REVERT: E 280 LYS cc_start: 0.7404 (mmmt) cc_final: 0.7175 (mmmt) REVERT: E 339 TRP cc_start: 0.6398 (OUTLIER) cc_final: 0.4559 (m100) REVERT: G 36 ASP cc_start: 0.8950 (t0) cc_final: 0.8467 (t0) REVERT: F 303 TYR cc_start: 0.8944 (t80) cc_final: 0.8725 (t80) REVERT: H 91 HIS cc_start: 0.6748 (m90) cc_final: 0.6507 (m-70) REVERT: H 211 TRP cc_start: 0.5724 (m100) cc_final: 0.5186 (m100) REVERT: H 235 PHE cc_start: 0.5335 (t80) cc_final: 0.4523 (t80) REVERT: H 256 ARG cc_start: 0.6185 (mtm180) cc_final: 0.5938 (mmm-85) REVERT: H 280 LYS cc_start: 0.7404 (mmmt) cc_final: 0.7178 (mmmt) REVERT: I 36 ASP cc_start: 0.8903 (t0) cc_final: 0.8422 (t0) outliers start: 37 outliers final: 19 residues processed: 210 average time/residue: 0.2734 time to fit residues: 83.8670 Evaluate side-chains 186 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 166 time to evaluate : 1.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 50 ASN Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 304 ILE Chi-restraints excluded: chain R residue 325 LEU Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 50 ASN Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 304 ILE Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 103 CYS Chi-restraints excluded: chain E residue 234 PHE Chi-restraints excluded: chain E residue 339 TRP Chi-restraints excluded: chain F residue 49 ILE Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 103 CYS Chi-restraints excluded: chain H residue 234 PHE Chi-restraints excluded: chain H residue 262 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 13 optimal weight: 0.7980 chunk 119 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 145 optimal weight: 8.9990 chunk 11 optimal weight: 2.9990 chunk 110 optimal weight: 10.0000 chunk 139 optimal weight: 0.0980 chunk 23 optimal weight: 1.9990 chunk 133 optimal weight: 10.0000 chunk 158 optimal weight: 9.9990 chunk 186 optimal weight: 6.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 ASN A 305 GLN E 91 HIS ** G 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.132748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 95)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.091807 restraints weight = 39064.071| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 3.56 r_work: 0.3198 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.4892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 15344 Z= 0.225 Angle : 0.615 7.190 20803 Z= 0.332 Chirality : 0.045 0.161 2440 Planarity : 0.004 0.062 2621 Dihedral : 4.395 35.873 2078 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.81 % Allowed : 13.88 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.20), residues: 1914 helix: 1.90 (0.18), residues: 806 sheet: 0.10 (0.26), residues: 368 loop : -0.68 (0.23), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP E 211 HIS 0.006 0.001 HIS G 44 PHE 0.022 0.002 PHE B 62 TYR 0.008 0.001 TYR R 197 ARG 0.007 0.001 ARG A 243 Details of bonding type rmsd hydrogen bonds : bond 0.05038 ( 774) hydrogen bonds : angle 4.68736 ( 2244) SS BOND : bond 0.00562 ( 10) SS BOND : angle 3.34391 ( 20) covalent geometry : bond 0.00534 (15334) covalent geometry : angle 0.60693 (20783) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 163 time to evaluate : 1.724 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: R 213 ILE cc_start: 0.9283 (OUTLIER) cc_final: 0.9052 (mt) REVERT: C 213 ILE cc_start: 0.9273 (OUTLIER) cc_final: 0.9044 (mt) REVERT: A 211 LYS cc_start: 0.8287 (mmtm) cc_final: 0.7984 (mmtt) REVERT: A 303 TYR cc_start: 0.8928 (t80) cc_final: 0.8726 (t80) REVERT: A 354 TYR cc_start: 0.7777 (t80) cc_final: 0.7479 (t80) REVERT: E 124 TYR cc_start: 0.7569 (m-10) cc_final: 0.7275 (m-10) REVERT: E 235 PHE cc_start: 0.5579 (t80) cc_final: 0.4666 (t80) REVERT: E 256 ARG cc_start: 0.6394 (mtm180) cc_final: 0.6109 (mmm-85) REVERT: E 339 TRP cc_start: 0.6554 (OUTLIER) cc_final: 0.4563 (m100) REVERT: G 36 ASP cc_start: 0.8914 (t0) cc_final: 0.8427 (t0) REVERT: G 44 HIS cc_start: 0.6014 (t-170) cc_final: 0.5603 (t70) REVERT: F 211 LYS cc_start: 0.8251 (mmtm) cc_final: 0.7989 (mmtt) REVERT: F 297 TYR cc_start: 0.6795 (t80) cc_final: 0.6409 (t80) REVERT: F 303 TYR cc_start: 0.8941 (t80) cc_final: 0.8728 (t80) REVERT: F 341 ASP cc_start: 0.8804 (OUTLIER) cc_final: 0.8562 (m-30) REVERT: F 354 TYR cc_start: 0.7816 (t80) cc_final: 0.7528 (t80) REVERT: H 235 PHE cc_start: 0.5583 (t80) cc_final: 0.4660 (t80) REVERT: H 256 ARG cc_start: 0.6374 (mtm180) cc_final: 0.6072 (mmm-85) REVERT: H 339 TRP cc_start: 0.6409 (OUTLIER) cc_final: 0.4625 (m100) REVERT: I 36 ASP cc_start: 0.8911 (t0) cc_final: 0.8430 (t0) REVERT: I 44 HIS cc_start: 0.5926 (t-170) cc_final: 0.5537 (t70) outliers start: 46 outliers final: 23 residues processed: 197 average time/residue: 0.2800 time to fit residues: 81.0117 Evaluate side-chains 174 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 146 time to evaluate : 1.713 ------------------------------------------------------------------------------- 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 213 ILE Chi-restraints excluded: chain R residue 304 ILE Chi-restraints excluded: chain R residue 316 PHE Chi-restraints excluded: chain R residue 325 LEU Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 50 ASN Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 304 ILE Chi-restraints excluded: chain C residue 316 PHE Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 103 CYS Chi-restraints excluded: chain E residue 234 PHE Chi-restraints excluded: chain E residue 262 MET Chi-restraints excluded: chain E residue 339 TRP Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain F residue 49 ILE Chi-restraints excluded: chain F residue 341 ASP Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 103 CYS Chi-restraints excluded: chain H residue 234 PHE Chi-restraints excluded: chain H residue 339 TRP Chi-restraints excluded: chain I residue 31 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 122 optimal weight: 10.0000 chunk 183 optimal weight: 10.0000 chunk 168 optimal weight: 0.9990 chunk 184 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 103 optimal weight: 9.9990 chunk 77 optimal weight: 0.3980 chunk 186 optimal weight: 0.9980 chunk 11 optimal weight: 0.5980 chunk 74 optimal weight: 10.0000 chunk 102 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 ASN E 6 GLN E 91 HIS H 6 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.133787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.096473 restraints weight = 38479.180| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 2.33 r_work: 0.3276 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.5108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15344 Z= 0.159 Angle : 0.565 6.755 20803 Z= 0.306 Chirality : 0.043 0.155 2440 Planarity : 0.004 0.062 2621 Dihedral : 4.273 34.317 2078 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.38 % Allowed : 15.22 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.20), residues: 1914 helix: 2.01 (0.18), residues: 808 sheet: 0.28 (0.26), residues: 368 loop : -0.63 (0.23), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 211 HIS 0.004 0.001 HIS C 247 PHE 0.019 0.001 PHE D 62 TYR 0.008 0.001 TYR E 59 ARG 0.004 0.000 ARG A 313 Details of bonding type rmsd hydrogen bonds : bond 0.04519 ( 774) hydrogen bonds : angle 4.53415 ( 2244) SS BOND : bond 0.00512 ( 10) SS BOND : angle 2.83820 ( 20) covalent geometry : bond 0.00375 (15334) covalent geometry : angle 0.55862 (20783) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 162 time to evaluate : 1.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 297 TYR cc_start: 0.6723 (t80) cc_final: 0.6303 (t80) REVERT: A 341 ASP cc_start: 0.8765 (OUTLIER) cc_final: 0.8552 (m-30) REVERT: E 124 TYR cc_start: 0.7419 (m-10) cc_final: 0.7139 (m-10) REVERT: E 235 PHE cc_start: 0.5565 (t80) cc_final: 0.4407 (t80) REVERT: E 256 ARG cc_start: 0.6340 (mtm180) cc_final: 0.6071 (mmm-85) REVERT: E 339 TRP cc_start: 0.6627 (OUTLIER) cc_final: 0.4559 (m100) REVERT: G 36 ASP cc_start: 0.8909 (t0) cc_final: 0.8556 (t0) REVERT: F 297 TYR cc_start: 0.6706 (t80) cc_final: 0.6461 (t80) REVERT: H 91 HIS cc_start: 0.6863 (m90) cc_final: 0.6582 (m-70) REVERT: H 211 TRP cc_start: 0.6009 (m100) cc_final: 0.5358 (m100) REVERT: H 235 PHE cc_start: 0.5545 (t80) cc_final: 0.4370 (t80) REVERT: H 256 ARG cc_start: 0.6353 (mtm180) cc_final: 0.6060 (mmm-85) REVERT: H 339 TRP cc_start: 0.6327 (OUTLIER) cc_final: 0.4456 (m100) REVERT: I 36 ASP cc_start: 0.8898 (t0) cc_final: 0.8535 (t0) outliers start: 39 outliers final: 24 residues processed: 191 average time/residue: 0.2927 time to fit residues: 83.2084 Evaluate side-chains 174 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 147 time to evaluate : 1.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 50 ASN Chi-restraints excluded: chain R residue 58 VAL 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 316 PHE Chi-restraints excluded: chain R residue 325 LEU Chi-restraints excluded: chain B residue 50 ASN Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 203 ASN Chi-restraints excluded: chain C residue 304 ILE Chi-restraints excluded: chain C residue 316 PHE Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 103 CYS Chi-restraints excluded: chain E residue 234 PHE Chi-restraints excluded: chain E residue 262 MET Chi-restraints excluded: chain E residue 339 TRP Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain F residue 49 ILE Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 103 CYS Chi-restraints excluded: chain H residue 234 PHE Chi-restraints excluded: chain H residue 339 TRP Chi-restraints excluded: chain I residue 31 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 135 optimal weight: 5.9990 chunk 33 optimal weight: 0.5980 chunk 95 optimal weight: 10.0000 chunk 92 optimal weight: 0.6980 chunk 167 optimal weight: 7.9990 chunk 26 optimal weight: 0.6980 chunk 189 optimal weight: 0.0370 chunk 173 optimal weight: 6.9990 chunk 50 optimal weight: 0.9980 chunk 105 optimal weight: 6.9990 chunk 61 optimal weight: 0.9990 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 ASN ** F 256 ASN ** 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 = 0.4255 r_free = 0.4255 target = 0.134371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.093962 restraints weight = 38660.435| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 3.24 r_work: 0.3264 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.5218 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= 0.124 Angle : 0.539 6.691 20803 Z= 0.290 Chirality : 0.042 0.151 2440 Planarity : 0.004 0.062 2621 Dihedral : 4.120 35.859 2078 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.57 % Allowed : 14.49 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.20), residues: 1914 helix: 2.08 (0.18), residues: 808 sheet: 0.43 (0.27), residues: 368 loop : -0.62 (0.23), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP E 211 HIS 0.004 0.001 HIS H 183 PHE 0.019 0.001 PHE E 235 TYR 0.023 0.001 TYR A 303 ARG 0.003 0.000 ARG H 219 Details of bonding type rmsd hydrogen bonds : bond 0.04166 ( 774) hydrogen bonds : angle 4.39641 ( 2244) SS BOND : bond 0.00502 ( 10) SS BOND : angle 2.62989 ( 20) covalent geometry : bond 0.00284 (15334) covalent geometry : angle 0.53283 (20783) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 158 time to evaluate : 2.118 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: R 143 ASP cc_start: 0.9083 (t70) cc_final: 0.8872 (t70) REVERT: C 143 ASP cc_start: 0.9078 (t70) cc_final: 0.8861 (t70) REVERT: A 211 LYS cc_start: 0.8228 (mmtm) cc_final: 0.7961 (mmtt) REVERT: A 297 TYR cc_start: 0.6681 (t80) cc_final: 0.6468 (t80) REVERT: A 341 ASP cc_start: 0.8799 (OUTLIER) cc_final: 0.8545 (m-30) REVERT: E 12 GLU cc_start: 0.9073 (pt0) cc_final: 0.8459 (pp20) REVERT: E 124 TYR cc_start: 0.7477 (m-10) cc_final: 0.7198 (m-10) REVERT: E 211 TRP cc_start: 0.6256 (m100) cc_final: 0.4913 (m100) REVERT: E 235 PHE cc_start: 0.5775 (t80) cc_final: 0.4572 (t80) REVERT: E 256 ARG cc_start: 0.6287 (mtm180) cc_final: 0.6021 (mmm-85) REVERT: E 339 TRP cc_start: 0.6653 (OUTLIER) cc_final: 0.4558 (m100) REVERT: G 36 ASP cc_start: 0.8899 (t0) cc_final: 0.8486 (t0) REVERT: F 297 TYR cc_start: 0.6708 (t80) cc_final: 0.6489 (t80) REVERT: F 341 ASP cc_start: 0.8785 (OUTLIER) cc_final: 0.8561 (m-30) REVERT: F 354 TYR cc_start: 0.7595 (t80) cc_final: 0.7325 (t80) REVERT: H 91 HIS cc_start: 0.6765 (m90) cc_final: 0.6490 (m-70) REVERT: H 211 TRP cc_start: 0.5745 (m100) cc_final: 0.5088 (m100) REVERT: H 235 PHE cc_start: 0.5657 (t80) cc_final: 0.4475 (t80) REVERT: H 256 ARG cc_start: 0.6368 (mtm180) cc_final: 0.6053 (mmm-85) REVERT: H 339 TRP cc_start: 0.6643 (OUTLIER) cc_final: 0.4575 (m100) REVERT: I 36 ASP cc_start: 0.8900 (t0) cc_final: 0.8493 (t0) outliers start: 42 outliers final: 28 residues processed: 189 average time/residue: 0.2646 time to fit residues: 74.9004 Evaluate side-chains 180 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 148 time to evaluate : 1.766 ------------------------------------------------------------------------------- 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 58 VAL 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 316 PHE Chi-restraints excluded: chain R residue 325 LEU Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 50 ASN Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 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 A residue 341 ASP Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 103 CYS Chi-restraints excluded: chain E residue 234 PHE Chi-restraints excluded: chain E residue 262 MET Chi-restraints excluded: chain E residue 278 PHE Chi-restraints excluded: chain E residue 339 TRP Chi-restraints excluded: chain F residue 49 ILE Chi-restraints excluded: chain F residue 341 ASP Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 103 CYS Chi-restraints excluded: chain H residue 234 PHE Chi-restraints excluded: chain H residue 262 MET Chi-restraints excluded: chain H residue 278 PHE Chi-restraints excluded: chain H residue 339 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 58 optimal weight: 1.9990 chunk 128 optimal weight: 7.9990 chunk 171 optimal weight: 0.8980 chunk 123 optimal weight: 20.0000 chunk 68 optimal weight: 0.8980 chunk 163 optimal weight: 4.9990 chunk 183 optimal weight: 6.9990 chunk 6 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 134 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.132349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.091513 restraints weight = 38413.738| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 3.33 r_work: 0.3208 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.5501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 15344 Z= 0.218 Angle : 0.614 7.340 20803 Z= 0.330 Chirality : 0.045 0.158 2440 Planarity : 0.004 0.064 2621 Dihedral : 4.379 46.133 2078 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.20 % Allowed : 15.53 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.20), residues: 1914 helix: 1.88 (0.18), residues: 806 sheet: 0.32 (0.27), residues: 372 loop : -0.68 (0.23), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP E 211 HIS 0.005 0.001 HIS C 247 PHE 0.021 0.002 PHE D 62 TYR 0.013 0.001 TYR F 303 ARG 0.003 0.000 ARG A 313 Details of bonding type rmsd hydrogen bonds : bond 0.04970 ( 774) hydrogen bonds : angle 4.65114 ( 2244) SS BOND : bond 0.00545 ( 10) SS BOND : angle 2.96463 ( 20) covalent geometry : bond 0.00517 (15334) covalent geometry : angle 0.60721 (20783) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 157 time to evaluate : 1.830 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: A 211 LYS cc_start: 0.8308 (mmtm) cc_final: 0.8051 (mmtt) REVERT: A 297 TYR cc_start: 0.6743 (t80) cc_final: 0.6530 (t80) REVERT: A 341 ASP cc_start: 0.8841 (OUTLIER) cc_final: 0.8606 (m-30) REVERT: E 124 TYR cc_start: 0.7473 (m-10) cc_final: 0.7198 (m-10) REVERT: E 211 TRP cc_start: 0.6184 (m100) cc_final: 0.4965 (m100) REVERT: E 235 PHE cc_start: 0.6093 (t80) cc_final: 0.4848 (t80) REVERT: E 256 ARG cc_start: 0.6505 (mtm180) cc_final: 0.6145 (mmm-85) REVERT: E 339 TRP cc_start: 0.6786 (OUTLIER) cc_final: 0.4568 (m100) REVERT: G 36 ASP cc_start: 0.8865 (t0) cc_final: 0.8458 (t0) REVERT: F 297 TYR cc_start: 0.6702 (t80) cc_final: 0.6470 (t80) REVERT: F 341 ASP cc_start: 0.8821 (OUTLIER) cc_final: 0.8592 (m-30) REVERT: H 235 PHE cc_start: 0.5969 (t80) cc_final: 0.4798 (t80) REVERT: H 256 ARG cc_start: 0.6481 (mtm180) cc_final: 0.6189 (mmm-85) REVERT: H 339 TRP cc_start: 0.6772 (OUTLIER) cc_final: 0.4583 (m100) REVERT: I 27 ARG cc_start: 0.6383 (mtp180) cc_final: 0.6003 (mtp180) REVERT: I 36 ASP cc_start: 0.8864 (t0) cc_final: 0.8470 (t0) outliers start: 36 outliers final: 22 residues processed: 186 average time/residue: 0.2762 time to fit residues: 76.6874 Evaluate side-chains 174 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 148 time to evaluate : 1.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 50 ASN Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 304 ILE Chi-restraints excluded: chain R residue 316 PHE Chi-restraints excluded: chain R residue 325 LEU Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 50 ASN Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 304 ILE Chi-restraints excluded: chain C residue 316 PHE Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 103 CYS Chi-restraints excluded: chain E residue 137 ARG Chi-restraints excluded: chain E residue 262 MET Chi-restraints excluded: chain E residue 278 PHE Chi-restraints excluded: chain E residue 339 TRP Chi-restraints excluded: chain F residue 49 ILE Chi-restraints excluded: chain F residue 341 ASP Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 103 CYS Chi-restraints excluded: chain H residue 278 PHE Chi-restraints excluded: chain H residue 339 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 52 optimal weight: 0.5980 chunk 22 optimal weight: 0.5980 chunk 187 optimal weight: 10.0000 chunk 43 optimal weight: 0.9980 chunk 0 optimal weight: 0.9980 chunk 100 optimal weight: 6.9990 chunk 32 optimal weight: 0.7980 chunk 102 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 28 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 ASN G 18 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.133457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 91)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.093523 restraints weight = 38676.965| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 3.15 r_work: 0.3245 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.5563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15344 Z= 0.134 Angle : 0.563 8.852 20803 Z= 0.302 Chirality : 0.043 0.152 2440 Planarity : 0.004 0.064 2621 Dihedral : 4.257 47.538 2078 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.02 % Allowed : 15.95 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.20), residues: 1914 helix: 2.03 (0.18), residues: 808 sheet: 0.53 (0.26), residues: 394 loop : -0.64 (0.24), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 211 HIS 0.004 0.001 HIS H 183 PHE 0.023 0.001 PHE E 235 TYR 0.019 0.001 TYR F 303 ARG 0.005 0.000 ARG A 313 Details of bonding type rmsd hydrogen bonds : bond 0.04320 ( 774) hydrogen bonds : angle 4.47335 ( 2244) SS BOND : bond 0.00509 ( 10) SS BOND : angle 2.61159 ( 20) covalent geometry : bond 0.00313 (15334) covalent geometry : angle 0.55740 (20783) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 161 time to evaluate : 1.838 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: R 143 ASP cc_start: 0.9124 (t70) cc_final: 0.8919 (t70) REVERT: C 143 ASP cc_start: 0.9126 (t70) cc_final: 0.8920 (t70) REVERT: A 341 ASP cc_start: 0.8748 (OUTLIER) cc_final: 0.8502 (m-30) REVERT: E 59 TYR cc_start: 0.6744 (m-10) cc_final: 0.6298 (m-10) REVERT: E 124 TYR cc_start: 0.7418 (m-10) cc_final: 0.7197 (m-10) REVERT: E 211 TRP cc_start: 0.6045 (m100) cc_final: 0.4702 (m100) REVERT: E 235 PHE cc_start: 0.6064 (t80) cc_final: 0.4920 (t80) REVERT: E 256 ARG cc_start: 0.6370 (mtm180) cc_final: 0.6082 (mmm-85) REVERT: E 339 TRP cc_start: 0.6897 (OUTLIER) cc_final: 0.4597 (m100) REVERT: G 36 ASP cc_start: 0.8842 (t0) cc_final: 0.8450 (t0) REVERT: F 341 ASP cc_start: 0.8739 (OUTLIER) cc_final: 0.8503 (m-30) REVERT: H 59 TYR cc_start: 0.6688 (m-10) cc_final: 0.6232 (m-10) REVERT: H 211 TRP cc_start: 0.5769 (m100) cc_final: 0.5037 (m100) REVERT: H 235 PHE cc_start: 0.6015 (t80) cc_final: 0.4856 (t80) REVERT: H 256 ARG cc_start: 0.6366 (mtm180) cc_final: 0.6041 (mmm-85) REVERT: H 339 TRP cc_start: 0.6854 (OUTLIER) cc_final: 0.4584 (m100) REVERT: I 27 ARG cc_start: 0.6419 (mtp180) cc_final: 0.6030 (mtp180) REVERT: I 36 ASP cc_start: 0.8855 (t0) cc_final: 0.8471 (t0) outliers start: 33 outliers final: 25 residues processed: 184 average time/residue: 0.2960 time to fit residues: 81.1244 Evaluate side-chains 179 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 150 time to evaluate : 2.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 50 ASN Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 304 ILE Chi-restraints excluded: chain R residue 316 PHE Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 50 ASN Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 304 ILE Chi-restraints excluded: chain C residue 316 PHE Chi-restraints excluded: chain C residue 323 HIS Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 103 CYS Chi-restraints excluded: chain E residue 137 ARG Chi-restraints excluded: chain E residue 262 MET Chi-restraints excluded: chain E residue 278 PHE Chi-restraints excluded: chain E residue 339 TRP Chi-restraints excluded: chain F residue 49 ILE Chi-restraints excluded: chain F residue 341 ASP Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 103 CYS Chi-restraints excluded: chain H residue 262 MET Chi-restraints excluded: chain H residue 278 PHE Chi-restraints excluded: chain H residue 339 TRP Chi-restraints excluded: chain I residue 31 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 142 optimal weight: 2.9990 chunk 117 optimal weight: 9.9990 chunk 45 optimal weight: 4.9990 chunk 46 optimal weight: 0.5980 chunk 150 optimal weight: 0.4980 chunk 103 optimal weight: 2.9990 chunk 186 optimal weight: 8.9990 chunk 170 optimal weight: 0.8980 chunk 54 optimal weight: 0.7980 chunk 57 optimal weight: 0.7980 chunk 137 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 91 HIS H 91 HIS I 18 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.133610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.093258 restraints weight = 38704.175| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 3.23 r_work: 0.3249 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.5687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15344 Z= 0.135 Angle : 0.565 7.794 20803 Z= 0.304 Chirality : 0.043 0.193 2440 Planarity : 0.004 0.064 2621 Dihedral : 4.181 48.018 2078 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.96 % Allowed : 15.89 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.20), residues: 1914 helix: 2.11 (0.18), residues: 806 sheet: 0.54 (0.27), residues: 370 loop : -0.64 (0.23), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 211 HIS 0.004 0.001 HIS H 183 PHE 0.024 0.001 PHE E 235 TYR 0.012 0.001 TYR F 303 ARG 0.005 0.000 ARG A 313 Details of bonding type rmsd hydrogen bonds : bond 0.04272 ( 774) hydrogen bonds : angle 4.43139 ( 2244) SS BOND : bond 0.00514 ( 10) SS BOND : angle 2.58103 ( 20) covalent geometry : bond 0.00314 (15334) covalent geometry : angle 0.55980 (20783) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 161 time to evaluate : 1.657 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 341 ASP cc_start: 0.8731 (OUTLIER) cc_final: 0.8507 (m-30) REVERT: E 12 GLU cc_start: 0.8702 (pp20) cc_final: 0.8035 (pp20) REVERT: E 59 TYR cc_start: 0.6766 (m-10) cc_final: 0.6366 (m-10) REVERT: E 124 TYR cc_start: 0.7422 (m-10) cc_final: 0.7205 (m-10) REVERT: E 235 PHE cc_start: 0.6124 (t80) cc_final: 0.5028 (t80) REVERT: E 256 ARG cc_start: 0.6372 (mtm180) cc_final: 0.6049 (mmm-85) REVERT: E 339 TRP cc_start: 0.6892 (OUTLIER) cc_final: 0.4596 (m100) REVERT: G 36 ASP cc_start: 0.8822 (t0) cc_final: 0.8485 (t0) REVERT: H 12 GLU cc_start: 0.8961 (pp20) cc_final: 0.8180 (pp20) REVERT: H 59 TYR cc_start: 0.6667 (m-10) cc_final: 0.6283 (m-10) REVERT: H 235 PHE cc_start: 0.6079 (t80) cc_final: 0.4965 (t80) REVERT: H 339 TRP cc_start: 0.6883 (OUTLIER) cc_final: 0.4599 (m100) REVERT: I 27 ARG cc_start: 0.6428 (mtp180) cc_final: 0.6074 (mtp180) outliers start: 32 outliers final: 27 residues processed: 184 average time/residue: 0.2721 time to fit residues: 74.7058 Evaluate side-chains 177 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 147 time to evaluate : 2.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 50 ASN Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 304 ILE Chi-restraints excluded: chain R residue 316 PHE Chi-restraints excluded: chain R residue 325 LEU Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 50 ASN Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 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 A residue 341 ASP Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 103 CYS Chi-restraints excluded: chain E residue 137 ARG Chi-restraints excluded: chain E residue 262 MET Chi-restraints excluded: chain E residue 278 PHE Chi-restraints excluded: chain E residue 339 TRP Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain F residue 49 ILE Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 103 CYS Chi-restraints excluded: chain H residue 262 MET Chi-restraints excluded: chain H residue 278 PHE Chi-restraints excluded: chain H residue 339 TRP Chi-restraints excluded: chain I residue 31 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 149 optimal weight: 4.9990 chunk 128 optimal weight: 6.9990 chunk 98 optimal weight: 5.9990 chunk 52 optimal weight: 0.9990 chunk 110 optimal weight: 10.0000 chunk 150 optimal weight: 0.6980 chunk 131 optimal weight: 0.1980 chunk 44 optimal weight: 2.9990 chunk 158 optimal weight: 9.9990 chunk 163 optimal weight: 5.9990 chunk 146 optimal weight: 4.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN E 91 HIS F 43 ASN ** H 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.131242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.089377 restraints weight = 38624.774| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 3.61 r_work: 0.3185 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.5978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 15344 Z= 0.267 Angle : 0.687 10.686 20803 Z= 0.368 Chirality : 0.047 0.203 2440 Planarity : 0.004 0.064 2621 Dihedral : 4.570 57.736 2078 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 2.14 % Allowed : 16.44 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.19), residues: 1914 helix: 1.72 (0.18), residues: 798 sheet: 0.35 (0.27), residues: 370 loop : -0.74 (0.23), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP E 211 HIS 0.007 0.001 HIS R 247 PHE 0.024 0.002 PHE D 33 TYR 0.018 0.002 TYR A 354 ARG 0.003 0.000 ARG C 144 Details of bonding type rmsd hydrogen bonds : bond 0.05380 ( 774) hydrogen bonds : angle 4.81888 ( 2244) SS BOND : bond 0.00567 ( 10) SS BOND : angle 3.06698 ( 20) covalent geometry : bond 0.00638 (15334) covalent geometry : angle 0.68121 (20783) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12283.32 seconds wall clock time: 210 minutes 4.43 seconds (12604.43 seconds total)