Starting phenix.real_space_refine on Thu May 15 05:06:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6v03_20968/05_2025/6v03_20968.cif Found real_map, /net/cci-nas-00/data/ceres_data/6v03_20968/05_2025/6v03_20968.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6v03_20968/05_2025/6v03_20968.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6v03_20968/05_2025/6v03_20968.map" model { file = "/net/cci-nas-00/data/ceres_data/6v03_20968/05_2025/6v03_20968.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6v03_20968/05_2025/6v03_20968.cif" } resolution = 3.3 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= 0.001 sd= 0.019 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 30 5.16 5 C 8371 2.51 5 N 2146 2.21 5 O 2261 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 49 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 12808 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2556 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 307, 2505 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 14, 'TRANS': 292} Conformer: "B" Number of residues, atoms: 307, 2505 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 14, 'TRANS': 292} bond proxies already assigned to first conformer: 2513 Chain: "B" Number of atoms: 2553 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 307, 2505 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 14, 'TRANS': 292} Conformer: "B" Number of residues, atoms: 307, 2505 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 14, 'TRANS': 292} bond proxies already assigned to first conformer: 2516 Chain: "C" Number of atoms: 2553 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 307, 2505 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 14, 'TRANS': 292} Conformer: "B" Number of residues, atoms: 307, 2505 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 14, 'TRANS': 292} bond proxies already assigned to first conformer: 2516 Chain: "D" Number of atoms: 2553 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 307, 2505 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 14, 'TRANS': 292} Conformer: "B" Number of residues, atoms: 307, 2505 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 14, 'TRANS': 292} bond proxies already assigned to first conformer: 2516 Chain: "E" Number of atoms: 2553 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 307, 2505 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 14, 'TRANS': 292} Conformer: "B" Number of residues, atoms: 307, 2505 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 14, 'TRANS': 292} bond proxies already assigned to first conformer: 2516 Chain: "A" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 8 Unusual residues: {'3CN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 8 Unusual residues: {'3CN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 8 Unusual residues: {'3CN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 8 Unusual residues: {'3CN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 8 Unusual residues: {'3CN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 11 residue: pdb=" N ATRP A 160 " occ=0.50 ... (26 atoms not shown) pdb=" CH2BTRP A 160 " occ=0.50 residue: pdb=" N AHIS A 169 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS A 169 " occ=0.50 residue: pdb=" N APHE A 282 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE A 282 " occ=0.50 residue: pdb=" N AHIS B 169 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS B 169 " occ=0.50 residue: pdb=" N APHE B 282 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE B 282 " occ=0.50 residue: pdb=" N AHIS C 169 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS C 169 " occ=0.50 residue: pdb=" N APHE C 282 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE C 282 " occ=0.50 residue: pdb=" N AHIS D 169 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS D 169 " occ=0.50 residue: pdb=" N APHE D 282 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE D 282 " occ=0.50 residue: pdb=" N AHIS E 169 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS E 169 " occ=0.50 residue: pdb=" N APHE E 282 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE E 282 " occ=0.50 Time building chain proxies: 12.94, per 1000 atoms: 1.01 Number of scatterers: 12808 At special positions: 0 Unit cell: (88.7841, 89.8802, 124.955, 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 30 16.00 O 2261 8.00 N 2146 7.00 C 8371 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.10 Conformation dependent library (CDL) restraints added in 3.1 seconds 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2960 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 18 sheets defined 28.6% alpha, 32.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.61 Creating SS restraints... Processing helix chain 'A' and resid 59 through 62 Processing helix chain 'A' and resid 63 through 68 removed outlier: 3.644A pdb=" N ASN A 68 " --> pdb=" O GLU A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 185 Processing helix chain 'A' and resid 201 through 204 Processing helix chain 'A' and resid 209 through 218 Processing helix chain 'A' and resid 219 through 224 removed outlier: 3.934A pdb=" N VAL A 222 " --> pdb=" O SER A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 232 removed outlier: 4.072A pdb=" N LEU A 232 " --> pdb=" O PHE A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 248 removed outlier: 3.936A pdb=" N LEU A 238 " --> pdb=" O THR A 234 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N PHE A 247 " --> pdb=" O VAL A 243 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N TYR A 248 " --> pdb=" O ALA A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 285 removed outlier: 3.956A pdb=" N MET A 265 " --> pdb=" O VAL A 261 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLY A 269 " --> pdb=" O MET A 265 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLY A 271 " --> pdb=" O ILE A 267 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER A 272 " --> pdb=" O ALA A 268 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ILE A 273 " --> pdb=" O GLY A 269 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ALA A 276 " --> pdb=" O SER A 272 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE A 277 " --> pdb=" O ILE A 273 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N APHE A 282 " --> pdb=" O LEU A 278 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ALA A 283 " --> pdb=" O LEU A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 299 removed outlier: 4.019A pdb=" N ARG A 299 " --> pdb=" O LEU A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 316 removed outlier: 3.914A pdb=" N ALA A 310 " --> pdb=" O LEU A 306 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ILE A 311 " --> pdb=" O GLY A 307 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N VAL A 316 " --> pdb=" O GLY A 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 69 removed outlier: 3.710A pdb=" N ASN B 69 " --> pdb=" O ARG B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 204 Processing helix chain 'B' and resid 209 through 218 Processing helix chain 'B' and resid 219 through 224 removed outlier: 4.004A pdb=" N VAL B 222 " --> pdb=" O SER B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 248 removed outlier: 4.106A pdb=" N GLN B 233 " --> pdb=" O SER B 229 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU B 240 " --> pdb=" O PHE B 236 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR B 241 " --> pdb=" O THR B 237 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA B 246 " --> pdb=" O VAL B 242 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N PHE B 247 " --> pdb=" O VAL B 243 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N TYR B 248 " --> pdb=" O ALA B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 282 removed outlier: 3.511A pdb=" N MET B 265 " --> pdb=" O VAL B 261 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE B 273 " --> pdb=" O GLY B 269 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N APHE B 282 " --> pdb=" O LEU B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 317 removed outlier: 4.177A pdb=" N GLY B 312 " --> pdb=" O PHE B 308 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N CYS B 313 " --> pdb=" O LEU B 309 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL B 314 " --> pdb=" O ALA B 310 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU B 315 " --> pdb=" O ILE B 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 61 No H-bonds generated for 'chain 'C' and resid 59 through 61' Processing helix chain 'C' and resid 62 through 70 removed outlier: 3.619A pdb=" N TRP C 66 " --> pdb=" O GLN C 62 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ASN C 68 " --> pdb=" O GLU C 64 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLY C 70 " --> pdb=" O TRP C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 157 removed outlier: 4.121A pdb=" N GLU C 156 " --> pdb=" O ASP C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 179 removed outlier: 3.538A pdb=" N SER C 179 " --> pdb=" O ASP C 176 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 176 through 179' Processing helix chain 'C' and resid 209 through 218 Processing helix chain 'C' and resid 219 through 224 removed outlier: 4.011A pdb=" N VAL C 222 " --> pdb=" O SER C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 248 removed outlier: 3.671A pdb=" N LEU C 232 " --> pdb=" O PHE C 228 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N GLN C 233 " --> pdb=" O SER C 229 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N THR C 234 " --> pdb=" O GLU C 230 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N SER C 235 " --> pdb=" O ARG C 231 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N PHE C 236 " --> pdb=" O LEU C 232 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU C 240 " --> pdb=" O PHE C 236 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR C 241 " --> pdb=" O THR C 237 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N PHE C 247 " --> pdb=" O VAL C 243 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TYR C 248 " --> pdb=" O ALA C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 286 removed outlier: 3.655A pdb=" N APHE C 282 " --> pdb=" O LEU C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 311 removed outlier: 3.629A pdb=" N LEU C 309 " --> pdb=" O PRO C 305 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE C 311 " --> pdb=" O GLY C 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 70 removed outlier: 3.568A pdb=" N TRP D 66 " --> pdb=" O GLN D 62 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASN D 68 " --> pdb=" O GLU D 64 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASN D 69 " --> pdb=" O ARG D 65 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY D 70 " --> pdb=" O TRP D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 201 through 204 Processing helix chain 'D' and resid 209 through 218 Processing helix chain 'D' and resid 219 through 224 removed outlier: 3.808A pdb=" N VAL D 222 " --> pdb=" O SER D 219 " (cutoff:3.500A) Processing helix chain 'D' and resid 232 through 248 removed outlier: 3.964A pdb=" N LEU D 238 " --> pdb=" O THR D 234 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N PHE D 247 " --> pdb=" O VAL D 243 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N TYR D 248 " --> pdb=" O ALA D 244 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 282 removed outlier: 3.626A pdb=" N ILE D 273 " --> pdb=" O GLY D 269 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N APHE D 282 " --> pdb=" O LEU D 278 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 308 removed outlier: 4.123A pdb=" N LEU D 306 " --> pdb=" O LEU D 302 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N PHE D 308 " --> pdb=" O PHE D 304 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 313 removed outlier: 4.379A pdb=" N GLY D 312 " --> pdb=" O PHE D 308 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N CYS D 313 " --> pdb=" O LEU D 309 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 308 through 313' Processing helix chain 'E' and resid 62 through 70 removed outlier: 3.933A pdb=" N ASN E 68 " --> pdb=" O GLU E 64 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASN E 69 " --> pdb=" O ARG E 65 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLY E 70 " --> pdb=" O TRP E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 201 through 204 Processing helix chain 'E' and resid 209 through 220 removed outlier: 3.668A pdb=" N ALA E 217 " --> pdb=" O GLY E 213 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N TRP E 220 " --> pdb=" O ILE E 216 " (cutoff:3.500A) Processing helix chain 'E' and resid 221 through 224 Processing helix chain 'E' and resid 227 through 232 removed outlier: 3.828A pdb=" N LEU E 232 " --> pdb=" O PHE E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 232 through 237 Processing helix chain 'E' and resid 238 through 243 removed outlier: 3.616A pdb=" N VAL E 243 " --> pdb=" O MET E 239 " (cutoff:3.500A) Processing helix chain 'E' and resid 243 through 248 removed outlier: 3.875A pdb=" N PHE E 247 " --> pdb=" O VAL E 243 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N TYR E 248 " --> pdb=" O ALA E 244 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 243 through 248' Processing helix chain 'E' and resid 260 through 283 Processing helix chain 'E' and resid 308 through 313 removed outlier: 4.322A pdb=" N GLY E 312 " --> pdb=" O PHE E 308 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N CYS E 313 " --> pdb=" O LEU E 309 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 308 through 313' Processing sheet with id=AA1, first strand: chain 'A' and resid 56 through 58 removed outlier: 6.366A pdb=" N THR A 32 " --> pdb=" O GLY A 25 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N GLY A 25 " --> pdb=" O THR A 32 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N LYS A 34 " --> pdb=" O ILE A 23 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N ILE A 23 " --> pdb=" O LYS A 34 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N ASP A 36 " --> pdb=" O ASN A 21 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N THR A 44 " --> pdb=" O ASP A 13 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N ASP A 13 " --> pdb=" O THR A 44 " (cutoff:3.500A) removed outlier: 9.761A pdb=" N VAL A 12 " --> pdb=" O LEU A 140 " (cutoff:3.500A) removed outlier: 9.381A pdb=" N PHE A 142 " --> pdb=" O VAL A 12 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N VAL A 14 " --> pdb=" O PHE A 142 " (cutoff:3.500A) removed outlier: 8.650A pdb=" N ASP A 144 " --> pdb=" O VAL A 14 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N VAL A 16 " --> pdb=" O ASP A 144 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N GLN A 146 " --> pdb=" O VAL A 16 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ILE A 18 " --> pdb=" O GLN A 146 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 76 through 78 removed outlier: 6.633A pdb=" N SER A 189 " --> pdb=" O PRO A 132 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 76 through 78 removed outlier: 6.633A pdb=" N SER A 189 " --> pdb=" O PRO A 132 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 13 through 14 Processing sheet with id=AA5, first strand: chain 'B' and resid 56 through 58 removed outlier: 6.448A pdb=" N THR B 32 " --> pdb=" O GLY B 25 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N GLY B 25 " --> pdb=" O THR B 32 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N LYS B 34 " --> pdb=" O ILE B 23 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N ILE B 23 " --> pdb=" O LYS B 34 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N ASP B 36 " --> pdb=" O ASN B 21 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 76 through 78 removed outlier: 6.600A pdb=" N SER B 189 " --> pdb=" O PRO B 132 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 76 through 78 removed outlier: 6.600A pdb=" N SER B 189 " --> pdb=" O PRO B 132 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 56 through 58 removed outlier: 3.567A pdb=" N ILE C 101 " --> pdb=" O MET C 93 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N TYR C 33 " --> pdb=" O PHE C 110 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N THR C 32 " --> pdb=" O GLY C 25 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N GLY C 25 " --> pdb=" O THR C 32 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N LYS C 34 " --> pdb=" O ILE C 23 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N ILE C 23 " --> pdb=" O LYS C 34 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N ASP C 36 " --> pdb=" O ASN C 21 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N THR C 44 " --> pdb=" O ASP C 13 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N ASP C 13 " --> pdb=" O THR C 44 " (cutoff:3.500A) removed outlier: 9.552A pdb=" N VAL C 12 " --> pdb=" O LEU C 140 " (cutoff:3.500A) removed outlier: 9.371A pdb=" N PHE C 142 " --> pdb=" O VAL C 12 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N VAL C 14 " --> pdb=" O PHE C 142 " (cutoff:3.500A) removed outlier: 8.451A pdb=" N ASP C 144 " --> pdb=" O VAL C 14 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N VAL C 16 " --> pdb=" O ASP C 144 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N GLN C 146 " --> pdb=" O VAL C 16 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ILE C 18 " --> pdb=" O GLN C 146 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 76 through 78 removed outlier: 6.627A pdb=" N SER C 189 " --> pdb=" O PRO C 132 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 76 through 78 removed outlier: 6.627A pdb=" N SER C 189 " --> pdb=" O PRO C 132 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 56 through 58 removed outlier: 6.250A pdb=" N THR D 32 " --> pdb=" O GLY D 25 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N GLY D 25 " --> pdb=" O THR D 32 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N LYS D 34 " --> pdb=" O ILE D 23 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N ILE D 23 " --> pdb=" O LYS D 34 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ASP D 36 " --> pdb=" O ASN D 21 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N THR D 44 " --> pdb=" O ASP D 13 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ASP D 13 " --> pdb=" O THR D 44 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N VAL D 14 " --> pdb=" O PHE D 142 " (cutoff:3.500A) removed outlier: 8.610A pdb=" N ASP D 144 " --> pdb=" O VAL D 14 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N VAL D 16 " --> pdb=" O ASP D 144 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N GLN D 146 " --> pdb=" O VAL D 16 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ILE D 18 " --> pdb=" O GLN D 146 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 76 through 78 removed outlier: 4.134A pdb=" N ASP D 196 " --> pdb=" O ARG D 163 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 76 through 78 Processing sheet with id=AB5, first strand: chain 'D' and resid 172 through 174 Processing sheet with id=AB6, first strand: chain 'E' and resid 13 through 14 Processing sheet with id=AB7, first strand: chain 'E' and resid 56 through 58 removed outlier: 6.398A pdb=" N THR E 32 " --> pdb=" O GLY E 25 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N GLY E 25 " --> pdb=" O THR E 32 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N LYS E 34 " --> pdb=" O ILE E 23 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N ILE E 23 " --> pdb=" O LYS E 34 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N ASP E 36 " --> pdb=" O ASN E 21 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ILE E 18 " --> pdb=" O GLN E 146 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 76 through 78 Processing sheet with id=AB9, first strand: chain 'E' and resid 76 through 78 476 hydrogen bonds defined for protein. 1344 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.70 Time building geometry restraints manager: 3.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.05 - 1.20: 10 1.20 - 1.35: 4077 1.35 - 1.50: 3990 1.50 - 1.66: 5056 1.66 - 1.81: 50 Bond restraints: 13183 Sorted by residual: bond pdb=" CB 3CN B 402 " pdb=" CC 3CN B 402 " ideal model delta sigma weight residual 1.521 1.045 0.476 2.00e-02 2.50e+03 5.66e+02 bond pdb=" CB 3CN C 402 " pdb=" CC 3CN C 402 " ideal model delta sigma weight residual 1.521 1.045 0.476 2.00e-02 2.50e+03 5.66e+02 bond pdb=" CB 3CN E 402 " pdb=" CC 3CN E 402 " ideal model delta sigma weight residual 1.521 1.045 0.476 2.00e-02 2.50e+03 5.66e+02 bond pdb=" CB 3CN A 402 " pdb=" CC 3CN A 402 " ideal model delta sigma weight residual 1.521 1.046 0.475 2.00e-02 2.50e+03 5.64e+02 bond pdb=" CB 3CN D 402 " pdb=" CC 3CN D 402 " ideal model delta sigma weight residual 1.521 1.046 0.475 2.00e-02 2.50e+03 5.64e+02 ... (remaining 13178 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.90: 17663 1.90 - 3.79: 259 3.79 - 5.69: 35 5.69 - 7.58: 12 7.58 - 9.48: 15 Bond angle restraints: 17984 Sorted by residual: angle pdb=" N ASN B 60 " pdb=" CA ASN B 60 " pdb=" C ASN B 60 " ideal model delta sigma weight residual 111.02 115.41 -4.39 1.22e+00 6.72e-01 1.29e+01 angle pdb=" N ILE E 209 " pdb=" CA ILE E 209 " pdb=" C ILE E 209 " ideal model delta sigma weight residual 111.81 108.90 2.91 8.60e-01 1.35e+00 1.14e+01 angle pdb=" N ASN A 60 " pdb=" CA ASN A 60 " pdb=" C ASN A 60 " ideal model delta sigma weight residual 111.02 115.05 -4.03 1.22e+00 6.72e-01 1.09e+01 angle pdb=" C GLU B 59 " pdb=" N ASN B 60 " pdb=" CA ASN B 60 " ideal model delta sigma weight residual 120.79 125.22 -4.43 1.39e+00 5.18e-01 1.01e+01 angle pdb=" CA 3CN A 402 " pdb=" CB 3CN A 402 " pdb=" CC 3CN A 402 " ideal model delta sigma weight residual 112.40 102.98 9.42 3.00e+00 1.11e-01 9.87e+00 ... (remaining 17979 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 7028 17.81 - 35.61: 552 35.61 - 53.42: 114 53.42 - 71.23: 16 71.23 - 89.03: 5 Dihedral angle restraints: 7715 sinusoidal: 3110 harmonic: 4605 Sorted by residual: dihedral pdb=" CA ASN D 137 " pdb=" C ASN D 137 " pdb=" N GLN D 138 " pdb=" CA GLN D 138 " ideal model delta harmonic sigma weight residual 180.00 158.84 21.16 0 5.00e+00 4.00e-02 1.79e+01 dihedral pdb=" CA ASN A 137 " pdb=" C ASN A 137 " pdb=" N GLN A 138 " pdb=" CA GLN A 138 " ideal model delta harmonic sigma weight residual 180.00 159.24 20.76 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" CA LEU A 118 " pdb=" C LEU A 118 " pdb=" N PHE A 119 " pdb=" CA PHE A 119 " ideal model delta harmonic sigma weight residual -180.00 -159.30 -20.70 0 5.00e+00 4.00e-02 1.71e+01 ... (remaining 7712 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1027 0.030 - 0.061: 599 0.061 - 0.091: 203 0.091 - 0.121: 125 0.121 - 0.151: 21 Chirality restraints: 1975 Sorted by residual: chirality pdb=" CA VAL C 291 " pdb=" N VAL C 291 " pdb=" C VAL C 291 " pdb=" CB VAL C 291 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.72e-01 chirality pdb=" CA ILE C 195 " pdb=" N ILE C 195 " pdb=" C ILE C 195 " pdb=" CB ILE C 195 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.05e-01 chirality pdb=" CA ILE B 195 " pdb=" N ILE B 195 " pdb=" C ILE B 195 " pdb=" CB ILE B 195 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.62e-01 ... (remaining 1972 not shown) Planarity restraints: 2296 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS D 54 " -0.021 5.00e-02 4.00e+02 3.21e-02 1.64e+00 pdb=" N PRO D 55 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO D 55 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO D 55 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 54 " -0.021 5.00e-02 4.00e+02 3.18e-02 1.61e+00 pdb=" N PRO B 55 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO B 55 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 55 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS C 54 " -0.020 5.00e-02 4.00e+02 2.97e-02 1.41e+00 pdb=" N PRO C 55 " 0.051 5.00e-02 4.00e+02 pdb=" CA PRO C 55 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO C 55 " -0.017 5.00e-02 4.00e+02 ... (remaining 2293 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 2230 2.77 - 3.30: 11614 3.30 - 3.83: 20058 3.83 - 4.37: 24706 4.37 - 4.90: 43125 Nonbonded interactions: 101733 Sorted by model distance: nonbonded pdb=" OH TYR A 148 " pdb=" OD2 ASP B 176 " model vdw 2.234 3.040 nonbonded pdb=" OD2 ASP D 122 " pdb=" NH1 ARG D 199 " model vdw 2.236 3.120 nonbonded pdb=" O GLU B 150 " pdb=" ND2 ASN B 154 " model vdw 2.254 3.120 nonbonded pdb=" OD1 ASP A 115 " pdb=" NH1 ARG A 117 " model vdw 2.294 3.120 nonbonded pdb=" O ARG D 299 " pdb=" NH1 ARG D 299 " model vdw 2.301 3.120 ... (remaining 101728 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' and (resid 11 through 64 or resid 66 through 122 or resid 124 through \ 159 or resid 161 through 168 or resid 170 through 281 or resid 283 through 317 \ or resid 401 through 402)) selection = (chain 'B' and (resid 11 through 64 or resid 66 through 122 or resid 124 through \ 159 or resid 161 through 168 or resid 170 through 281 or resid 283 through 317 \ or resid 401 through 402)) selection = (chain 'C' and (resid 11 through 64 or resid 66 through 122 or resid 124 through \ 159 or resid 161 through 168 or resid 170 through 281 or resid 283 through 317 \ or resid 401 through 402)) selection = (chain 'D' and (resid 11 through 64 or resid 66 through 122 or resid 124 through \ 159 or resid 161 through 168 or resid 170 through 281 or resid 283 through 317 \ or resid 401 through 402)) selection = (chain 'E' and (resid 11 through 64 or resid 66 through 122 or resid 124 through \ 159 or resid 161 through 168 or resid 170 through 281 or resid 283 through 317 \ or resid 401 through 402)) } 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=0.50 max=1.00 mean=0.98 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: 0.480 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: 0.520 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 37.800 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 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 : 0.014 0.476 13183 Z= 0.677 Angle : 0.670 9.480 17984 Z= 0.352 Chirality : 0.047 0.151 1975 Planarity : 0.003 0.032 2296 Dihedral : 13.488 89.035 4755 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 0.79 % Allowed : 4.21 % Favored : 95.00 % 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: -4.30 (0.18), residues: 1572 helix: -3.03 (0.19), residues: 415 sheet: -1.93 (0.21), residues: 519 loop : -3.39 (0.22), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 224 HIS 0.006 0.001 HIS B 177 PHE 0.017 0.001 PHE D 142 TYR 0.007 0.001 TYR A 245 ARG 0.007 0.000 ARG A 199 Details of bonding type rmsd hydrogen bonds : bond 0.15586 ( 430) hydrogen bonds : angle 6.86434 ( 1344) covalent geometry : bond 0.01364 (13183) covalent geometry : angle 0.66962 (17984) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 1.494 Fit side-chains revert: symmetry clash REVERT: C 86 ASP cc_start: 0.7753 (t70) cc_final: 0.7489 (t70) REVERT: C 258 TYR cc_start: 0.8711 (p90) cc_final: 0.7962 (p90) REVERT: D 36 ASP cc_start: 0.8028 (t0) cc_final: 0.7728 (t0) REVERT: E 216 ILE cc_start: 0.7802 (mm) cc_final: 0.7496 (mt) REVERT: E 231 ARG cc_start: 0.7194 (mtp-110) cc_final: 0.6965 (mtp85) REVERT: E 247 PHE cc_start: 0.7463 (t80) cc_final: 0.7228 (t80) outliers start: 0 outliers final: 0 residues processed: 157 average time/residue: 0.2697 time to fit residues: 60.2657 Evaluate side-chains 131 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 1.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 126 optimal weight: 0.7980 chunk 113 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 117 optimal weight: 8.9990 chunk 45 optimal weight: 6.9990 chunk 71 optimal weight: 4.9990 chunk 87 optimal weight: 9.9990 chunk 136 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN A 69 ASN A 89 ASN ** A 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 151 ASN B 62 GLN B 124 GLN B 169 HIS B ** B 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 62 GLN C 284 HIS D 62 GLN D 151 ASN D 284 HIS E 60 ASN E 62 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.172944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.131149 restraints weight = 76942.891| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 3.85 r_work: 0.3049 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3044 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3044 r_free = 0.3044 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3042 r_free = 0.3042 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3042 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.0804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 13183 Z= 0.167 Angle : 0.594 8.009 17984 Z= 0.304 Chirality : 0.048 0.156 1975 Planarity : 0.004 0.038 2296 Dihedral : 5.215 30.277 1755 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 1.29 % Allowed : 8.86 % Favored : 89.86 % 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: -3.27 (0.20), residues: 1572 helix: -2.10 (0.22), residues: 428 sheet: -1.28 (0.22), residues: 532 loop : -2.91 (0.23), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 224 HIS 0.006 0.002 HIS B 177 PHE 0.029 0.001 PHE E 228 TYR 0.011 0.001 TYR B 270 ARG 0.005 0.001 ARG B 231 Details of bonding type rmsd hydrogen bonds : bond 0.03773 ( 430) hydrogen bonds : angle 5.13460 ( 1344) covalent geometry : bond 0.00405 (13183) covalent geometry : angle 0.59359 (17984) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 153 time to evaluate : 1.327 Fit side-chains revert: symmetry clash REVERT: A 284 HIS cc_start: 0.6409 (t70) cc_final: 0.6185 (t-90) REVERT: C 86 ASP cc_start: 0.8336 (t70) cc_final: 0.8091 (t70) REVERT: C 247 PHE cc_start: 0.7571 (t80) cc_final: 0.7201 (t80) REVERT: C 258 TYR cc_start: 0.8936 (p90) cc_final: 0.8031 (p90) REVERT: D 36 ASP cc_start: 0.8563 (t0) cc_final: 0.8360 (t0) REVERT: E 115 ASP cc_start: 0.8159 (t70) cc_final: 0.7919 (t0) REVERT: E 216 ILE cc_start: 0.7457 (mm) cc_final: 0.7203 (mt) REVERT: E 247 PHE cc_start: 0.7560 (t80) cc_final: 0.7331 (t80) outliers start: 7 outliers final: 3 residues processed: 155 average time/residue: 0.2630 time to fit residues: 58.1059 Evaluate side-chains 140 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 137 time to evaluate : 1.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 TYR Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain C residue 30 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 26 optimal weight: 3.9990 chunk 127 optimal weight: 0.5980 chunk 112 optimal weight: 10.0000 chunk 90 optimal weight: 5.9990 chunk 75 optimal weight: 7.9990 chunk 53 optimal weight: 9.9990 chunk 74 optimal weight: 7.9990 chunk 73 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 99 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 overall best weight: 2.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 ASN ** A 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 287 GLN C 284 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.170992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.127370 restraints weight = 66711.138| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 4.01 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3407 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3407 r_free = 0.3407 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3407 r_free = 0.3407 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3407 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.1051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 13183 Z= 0.226 Angle : 0.629 7.321 17984 Z= 0.324 Chirality : 0.049 0.150 1975 Planarity : 0.004 0.035 2296 Dihedral : 5.371 27.438 1755 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 1.93 % Allowed : 11.00 % Favored : 87.07 % 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: -2.85 (0.20), residues: 1572 helix: -1.78 (0.23), residues: 428 sheet: -0.94 (0.23), residues: 525 loop : -2.73 (0.23), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 43 HIS 0.008 0.002 HIS A 285 PHE 0.019 0.002 PHE D 228 TYR 0.011 0.001 TYR B 148 ARG 0.006 0.000 ARG D 190 Details of bonding type rmsd hydrogen bonds : bond 0.03716 ( 430) hydrogen bonds : angle 5.00281 ( 1344) covalent geometry : bond 0.00555 (13183) covalent geometry : angle 0.62941 (17984) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 137 time to evaluate : 1.296 Fit side-chains revert: symmetry clash REVERT: C 86 ASP cc_start: 0.7944 (t70) cc_final: 0.7712 (t70) REVERT: C 258 TYR cc_start: 0.8647 (p90) cc_final: 0.7982 (p90) REVERT: D 36 ASP cc_start: 0.8044 (t0) cc_final: 0.7801 (t0) REVERT: E 115 ASP cc_start: 0.7768 (t70) cc_final: 0.7536 (t0) REVERT: E 216 ILE cc_start: 0.7954 (mm) cc_final: 0.7754 (mt) REVERT: E 247 PHE cc_start: 0.7843 (t80) cc_final: 0.7616 (t80) outliers start: 15 outliers final: 8 residues processed: 145 average time/residue: 0.2596 time to fit residues: 53.9750 Evaluate side-chains 142 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 134 time to evaluate : 1.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain C residue 30 GLU Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain D residue 196 ASP Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 196 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 94 optimal weight: 0.8980 chunk 82 optimal weight: 9.9990 chunk 124 optimal weight: 0.8980 chunk 98 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 11 optimal weight: 0.0570 chunk 78 optimal weight: 0.9980 chunk 112 optimal weight: 3.9990 overall best weight: 0.9700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 138 GLN B 138 GLN ** C 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 GLN D 138 GLN E 69 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.173879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.129066 restraints weight = 74341.011| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 4.24 r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3444 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3444 r_free = 0.3444 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3444 r_free = 0.3444 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| r_final: 0.3444 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.1281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13183 Z= 0.116 Angle : 0.546 8.134 17984 Z= 0.277 Chirality : 0.046 0.151 1975 Planarity : 0.003 0.032 2296 Dihedral : 4.789 19.976 1755 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 1.79 % Allowed : 12.36 % Favored : 85.86 % 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: -2.28 (0.21), residues: 1572 helix: -1.48 (0.24), residues: 430 sheet: -0.49 (0.24), residues: 520 loop : -2.34 (0.24), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 224 HIS 0.009 0.002 HIS A 285 PHE 0.018 0.001 PHE D 228 TYR 0.010 0.001 TYR A 203 ARG 0.003 0.000 ARG D 255 Details of bonding type rmsd hydrogen bonds : bond 0.03165 ( 430) hydrogen bonds : angle 4.57440 ( 1344) covalent geometry : bond 0.00274 (13183) covalent geometry : angle 0.54564 (17984) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 158 time to evaluate : 1.399 Fit side-chains REVERT: B 159 GLU cc_start: 0.7245 (tt0) cc_final: 0.6987 (tp30) REVERT: C 86 ASP cc_start: 0.7942 (t70) cc_final: 0.7708 (t70) REVERT: C 258 TYR cc_start: 0.8658 (p90) cc_final: 0.7954 (p90) REVERT: D 36 ASP cc_start: 0.7983 (t0) cc_final: 0.7726 (t0) REVERT: D 258 TYR cc_start: 0.8447 (p90) cc_final: 0.7901 (p90) REVERT: E 115 ASP cc_start: 0.7789 (t70) cc_final: 0.7565 (t0) REVERT: E 247 PHE cc_start: 0.7770 (t80) cc_final: 0.7554 (t80) outliers start: 14 outliers final: 11 residues processed: 167 average time/residue: 0.2228 time to fit residues: 55.8416 Evaluate side-chains 160 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 149 time to evaluate : 1.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 138 GLN Chi-restraints excluded: chain B residue 138 GLN Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 245 TYR Chi-restraints excluded: chain C residue 30 GLU Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 138 GLN Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 147 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 81 optimal weight: 10.0000 chunk 54 optimal weight: 0.9980 chunk 31 optimal weight: 5.9990 chunk 77 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 112 optimal weight: 10.0000 chunk 117 optimal weight: 5.9990 chunk 133 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 115 optimal weight: 4.9990 chunk 76 optimal weight: 0.4980 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 284 HIS D 103 ASN D 233 GLN E 103 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.171309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.128612 restraints weight = 76322.657| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 3.93 r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3442 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3442 r_free = 0.3442 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3442 r_free = 0.3442 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 36 | |-----------------------------------------------------------------------------| r_final: 0.3442 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.1347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 13183 Z= 0.214 Angle : 0.610 7.318 17984 Z= 0.313 Chirality : 0.049 0.195 1975 Planarity : 0.004 0.034 2296 Dihedral : 5.091 22.464 1755 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 1.71 % Allowed : 13.43 % Favored : 84.86 % 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: -2.20 (0.21), residues: 1572 helix: -1.38 (0.24), residues: 430 sheet: -0.46 (0.24), residues: 517 loop : -2.30 (0.24), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 206 HIS 0.008 0.002 HIS A 285 PHE 0.039 0.002 PHE A 228 TYR 0.010 0.001 TYR A 148 ARG 0.003 0.000 ARG D 190 Details of bonding type rmsd hydrogen bonds : bond 0.03435 ( 430) hydrogen bonds : angle 4.74976 ( 1344) covalent geometry : bond 0.00526 (13183) covalent geometry : angle 0.61012 (17984) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 148 time to evaluate : 1.433 Fit side-chains REVERT: C 86 ASP cc_start: 0.7903 (t70) cc_final: 0.7694 (t70) REVERT: C 258 TYR cc_start: 0.8626 (p90) cc_final: 0.7965 (p90) REVERT: D 258 TYR cc_start: 0.8447 (p90) cc_final: 0.7988 (p90) REVERT: E 115 ASP cc_start: 0.7765 (t70) cc_final: 0.7534 (t0) REVERT: E 216 ILE cc_start: 0.7917 (mm) cc_final: 0.7647 (mt) outliers start: 12 outliers final: 10 residues processed: 157 average time/residue: 0.2392 time to fit residues: 55.2447 Evaluate side-chains 152 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 142 time to evaluate : 1.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain C residue 30 GLU Chi-restraints excluded: chain C residue 202 SER Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 196 ASP Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 147 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 28 optimal weight: 8.9990 chunk 112 optimal weight: 9.9990 chunk 101 optimal weight: 0.9980 chunk 21 optimal weight: 10.0000 chunk 146 optimal weight: 0.6980 chunk 68 optimal weight: 1.9990 chunk 31 optimal weight: 0.0870 chunk 3 optimal weight: 9.9990 chunk 127 optimal weight: 0.0020 chunk 107 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 overall best weight: 0.7568 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 138 GLN ** C 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 27 ASN E 103 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.175690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.121691 restraints weight = 62746.320| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 5.41 r_work: 0.3113 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3120 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3120 r_free = 0.3120 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 36 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3120 r_free = 0.3120 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3120 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.1565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 13183 Z= 0.105 Angle : 0.536 7.981 17984 Z= 0.271 Chirality : 0.046 0.153 1975 Planarity : 0.003 0.030 2296 Dihedral : 4.579 17.670 1755 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 1.64 % Allowed : 13.71 % Favored : 84.64 % 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: -1.68 (0.22), residues: 1572 helix: -0.91 (0.26), residues: 411 sheet: -0.20 (0.24), residues: 521 loop : -1.96 (0.24), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 206 HIS 0.008 0.002 HIS A 285 PHE 0.037 0.001 PHE A 228 TYR 0.011 0.001 TYR B 203 ARG 0.002 0.000 ARG D 255 Details of bonding type rmsd hydrogen bonds : bond 0.03011 ( 430) hydrogen bonds : angle 4.39748 ( 1344) covalent geometry : bond 0.00243 (13183) covalent geometry : angle 0.53558 (17984) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 160 time to evaluate : 1.551 Fit side-chains REVERT: B 159 GLU cc_start: 0.7346 (tt0) cc_final: 0.6785 (tp30) REVERT: C 86 ASP cc_start: 0.8305 (t70) cc_final: 0.8087 (t70) REVERT: C 186 ASN cc_start: 0.8482 (p0) cc_final: 0.8269 (p0) REVERT: C 247 PHE cc_start: 0.7394 (t80) cc_final: 0.7052 (t80) REVERT: C 258 TYR cc_start: 0.8782 (p90) cc_final: 0.7793 (p90) REVERT: D 239 MET cc_start: 0.7011 (tpp) cc_final: 0.6615 (mmt) REVERT: D 258 TYR cc_start: 0.8397 (p90) cc_final: 0.7680 (p90) REVERT: E 115 ASP cc_start: 0.7970 (t70) cc_final: 0.7683 (t0) outliers start: 12 outliers final: 11 residues processed: 168 average time/residue: 0.2372 time to fit residues: 59.3326 Evaluate side-chains 167 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 156 time to evaluate : 1.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain B residue 138 GLN Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 245 TYR Chi-restraints excluded: chain C residue 30 GLU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 147 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 21 optimal weight: 10.0000 chunk 35 optimal weight: 2.9990 chunk 138 optimal weight: 5.9990 chunk 69 optimal weight: 5.9990 chunk 67 optimal weight: 0.0270 chunk 89 optimal weight: 10.0000 chunk 145 optimal weight: 3.9990 chunk 43 optimal weight: 0.2980 chunk 77 optimal weight: 4.9990 overall best weight: 1.4644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 60 ASN C 60 ASN C 124 GLN C 284 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.173627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.129202 restraints weight = 82457.419| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 4.32 r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3435 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3435 r_free = 0.3435 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3435 r_free = 0.3435 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 36 | |-----------------------------------------------------------------------------| r_final: 0.3435 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 13183 Z= 0.142 Angle : 0.551 7.325 17984 Z= 0.281 Chirality : 0.047 0.221 1975 Planarity : 0.003 0.031 2296 Dihedral : 4.661 19.493 1755 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 1.64 % Allowed : 14.64 % Favored : 83.71 % 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: -1.57 (0.22), residues: 1572 helix: -0.81 (0.26), residues: 414 sheet: -0.10 (0.24), residues: 521 loop : -1.94 (0.24), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 206 HIS 0.009 0.002 HIS A 285 PHE 0.038 0.001 PHE A 228 TYR 0.009 0.001 TYR B 203 ARG 0.002 0.000 ARG D 255 Details of bonding type rmsd hydrogen bonds : bond 0.03082 ( 430) hydrogen bonds : angle 4.44496 ( 1344) covalent geometry : bond 0.00343 (13183) covalent geometry : angle 0.55056 (17984) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 151 time to evaluate : 1.359 Fit side-chains REVERT: B 159 GLU cc_start: 0.7219 (tt0) cc_final: 0.6985 (tp30) REVERT: C 86 ASP cc_start: 0.7964 (t70) cc_final: 0.7744 (t70) REVERT: C 247 PHE cc_start: 0.7780 (t80) cc_final: 0.7480 (t80) REVERT: C 258 TYR cc_start: 0.8624 (p90) cc_final: 0.7908 (p90) REVERT: D 258 TYR cc_start: 0.8339 (p90) cc_final: 0.7851 (p90) REVERT: E 115 ASP cc_start: 0.7673 (t70) cc_final: 0.7453 (t0) outliers start: 12 outliers final: 11 residues processed: 159 average time/residue: 0.2451 time to fit residues: 57.7908 Evaluate side-chains 159 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 148 time to evaluate : 1.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 141 ARG Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain C residue 30 GLU Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 147 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.7042 > 50: distance: 65 - 70: 34.599 distance: 70 - 71: 41.075 distance: 71 - 72: 40.201 distance: 71 - 74: 55.903 distance: 72 - 73: 68.255 distance: 72 - 76: 39.107 distance: 74 - 75: 41.253 distance: 76 - 77: 41.085 distance: 77 - 78: 57.958 distance: 77 - 80: 40.651 distance: 78 - 79: 24.183 distance: 78 - 84: 50.362 distance: 80 - 81: 11.485 distance: 81 - 82: 58.955 distance: 81 - 83: 26.639 distance: 84 - 85: 31.724 distance: 85 - 88: 70.812 distance: 86 - 87: 39.565 distance: 86 - 92: 70.120 distance: 88 - 89: 56.710 distance: 88 - 90: 40.570 distance: 89 - 91: 69.859 distance: 92 - 93: 42.141 distance: 93 - 94: 42.565 distance: 93 - 96: 22.861 distance: 94 - 95: 70.116 distance: 94 - 100: 41.854 distance: 96 - 97: 40.338 distance: 97 - 98: 59.558 distance: 97 - 99: 40.098 distance: 100 - 101: 49.777 distance: 100 - 106: 41.405 distance: 101 - 102: 30.766 distance: 101 - 104: 56.210 distance: 102 - 103: 58.161 distance: 102 - 107: 32.412 distance: 104 - 105: 40.014 distance: 105 - 106: 57.053 distance: 107 - 108: 57.648 distance: 108 - 109: 55.752 distance: 109 - 110: 38.861 distance: 111 - 112: 56.521 distance: 112 - 113: 57.283 distance: 113 - 114: 56.463 distance: 114 - 115: 40.680 distance: 115 - 116: 57.294 distance: 115 - 117: 56.766 distance: 118 - 119: 41.009 distance: 119 - 120: 57.592 distance: 119 - 122: 39.634 distance: 120 - 121: 70.198 distance: 120 - 126: 55.331 distance: 122 - 123: 68.378 distance: 123 - 124: 39.491 distance: 123 - 125: 41.257 distance: 126 - 127: 42.507 distance: 126 - 132: 50.316 distance: 127 - 128: 29.637 distance: 127 - 130: 40.838 distance: 128 - 129: 56.533 distance: 128 - 133: 39.983 distance: 130 - 131: 57.152 distance: 131 - 132: 57.358 distance: 133 - 134: 39.108 distance: 134 - 135: 49.841 distance: 135 - 136: 28.758 distance: 135 - 145: 42.365 distance: 137 - 138: 41.303 distance: 138 - 139: 44.096 distance: 138 - 140: 53.760 distance: 139 - 141: 35.860 distance: 140 - 142: 54.322 distance: 141 - 143: 28.067 distance: 142 - 143: 9.271 distance: 143 - 144: 66.229 distance: 146 - 147: 57.691 distance: 146 - 149: 56.428 distance: 147 - 148: 56.838 distance: 147 - 152: 34.063 distance: 149 - 150: 36.338 distance: 149 - 151: 52.305