Starting phenix.real_space_refine on Fri Feb 6 02:01:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9zbp_73996/02_2026/9zbp_73996.cif Found real_map, /net/cci-nas-00/data/ceres_data/9zbp_73996/02_2026/9zbp_73996.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9zbp_73996/02_2026/9zbp_73996.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9zbp_73996/02_2026/9zbp_73996.map" model { file = "/net/cci-nas-00/data/ceres_data/9zbp_73996/02_2026/9zbp_73996.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9zbp_73996/02_2026/9zbp_73996.cif" } resolution = 3.12 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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: 6 Type Number sf(0) Gaussians P 12 5.49 5 Mg 6 5.21 5 S 132 5.16 5 C 13504 2.51 5 N 3656 2.21 5 O 4260 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21570 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2897 Classifications: {'peptide': 371} Link IDs: {'PTRANS': 19, 'TRANS': 351} Chain: "B" Number of atoms: 2897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2897 Classifications: {'peptide': 371} Link IDs: {'PTRANS': 19, 'TRANS': 351} Chain: "C" Number of atoms: 2897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2897 Classifications: {'peptide': 371} Link IDs: {'PTRANS': 19, 'TRANS': 351} Chain: "D" Number of atoms: 2897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2897 Classifications: {'peptide': 371} Link IDs: {'PTRANS': 19, 'TRANS': 351} Chain: "E" Number of atoms: 2897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2897 Classifications: {'peptide': 371} Link IDs: {'PTRANS': 19, 'TRANS': 351} Chain: "F" Number of atoms: 2897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2897 Classifications: {'peptide': 371} Link IDs: {'PTRANS': 19, 'TRANS': 351} Chain: "M" Number of atoms: 1005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1005 Classifications: {'peptide': 124} Link IDs: {'TRANS': 123} Chain: "N" Number of atoms: 1005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1005 Classifications: {'peptide': 124} Link IDs: {'TRANS': 123} Chain: "O" Number of atoms: 1005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1005 Classifications: {'peptide': 124} Link IDs: {'TRANS': 123} Chain: "P" Number of atoms: 1005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1005 Classifications: {'peptide': 124} Link IDs: {'TRANS': 123} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.99, per 1000 atoms: 0.28 Number of scatterers: 21570 At special positions: 0 Unit cell: (98.79, 102.35, 218.94, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 132 16.00 P 12 15.00 Mg 6 11.99 O 4260 8.00 N 3656 7.00 C 13504 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.04 Conformation dependent library (CDL) restraints added in 1.2 seconds 5404 Ramachandran restraints generated. 2702 Oldfield, 0 Emsley, 2702 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5092 Finding SS restraints... Secondary structure from input PDB file: 131 helices and 36 sheets defined 59.9% alpha, 13.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.11 Creating SS restraints... Processing helix chain 'A' and resid 55 through 61 Processing helix chain 'A' and resid 78 through 92 Processing helix chain 'A' and resid 97 through 101 Processing helix chain 'A' and resid 112 through 127 removed outlier: 3.892A pdb=" N ARG A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 145 Processing helix chain 'A' and resid 172 through 175 Processing helix chain 'A' and resid 181 through 195 removed outlier: 3.962A pdb=" N GLU A 195 " --> pdb=" O LYS A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 216 Processing helix chain 'A' and resid 222 through 232 removed outlier: 3.658A pdb=" N SER A 232 " --> pdb=" O ALA A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 257 Processing helix chain 'A' and resid 258 through 262 Processing helix chain 'A' and resid 263 through 268 Processing helix chain 'A' and resid 273 through 285 Processing helix chain 'A' and resid 286 through 288 No H-bonds generated for 'chain 'A' and resid 286 through 288' Processing helix chain 'A' and resid 289 through 296 Processing helix chain 'A' and resid 302 through 306 removed outlier: 3.729A pdb=" N TYR A 306 " --> pdb=" O THR A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 321 Processing helix chain 'A' and resid 337 through 349 Processing helix chain 'A' and resid 350 through 356 removed outlier: 3.728A pdb=" N GLN A 354 " --> pdb=" O THR A 351 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N TRP A 356 " --> pdb=" O GLN A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 365 Processing helix chain 'A' and resid 368 through 374 removed outlier: 3.688A pdb=" N ARG A 372 " --> pdb=" O SER A 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 61 Processing helix chain 'B' and resid 78 through 92 Processing helix chain 'B' and resid 97 through 101 Processing helix chain 'B' and resid 112 through 127 removed outlier: 3.879A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 145 Processing helix chain 'B' and resid 172 through 175 Processing helix chain 'B' and resid 181 through 194 Processing helix chain 'B' and resid 195 through 197 No H-bonds generated for 'chain 'B' and resid 195 through 197' Processing helix chain 'B' and resid 202 through 216 Processing helix chain 'B' and resid 222 through 232 Processing helix chain 'B' and resid 252 through 257 Processing helix chain 'B' and resid 258 through 262 Processing helix chain 'B' and resid 263 through 268 Processing helix chain 'B' and resid 273 through 284 Processing helix chain 'B' and resid 289 through 296 Processing helix chain 'B' and resid 302 through 306 removed outlier: 3.706A pdb=" N TYR B 306 " --> pdb=" O THR B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 321 Processing helix chain 'B' and resid 337 through 349 Processing helix chain 'B' and resid 350 through 356 removed outlier: 3.813A pdb=" N GLN B 354 " --> pdb=" O THR B 351 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N TRP B 356 " --> pdb=" O GLN B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 365 Processing helix chain 'B' and resid 368 through 374 removed outlier: 3.787A pdb=" N ARG B 372 " --> pdb=" O SER B 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 61 Processing helix chain 'C' and resid 78 through 92 Processing helix chain 'C' and resid 97 through 101 Processing helix chain 'C' and resid 112 through 126 removed outlier: 3.891A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 145 Processing helix chain 'C' and resid 172 through 175 Processing helix chain 'C' and resid 181 through 195 removed outlier: 3.984A pdb=" N GLU C 195 " --> pdb=" O LYS C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 216 Processing helix chain 'C' and resid 222 through 232 removed outlier: 3.660A pdb=" N SER C 232 " --> pdb=" O ALA C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 257 Processing helix chain 'C' and resid 258 through 262 Processing helix chain 'C' and resid 263 through 268 Processing helix chain 'C' and resid 273 through 285 Processing helix chain 'C' and resid 289 through 296 Processing helix chain 'C' and resid 302 through 306 removed outlier: 3.732A pdb=" N TYR C 306 " --> pdb=" O THR C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 321 Processing helix chain 'C' and resid 334 through 336 No H-bonds generated for 'chain 'C' and resid 334 through 336' Processing helix chain 'C' and resid 337 through 349 Processing helix chain 'C' and resid 350 through 356 removed outlier: 3.798A pdb=" N GLN C 354 " --> pdb=" O THR C 351 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N TRP C 356 " --> pdb=" O GLN C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 365 Processing helix chain 'C' and resid 368 through 374 removed outlier: 3.797A pdb=" N ARG C 372 " --> pdb=" O SER C 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 61 Processing helix chain 'D' and resid 78 through 92 Processing helix chain 'D' and resid 97 through 101 Processing helix chain 'D' and resid 112 through 126 removed outlier: 3.921A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 145 Processing helix chain 'D' and resid 172 through 175 Processing helix chain 'D' and resid 181 through 194 Processing helix chain 'D' and resid 195 through 197 No H-bonds generated for 'chain 'D' and resid 195 through 197' Processing helix chain 'D' and resid 202 through 216 Processing helix chain 'D' and resid 222 through 232 removed outlier: 3.635A pdb=" N SER D 232 " --> pdb=" O ALA D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 257 Processing helix chain 'D' and resid 258 through 262 Processing helix chain 'D' and resid 263 through 268 Processing helix chain 'D' and resid 273 through 285 Processing helix chain 'D' and resid 286 through 295 removed outlier: 4.316A pdb=" N LYS D 291 " --> pdb=" O ILE D 287 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N ASP D 292 " --> pdb=" O ASP D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 306 removed outlier: 3.745A pdb=" N TYR D 306 " --> pdb=" O THR D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 321 Processing helix chain 'D' and resid 337 through 349 Processing helix chain 'D' and resid 350 through 355 removed outlier: 3.895A pdb=" N GLN D 354 " --> pdb=" O THR D 351 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 365 Processing helix chain 'D' and resid 368 through 374 removed outlier: 4.142A pdb=" N ARG D 372 " --> pdb=" O SER D 368 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 61 Processing helix chain 'E' and resid 78 through 92 Processing helix chain 'E' and resid 97 through 101 Processing helix chain 'E' and resid 112 through 127 removed outlier: 3.893A pdb=" N ARG E 116 " --> pdb=" O PRO E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 145 Processing helix chain 'E' and resid 172 through 175 Processing helix chain 'E' and resid 181 through 194 Processing helix chain 'E' and resid 195 through 197 No H-bonds generated for 'chain 'E' and resid 195 through 197' Processing helix chain 'E' and resid 202 through 216 Processing helix chain 'E' and resid 222 through 232 removed outlier: 3.625A pdb=" N SER E 232 " --> pdb=" O ALA E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 252 through 257 Processing helix chain 'E' and resid 258 through 262 Processing helix chain 'E' and resid 263 through 268 Processing helix chain 'E' and resid 273 through 285 Processing helix chain 'E' and resid 289 through 296 Processing helix chain 'E' and resid 302 through 306 removed outlier: 3.693A pdb=" N TYR E 306 " --> pdb=" O THR E 303 " (cutoff:3.500A) Processing helix chain 'E' and resid 308 through 321 Processing helix chain 'E' and resid 337 through 349 Processing helix chain 'E' and resid 350 through 355 removed outlier: 3.808A pdb=" N GLN E 354 " --> pdb=" O THR E 351 " (cutoff:3.500A) Processing helix chain 'E' and resid 359 through 365 Processing helix chain 'E' and resid 368 through 374 removed outlier: 3.915A pdb=" N ARG E 372 " --> pdb=" O SER E 368 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 61 Processing helix chain 'F' and resid 78 through 92 Processing helix chain 'F' and resid 97 through 101 Processing helix chain 'F' and resid 112 through 126 removed outlier: 3.846A pdb=" N ARG F 116 " --> pdb=" O PRO F 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 145 Processing helix chain 'F' and resid 172 through 175 Processing helix chain 'F' and resid 181 through 194 Processing helix chain 'F' and resid 195 through 197 No H-bonds generated for 'chain 'F' and resid 195 through 197' Processing helix chain 'F' and resid 202 through 216 Processing helix chain 'F' and resid 222 through 232 removed outlier: 3.681A pdb=" N SER F 232 " --> pdb=" O ALA F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 252 through 257 Processing helix chain 'F' and resid 258 through 262 Processing helix chain 'F' and resid 263 through 268 Processing helix chain 'F' and resid 273 through 285 Processing helix chain 'F' and resid 289 through 296 Processing helix chain 'F' and resid 302 through 306 removed outlier: 3.737A pdb=" N TYR F 306 " --> pdb=" O THR F 303 " (cutoff:3.500A) Processing helix chain 'F' and resid 308 through 321 Processing helix chain 'F' and resid 337 through 349 Processing helix chain 'F' and resid 350 through 355 removed outlier: 3.725A pdb=" N GLN F 354 " --> pdb=" O THR F 351 " (cutoff:3.500A) Processing helix chain 'F' and resid 359 through 365 Processing helix chain 'F' and resid 366 through 368 No H-bonds generated for 'chain 'F' and resid 366 through 368' Processing helix chain 'F' and resid 369 through 374 Processing helix chain 'M' and resid 103 through 225 removed outlier: 3.669A pdb=" N ILE M 225 " --> pdb=" O TYR M 221 " (cutoff:3.500A) Processing helix chain 'N' and resid 103 through 225 Processing helix chain 'O' and resid 103 through 225 Processing helix chain 'P' and resid 103 through 225 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32 removed outlier: 6.716A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.471A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.445A pdb=" N CYS A 10 " --> pdb=" O THR A 106 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AA3, first strand: chain 'A' and resid 71 through 72 Processing sheet with id=AA4, first strand: chain 'A' and resid 169 through 170 Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 170 removed outlier: 6.068A pdb=" N ILE A 151 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N SER A 300 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N LEU A 153 " --> pdb=" O SER A 300 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ASN A 297 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 238 through 241 Processing sheet with id=AA7, first strand: chain 'B' and resid 29 through 31 removed outlier: 6.764A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.506A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.417A pdb=" N CYS B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AA9, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AB1, first strand: chain 'B' and resid 169 through 170 Processing sheet with id=AB2, first strand: chain 'B' and resid 169 through 170 removed outlier: 6.143A pdb=" N ILE B 151 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N SER B 300 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N LEU B 153 " --> pdb=" O SER B 300 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ASN B 297 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 238 through 241 Processing sheet with id=AB4, first strand: chain 'C' and resid 29 through 31 removed outlier: 6.759A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.501A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.435A pdb=" N CYS C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB6, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AB7, first strand: chain 'C' and resid 169 through 170 Processing sheet with id=AB8, first strand: chain 'C' and resid 169 through 170 removed outlier: 6.251A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N LEU C 153 " --> pdb=" O SER C 300 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ASN C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AC1, first strand: chain 'D' and resid 29 through 32 removed outlier: 4.216A pdb=" N THR D 106 " --> pdb=" O CYS D 10 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N ASN D 12 " --> pdb=" O THR D 106 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AC3, first strand: chain 'D' and resid 71 through 72 Processing sheet with id=AC4, first strand: chain 'D' and resid 169 through 170 Processing sheet with id=AC5, first strand: chain 'D' and resid 169 through 170 removed outlier: 6.767A pdb=" N ASN D 297 " --> pdb=" O ILE D 330 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 238 through 241 Processing sheet with id=AC7, first strand: chain 'E' and resid 29 through 32 removed outlier: 6.746A pdb=" N LEU E 8 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 8.488A pdb=" N THR E 106 " --> pdb=" O LEU E 8 " (cutoff:3.500A) removed outlier: 8.454A pdb=" N CYS E 10 " --> pdb=" O THR E 106 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 53 through 54 removed outlier: 3.686A pdb=" N ARG E 37 " --> pdb=" O THR E 66 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 71 through 72 Processing sheet with id=AD1, first strand: chain 'E' and resid 169 through 170 Processing sheet with id=AD2, first strand: chain 'E' and resid 169 through 170 removed outlier: 6.282A pdb=" N ILE E 151 " --> pdb=" O VAL E 298 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N SER E 300 " --> pdb=" O ILE E 151 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N LEU E 153 " --> pdb=" O SER E 300 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ASN E 297 " --> pdb=" O ILE E 330 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 238 through 241 Processing sheet with id=AD4, first strand: chain 'F' and resid 29 through 32 removed outlier: 6.785A pdb=" N LEU F 8 " --> pdb=" O LEU F 104 " (cutoff:3.500A) removed outlier: 8.528A pdb=" N THR F 106 " --> pdb=" O LEU F 8 " (cutoff:3.500A) removed outlier: 8.421A pdb=" N CYS F 10 " --> pdb=" O THR F 106 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 53 through 54 Processing sheet with id=AD6, first strand: chain 'F' and resid 71 through 72 Processing sheet with id=AD7, first strand: chain 'F' and resid 169 through 170 Processing sheet with id=AD8, first strand: chain 'F' and resid 169 through 170 removed outlier: 6.782A pdb=" N ASN F 297 " --> pdb=" O ILE F 330 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 238 through 241 1369 hydrogen bonds defined for protein. 3687 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: 4.72 Time building geometry restraints manager: 2.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7190 1.34 - 1.46: 3588 1.46 - 1.58: 10940 1.58 - 1.69: 18 1.69 - 1.81: 230 Bond restraints: 21966 Sorted by residual: bond pdb=" C4 ADP E 401 " pdb=" C5 ADP E 401 " ideal model delta sigma weight residual 1.490 1.465 0.025 2.00e-02 2.50e+03 1.55e+00 bond pdb=" C4 ADP F 401 " pdb=" C5 ADP F 401 " ideal model delta sigma weight residual 1.490 1.466 0.024 2.00e-02 2.50e+03 1.49e+00 bond pdb=" C4 ADP C 401 " pdb=" C5 ADP C 401 " ideal model delta sigma weight residual 1.490 1.466 0.024 2.00e-02 2.50e+03 1.43e+00 bond pdb=" C4 ADP D 401 " pdb=" C5 ADP D 401 " ideal model delta sigma weight residual 1.490 1.466 0.024 2.00e-02 2.50e+03 1.42e+00 bond pdb=" C4 ADP B 401 " pdb=" C5 ADP B 401 " ideal model delta sigma weight residual 1.490 1.466 0.024 2.00e-02 2.50e+03 1.40e+00 ... (remaining 21961 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.22: 29332 2.22 - 4.45: 312 4.45 - 6.67: 63 6.67 - 8.89: 6 8.89 - 11.12: 3 Bond angle restraints: 29716 Sorted by residual: angle pdb=" CB ARG P 160 " pdb=" CG ARG P 160 " pdb=" CD ARG P 160 " ideal model delta sigma weight residual 111.30 121.56 -10.26 2.30e+00 1.89e-01 1.99e+01 angle pdb=" CA MET M 141 " pdb=" CB MET M 141 " pdb=" CG MET M 141 " ideal model delta sigma weight residual 114.10 121.17 -7.07 2.00e+00 2.50e-01 1.25e+01 angle pdb=" CA GLU M 208 " pdb=" CB GLU M 208 " pdb=" CG GLU M 208 " ideal model delta sigma weight residual 114.10 120.66 -6.56 2.00e+00 2.50e-01 1.08e+01 angle pdb=" CA MET O 141 " pdb=" CB MET O 141 " pdb=" CG MET O 141 " ideal model delta sigma weight residual 114.10 120.60 -6.50 2.00e+00 2.50e-01 1.06e+01 angle pdb=" CA LEU N 176 " pdb=" CB LEU N 176 " pdb=" CG LEU N 176 " ideal model delta sigma weight residual 116.30 127.42 -11.12 3.50e+00 8.16e-02 1.01e+01 ... (remaining 29711 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.61: 11284 17.61 - 35.23: 1468 35.23 - 52.84: 501 52.84 - 70.45: 100 70.45 - 88.07: 63 Dihedral angle restraints: 13416 sinusoidal: 5504 harmonic: 7912 Sorted by residual: dihedral pdb=" CA ASP F 288 " pdb=" CB ASP F 288 " pdb=" CG ASP F 288 " pdb=" OD1 ASP F 288 " ideal model delta sinusoidal sigma weight residual -30.00 -88.68 58.68 1 2.00e+01 2.50e-03 1.15e+01 dihedral pdb=" CA ASP F 80 " pdb=" CB ASP F 80 " pdb=" CG ASP F 80 " pdb=" OD1 ASP F 80 " ideal model delta sinusoidal sigma weight residual -30.00 -88.48 58.48 1 2.00e+01 2.50e-03 1.15e+01 dihedral pdb=" CA ASP O 137 " pdb=" CB ASP O 137 " pdb=" CG ASP O 137 " pdb=" OD1 ASP O 137 " ideal model delta sinusoidal sigma weight residual -30.00 -88.02 58.02 1 2.00e+01 2.50e-03 1.13e+01 ... (remaining 13413 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 2417 0.044 - 0.087: 630 0.087 - 0.131: 239 0.131 - 0.174: 7 0.174 - 0.218: 1 Chirality restraints: 3294 Sorted by residual: chirality pdb=" CB THR P 201 " pdb=" CA THR P 201 " pdb=" OG1 THR P 201 " pdb=" CG2 THR P 201 " both_signs ideal model delta sigma weight residual False 2.55 2.33 0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CB ILE O 130 " pdb=" CA ILE O 130 " pdb=" CG1 ILE O 130 " pdb=" CG2 ILE O 130 " both_signs ideal model delta sigma weight residual False 2.64 2.81 -0.17 2.00e-01 2.50e+01 6.99e-01 chirality pdb=" CA LYS O 140 " pdb=" N LYS O 140 " pdb=" C LYS O 140 " pdb=" CB LYS O 140 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.30e-01 ... (remaining 3291 not shown) Planarity restraints: 3844 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR O 221 " -0.022 2.00e-02 2.50e+03 2.07e-02 8.53e+00 pdb=" CG TYR O 221 " 0.051 2.00e-02 2.50e+03 pdb=" CD1 TYR O 221 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TYR O 221 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 TYR O 221 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR O 221 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR O 221 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR O 221 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU M 208 " -0.008 2.00e-02 2.50e+03 1.57e-02 2.47e+00 pdb=" CD GLU M 208 " 0.027 2.00e-02 2.50e+03 pdb=" OE1 GLU M 208 " -0.010 2.00e-02 2.50e+03 pdb=" OE2 GLU M 208 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR P 221 " -0.015 2.00e-02 2.50e+03 1.02e-02 2.10e+00 pdb=" CG TYR P 221 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 TYR P 221 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR P 221 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR P 221 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR P 221 " -0.007 2.00e-02 2.50e+03 pdb=" CZ TYR P 221 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR P 221 " -0.000 2.00e-02 2.50e+03 ... (remaining 3841 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 29 2.59 - 3.17: 18504 3.17 - 3.75: 35428 3.75 - 4.32: 48244 4.32 - 4.90: 80669 Nonbonded interactions: 182874 Sorted by model distance: nonbonded pdb=" O3B ADP A 401 " pdb="MG MG A 402 " model vdw 2.017 2.170 nonbonded pdb=" O3B ADP F 401 " pdb="MG MG F 402 " model vdw 2.022 2.170 nonbonded pdb=" O3B ADP B 401 " pdb="MG MG B 402 " model vdw 2.035 2.170 nonbonded pdb=" O3B ADP D 401 " pdb="MG MG D 402 " model vdw 2.081 2.170 nonbonded pdb=" O2B ADP C 401 " pdb="MG MG C 402 " model vdw 2.082 2.170 ... (remaining 182869 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' } 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: 2.800 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: 0.320 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 23.490 Find NCS groups from input model: 0.520 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:1.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8925 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 0.038 21966 Z= 0.182 Angle : 0.583 11.118 29716 Z= 0.287 Chirality : 0.043 0.218 3294 Planarity : 0.003 0.029 3844 Dihedral : 18.638 88.067 8324 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.60 % Allowed : 26.26 % Favored : 72.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.95 (0.17), residues: 2702 helix: 1.76 (0.14), residues: 1416 sheet: 0.65 (0.27), residues: 390 loop : 1.06 (0.22), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG P 160 TYR 0.051 0.001 TYR O 221 PHE 0.007 0.001 PHE F 255 TRP 0.009 0.001 TRP D 79 HIS 0.007 0.001 HIS P 153 Details of bonding type rmsd covalent geometry : bond 0.00405 (21966) covalent geometry : angle 0.58340 (29716) hydrogen bonds : bond 0.11446 ( 1357) hydrogen bonds : angle 5.15136 ( 3687) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5404 Ramachandran restraints generated. 2702 Oldfield, 0 Emsley, 2702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5404 Ramachandran restraints generated. 2702 Oldfield, 0 Emsley, 2702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 2308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 172 time to evaluate : 0.930 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 LEU cc_start: 0.9343 (OUTLIER) cc_final: 0.9075 (pp) REVERT: A 162 ASN cc_start: 0.8739 (t0) cc_final: 0.8450 (t0) REVERT: B 192 ILE cc_start: 0.9285 (tp) cc_final: 0.9031 (pt) REVERT: C 256 ARG cc_start: 0.9123 (OUTLIER) cc_final: 0.8802 (mtm180) REVERT: E 373 LYS cc_start: 0.9108 (OUTLIER) cc_final: 0.8860 (tptt) REVERT: F 64 ILE cc_start: 0.9700 (OUTLIER) cc_final: 0.9475 (pp) REVERT: F 78 ASN cc_start: 0.9081 (t0) cc_final: 0.8619 (t0) REVERT: F 225 ASN cc_start: 0.9403 (t0) cc_final: 0.9075 (t0) REVERT: F 297 ASN cc_start: 0.9250 (t0) cc_final: 0.9027 (t0) REVERT: M 127 MET cc_start: 0.7018 (tpp) cc_final: 0.6467 (mmm) REVERT: M 133 ARG cc_start: 0.8866 (tmm160) cc_final: 0.8467 (tmm160) REVERT: N 127 MET cc_start: 0.7740 (tpt) cc_final: 0.7267 (tpt) REVERT: N 130 ILE cc_start: 0.9260 (mm) cc_final: 0.8895 (tt) REVERT: N 153 HIS cc_start: 0.9501 (OUTLIER) cc_final: 0.9136 (p-80) REVERT: O 141 MET cc_start: 0.8092 (mmm) cc_final: 0.7547 (mmm) outliers start: 37 outliers final: 27 residues processed: 201 average time/residue: 0.1458 time to fit residues: 47.6605 Evaluate side-chains 202 residues out of total 2308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 170 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 256 ARG Chi-restraints excluded: chain C residue 344 SER Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain E residue 373 LYS Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 236 LEU Chi-restraints excluded: chain F residue 324 THR Chi-restraints excluded: chain F residue 344 SER Chi-restraints excluded: chain M residue 173 GLU Chi-restraints excluded: chain N residue 153 HIS Chi-restraints excluded: chain N residue 221 TYR Chi-restraints excluded: chain P residue 162 TYR Chi-restraints excluded: chain P residue 197 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 197 optimal weight: 0.0050 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 0.9980 chunk 111 optimal weight: 7.9990 overall best weight: 1.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 297 ASN ** F 162 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 = 0.3373 r_free = 0.3373 target = 0.091959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2654 r_free = 0.2654 target = 0.057837 restraints weight = 51488.525| |-----------------------------------------------------------------------------| r_work (start): 0.2571 rms_B_bonded: 2.76 r_work: 0.2393 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.0405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 21966 Z= 0.148 Angle : 0.530 6.312 29716 Z= 0.262 Chirality : 0.042 0.145 3294 Planarity : 0.003 0.027 3844 Dihedral : 5.982 55.659 3085 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.64 % Allowed : 24.74 % Favored : 72.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.24 (0.17), residues: 2702 helix: 2.03 (0.14), residues: 1356 sheet: 0.71 (0.27), residues: 390 loop : 1.24 (0.22), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 256 TYR 0.036 0.001 TYR O 221 PHE 0.006 0.001 PHE F 255 TRP 0.009 0.001 TRP D 79 HIS 0.007 0.001 HIS P 153 Details of bonding type rmsd covalent geometry : bond 0.00326 (21966) covalent geometry : angle 0.53027 (29716) hydrogen bonds : bond 0.04258 ( 1357) hydrogen bonds : angle 4.34561 ( 3687) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5404 Ramachandran restraints generated. 2702 Oldfield, 0 Emsley, 2702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5404 Ramachandran restraints generated. 2702 Oldfield, 0 Emsley, 2702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 173 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8747 (pp) REVERT: A 162 ASN cc_start: 0.8575 (t0) cc_final: 0.8304 (t0) REVERT: B 192 ILE cc_start: 0.9074 (tp) cc_final: 0.8780 (pt) REVERT: D 64 ILE cc_start: 0.9685 (OUTLIER) cc_final: 0.9432 (pp) REVERT: E 180 LEU cc_start: 0.9445 (OUTLIER) cc_final: 0.9183 (pt) REVERT: F 78 ASN cc_start: 0.8366 (t0) cc_final: 0.7753 (t0) REVERT: F 225 ASN cc_start: 0.9299 (t0) cc_final: 0.8995 (t0) REVERT: F 297 ASN cc_start: 0.9158 (t0) cc_final: 0.8881 (t0) REVERT: M 127 MET cc_start: 0.6883 (tpp) cc_final: 0.6442 (mmm) REVERT: M 133 ARG cc_start: 0.8896 (tmm160) cc_final: 0.8542 (tmm160) REVERT: M 148 LEU cc_start: 0.8087 (OUTLIER) cc_final: 0.7746 (mt) REVERT: M 162 TYR cc_start: 0.8946 (OUTLIER) cc_final: 0.8433 (t80) REVERT: N 127 MET cc_start: 0.7668 (tpt) cc_final: 0.7247 (tpp) REVERT: N 130 ILE cc_start: 0.9258 (mm) cc_final: 0.8858 (tt) REVERT: N 153 HIS cc_start: 0.9506 (OUTLIER) cc_final: 0.9194 (p-80) REVERT: N 190 CYS cc_start: 0.7993 (p) cc_final: 0.7730 (p) REVERT: O 141 MET cc_start: 0.8489 (mmm) cc_final: 0.8158 (mmm) outliers start: 61 outliers final: 31 residues processed: 223 average time/residue: 0.1448 time to fit residues: 53.5452 Evaluate side-chains 208 residues out of total 2308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 171 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 217 CYS Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 338 SER Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 71 ILE Chi-restraints excluded: chain F residue 132 MET Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 217 CYS Chi-restraints excluded: chain F residue 324 THR Chi-restraints excluded: chain F residue 351 THR Chi-restraints excluded: chain M residue 148 LEU Chi-restraints excluded: chain M residue 162 TYR Chi-restraints excluded: chain M residue 173 GLU Chi-restraints excluded: chain N residue 153 HIS Chi-restraints excluded: chain O residue 144 GLN Chi-restraints excluded: chain P residue 162 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 142 optimal weight: 5.9990 chunk 63 optimal weight: 5.9990 chunk 55 optimal weight: 4.9990 chunk 252 optimal weight: 8.9990 chunk 245 optimal weight: 20.0000 chunk 261 optimal weight: 5.9990 chunk 52 optimal weight: 9.9990 chunk 14 optimal weight: 10.0000 chunk 219 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 93 optimal weight: 6.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 101 HIS ** F 162 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 = 0.3330 r_free = 0.3330 target = 0.090421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2589 r_free = 0.2589 target = 0.055367 restraints weight = 52147.306| |-----------------------------------------------------------------------------| r_work (start): 0.2509 rms_B_bonded: 2.76 r_work: 0.2331 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.0695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 21966 Z= 0.291 Angle : 0.605 15.143 29716 Z= 0.298 Chirality : 0.045 0.182 3294 Planarity : 0.003 0.034 3844 Dihedral : 5.580 59.853 3051 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.47 % Allowed : 24.22 % Favored : 72.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.09 (0.17), residues: 2702 helix: 2.00 (0.14), residues: 1362 sheet: 0.64 (0.27), residues: 390 loop : 1.00 (0.21), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG P 160 TYR 0.038 0.001 TYR O 221 PHE 0.008 0.001 PHE E 127 TRP 0.013 0.002 TRP D 79 HIS 0.006 0.001 HIS P 153 Details of bonding type rmsd covalent geometry : bond 0.00670 (21966) covalent geometry : angle 0.60459 (29716) hydrogen bonds : bond 0.04532 ( 1357) hydrogen bonds : angle 4.34304 ( 3687) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5404 Ramachandran restraints generated. 2702 Oldfield, 0 Emsley, 2702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5404 Ramachandran restraints generated. 2702 Oldfield, 0 Emsley, 2702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 167 time to evaluate : 0.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 LEU cc_start: 0.9143 (OUTLIER) cc_final: 0.8809 (pp) REVERT: A 162 ASN cc_start: 0.8735 (t0) cc_final: 0.8503 (t0) REVERT: B 64 ILE cc_start: 0.9712 (OUTLIER) cc_final: 0.9338 (pp) REVERT: B 180 LEU cc_start: 0.9431 (OUTLIER) cc_final: 0.9208 (pt) REVERT: D 64 ILE cc_start: 0.9682 (OUTLIER) cc_final: 0.9413 (pp) REVERT: E 123 MET cc_start: 0.9190 (OUTLIER) cc_final: 0.7617 (mpm) REVERT: F 82 MET cc_start: 0.9196 (OUTLIER) cc_final: 0.8996 (tpt) REVERT: F 297 ASN cc_start: 0.9183 (t0) cc_final: 0.8909 (t0) REVERT: M 127 MET cc_start: 0.6844 (tpp) cc_final: 0.6454 (mmm) REVERT: M 133 ARG cc_start: 0.8927 (tmm160) cc_final: 0.8617 (tmm160) REVERT: M 162 TYR cc_start: 0.8924 (OUTLIER) cc_final: 0.8435 (t80) REVERT: M 173 GLU cc_start: 0.9604 (OUTLIER) cc_final: 0.9274 (mp0) REVERT: N 127 MET cc_start: 0.7597 (tpt) cc_final: 0.7197 (tpp) REVERT: N 130 ILE cc_start: 0.9230 (mm) cc_final: 0.8766 (tt) REVERT: N 153 HIS cc_start: 0.9485 (OUTLIER) cc_final: 0.9259 (p-80) REVERT: N 190 CYS cc_start: 0.7916 (p) cc_final: 0.7657 (p) REVERT: O 162 TYR cc_start: 0.8630 (OUTLIER) cc_final: 0.8333 (t80) outliers start: 80 outliers final: 38 residues processed: 233 average time/residue: 0.1399 time to fit residues: 53.7600 Evaluate side-chains 212 residues out of total 2308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 164 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 217 CYS Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 123 MET Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 338 SER Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 71 ILE Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 132 MET Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 216 LEU Chi-restraints excluded: chain F residue 217 CYS Chi-restraints excluded: chain F residue 324 THR Chi-restraints excluded: chain F residue 351 THR Chi-restraints excluded: chain M residue 162 TYR Chi-restraints excluded: chain M residue 173 GLU Chi-restraints excluded: chain N residue 153 HIS Chi-restraints excluded: chain O residue 144 GLN Chi-restraints excluded: chain O residue 162 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 124 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 122 optimal weight: 0.8980 chunk 169 optimal weight: 0.9990 chunk 201 optimal weight: 2.9990 chunk 257 optimal weight: 50.0000 chunk 142 optimal weight: 0.8980 chunk 28 optimal weight: 5.9990 chunk 266 optimal weight: 20.0000 chunk 242 optimal weight: 50.0000 chunk 56 optimal weight: 3.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.089287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2632 r_free = 0.2632 target = 0.053852 restraints weight = 51126.901| |-----------------------------------------------------------------------------| r_work (start): 0.2553 rms_B_bonded: 2.85 r_work: 0.2367 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.0693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 21966 Z= 0.152 Angle : 0.545 8.621 29716 Z= 0.268 Chirality : 0.042 0.173 3294 Planarity : 0.003 0.066 3844 Dihedral : 5.315 55.615 3046 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 3.12 % Allowed : 25.04 % Favored : 71.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.15 (0.17), residues: 2702 helix: 2.04 (0.14), residues: 1370 sheet: 0.66 (0.27), residues: 390 loop : 1.04 (0.21), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG O 133 TYR 0.027 0.001 TYR O 221 PHE 0.008 0.001 PHE E 127 TRP 0.011 0.001 TRP E 79 HIS 0.007 0.001 HIS P 153 Details of bonding type rmsd covalent geometry : bond 0.00334 (21966) covalent geometry : angle 0.54485 (29716) hydrogen bonds : bond 0.04248 ( 1357) hydrogen bonds : angle 4.20101 ( 3687) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5404 Ramachandran restraints generated. 2702 Oldfield, 0 Emsley, 2702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5404 Ramachandran restraints generated. 2702 Oldfield, 0 Emsley, 2702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 175 time to evaluate : 1.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8793 (pp) REVERT: A 162 ASN cc_start: 0.8692 (t0) cc_final: 0.8444 (t0) REVERT: B 64 ILE cc_start: 0.9725 (OUTLIER) cc_final: 0.9378 (pp) REVERT: C 78 ASN cc_start: 0.8690 (t0) cc_final: 0.8398 (t0) REVERT: C 128 ASN cc_start: 0.9139 (t0) cc_final: 0.8929 (t0) REVERT: D 64 ILE cc_start: 0.9684 (OUTLIER) cc_final: 0.9432 (pp) REVERT: F 64 ILE cc_start: 0.9544 (OUTLIER) cc_final: 0.9321 (pp) REVERT: F 78 ASN cc_start: 0.8379 (t0) cc_final: 0.7707 (t0) REVERT: F 225 ASN cc_start: 0.9313 (t0) cc_final: 0.9006 (t0) REVERT: F 297 ASN cc_start: 0.9161 (t0) cc_final: 0.8865 (t0) REVERT: M 127 MET cc_start: 0.6862 (tpp) cc_final: 0.6562 (mmm) REVERT: M 133 ARG cc_start: 0.8928 (tmm160) cc_final: 0.8624 (tmm160) REVERT: M 162 TYR cc_start: 0.8898 (OUTLIER) cc_final: 0.8428 (t80) REVERT: M 173 GLU cc_start: 0.9614 (OUTLIER) cc_final: 0.9312 (mp0) REVERT: N 127 MET cc_start: 0.7592 (tpt) cc_final: 0.7264 (tpp) REVERT: N 130 ILE cc_start: 0.9247 (mm) cc_final: 0.8854 (tt) REVERT: N 153 HIS cc_start: 0.9500 (OUTLIER) cc_final: 0.9269 (p-80) REVERT: N 190 CYS cc_start: 0.7933 (p) cc_final: 0.7670 (p) REVERT: O 141 MET cc_start: 0.8278 (mmm) cc_final: 0.7922 (mmm) REVERT: O 162 TYR cc_start: 0.8588 (OUTLIER) cc_final: 0.8322 (t80) REVERT: P 173 GLU cc_start: 0.9070 (OUTLIER) cc_final: 0.8831 (mm-30) outliers start: 72 outliers final: 41 residues processed: 230 average time/residue: 0.1406 time to fit residues: 53.6795 Evaluate side-chains 222 residues out of total 2308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 172 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 217 CYS Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 123 MET Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 338 SER Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 71 ILE Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 217 CYS Chi-restraints excluded: chain F residue 236 LEU Chi-restraints excluded: chain F residue 324 THR Chi-restraints excluded: chain F residue 351 THR Chi-restraints excluded: chain M residue 144 GLN Chi-restraints excluded: chain M residue 162 TYR Chi-restraints excluded: chain M residue 173 GLU Chi-restraints excluded: chain N residue 153 HIS Chi-restraints excluded: chain O residue 133 ARG Chi-restraints excluded: chain O residue 144 GLN Chi-restraints excluded: chain O residue 162 TYR Chi-restraints excluded: chain P residue 162 TYR Chi-restraints excluded: chain P residue 173 GLU Chi-restraints excluded: chain P residue 197 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 127 optimal weight: 1.9990 chunk 113 optimal weight: 0.5980 chunk 14 optimal weight: 10.0000 chunk 246 optimal weight: 20.0000 chunk 119 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 253 optimal weight: 20.0000 chunk 130 optimal weight: 5.9990 chunk 137 optimal weight: 6.9990 chunk 255 optimal weight: 10.0000 chunk 219 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.092433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2644 r_free = 0.2644 target = 0.057599 restraints weight = 51510.857| |-----------------------------------------------------------------------------| r_work (start): 0.2564 rms_B_bonded: 2.78 r_work: 0.2387 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.0729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 21966 Z= 0.135 Angle : 0.534 11.206 29716 Z= 0.261 Chirality : 0.042 0.183 3294 Planarity : 0.003 0.056 3844 Dihedral : 5.263 55.173 3046 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.86 % Allowed : 25.43 % Favored : 71.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.21 (0.17), residues: 2702 helix: 2.06 (0.14), residues: 1372 sheet: 0.68 (0.27), residues: 390 loop : 1.11 (0.22), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG O 133 TYR 0.044 0.001 TYR O 221 PHE 0.008 0.001 PHE E 127 TRP 0.009 0.001 TRP D 340 HIS 0.007 0.001 HIS P 153 Details of bonding type rmsd covalent geometry : bond 0.00294 (21966) covalent geometry : angle 0.53368 (29716) hydrogen bonds : bond 0.04121 ( 1357) hydrogen bonds : angle 4.10540 ( 3687) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5404 Ramachandran restraints generated. 2702 Oldfield, 0 Emsley, 2702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5404 Ramachandran restraints generated. 2702 Oldfield, 0 Emsley, 2702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 179 time to evaluate : 0.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8716 (pp) REVERT: A 162 ASN cc_start: 0.8654 (t0) cc_final: 0.8398 (t0) REVERT: B 64 ILE cc_start: 0.9723 (OUTLIER) cc_final: 0.9383 (pp) REVERT: B 180 LEU cc_start: 0.9422 (OUTLIER) cc_final: 0.9201 (pt) REVERT: C 78 ASN cc_start: 0.8666 (t0) cc_final: 0.8391 (t0) REVERT: C 113 LYS cc_start: 0.8613 (OUTLIER) cc_final: 0.8177 (mmtp) REVERT: C 128 ASN cc_start: 0.9135 (t0) cc_final: 0.8921 (t0) REVERT: C 244 ASP cc_start: 0.9165 (t0) cc_final: 0.8849 (t0) REVERT: D 64 ILE cc_start: 0.9694 (OUTLIER) cc_final: 0.9448 (pp) REVERT: F 64 ILE cc_start: 0.9557 (OUTLIER) cc_final: 0.9336 (pp) REVERT: F 225 ASN cc_start: 0.9314 (t0) cc_final: 0.9006 (t0) REVERT: F 297 ASN cc_start: 0.9169 (t0) cc_final: 0.8868 (t0) REVERT: M 127 MET cc_start: 0.6874 (tpp) cc_final: 0.6566 (mmm) REVERT: M 133 ARG cc_start: 0.8935 (tmm160) cc_final: 0.8669 (tmm160) REVERT: M 162 TYR cc_start: 0.8922 (OUTLIER) cc_final: 0.8445 (t80) REVERT: M 173 GLU cc_start: 0.9601 (OUTLIER) cc_final: 0.9294 (mp0) REVERT: N 127 MET cc_start: 0.7554 (tpt) cc_final: 0.7227 (tpp) REVERT: N 130 ILE cc_start: 0.9244 (mm) cc_final: 0.8868 (tt) REVERT: N 153 HIS cc_start: 0.9503 (OUTLIER) cc_final: 0.9242 (p-80) REVERT: N 190 CYS cc_start: 0.7925 (p) cc_final: 0.7657 (p) REVERT: O 141 MET cc_start: 0.8514 (mmm) cc_final: 0.8152 (mmm) REVERT: P 173 GLU cc_start: 0.9057 (OUTLIER) cc_final: 0.8821 (mm-30) outliers start: 66 outliers final: 43 residues processed: 229 average time/residue: 0.1291 time to fit residues: 48.7472 Evaluate side-chains 228 residues out of total 2308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 175 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 113 LYS Chi-restraints excluded: chain C residue 217 CYS Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 123 MET Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain E residue 338 SER Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 71 ILE Chi-restraints excluded: chain F residue 132 MET Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 217 CYS Chi-restraints excluded: chain F residue 236 LEU Chi-restraints excluded: chain F residue 324 THR Chi-restraints excluded: chain F residue 351 THR Chi-restraints excluded: chain M residue 162 TYR Chi-restraints excluded: chain M residue 173 GLU Chi-restraints excluded: chain N residue 153 HIS Chi-restraints excluded: chain N residue 221 TYR Chi-restraints excluded: chain O residue 133 ARG Chi-restraints excluded: chain O residue 144 GLN Chi-restraints excluded: chain P residue 162 TYR Chi-restraints excluded: chain P residue 173 GLU Chi-restraints excluded: chain P residue 197 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 61 optimal weight: 5.9990 chunk 219 optimal weight: 0.9990 chunk 66 optimal weight: 8.9990 chunk 189 optimal weight: 0.0970 chunk 235 optimal weight: 0.7980 chunk 175 optimal weight: 3.9990 chunk 215 optimal weight: 5.9990 chunk 224 optimal weight: 30.0000 chunk 197 optimal weight: 2.9990 chunk 9 optimal weight: 10.0000 chunk 122 optimal weight: 6.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 203 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.089709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2646 r_free = 0.2646 target = 0.054042 restraints weight = 51638.605| |-----------------------------------------------------------------------------| r_work (start): 0.2565 rms_B_bonded: 2.81 r_work: 0.2385 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.0768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 21966 Z= 0.147 Angle : 0.535 9.620 29716 Z= 0.262 Chirality : 0.042 0.191 3294 Planarity : 0.003 0.051 3844 Dihedral : 5.260 55.679 3046 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.90 % Allowed : 25.65 % Favored : 71.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.25 (0.17), residues: 2702 helix: 2.09 (0.14), residues: 1366 sheet: 0.68 (0.27), residues: 390 loop : 1.15 (0.22), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG O 133 TYR 0.038 0.001 TYR O 221 PHE 0.008 0.001 PHE E 127 TRP 0.009 0.001 TRP D 340 HIS 0.007 0.001 HIS P 153 Details of bonding type rmsd covalent geometry : bond 0.00325 (21966) covalent geometry : angle 0.53520 (29716) hydrogen bonds : bond 0.04098 ( 1357) hydrogen bonds : angle 4.07305 ( 3687) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5404 Ramachandran restraints generated. 2702 Oldfield, 0 Emsley, 2702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5404 Ramachandran restraints generated. 2702 Oldfield, 0 Emsley, 2702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 167 time to evaluate : 0.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8747 (pp) REVERT: A 162 ASN cc_start: 0.8642 (t0) cc_final: 0.8400 (t0) REVERT: B 64 ILE cc_start: 0.9719 (OUTLIER) cc_final: 0.9372 (pp) REVERT: B 180 LEU cc_start: 0.9420 (OUTLIER) cc_final: 0.9184 (pt) REVERT: B 192 ILE cc_start: 0.9051 (tp) cc_final: 0.8786 (pt) REVERT: C 113 LYS cc_start: 0.8631 (OUTLIER) cc_final: 0.8193 (mmtp) REVERT: D 64 ILE cc_start: 0.9690 (OUTLIER) cc_final: 0.9444 (pp) REVERT: F 64 ILE cc_start: 0.9558 (OUTLIER) cc_final: 0.9341 (pp) REVERT: F 297 ASN cc_start: 0.9171 (t0) cc_final: 0.8867 (t0) REVERT: M 127 MET cc_start: 0.6888 (tpp) cc_final: 0.6581 (mmm) REVERT: M 133 ARG cc_start: 0.8957 (OUTLIER) cc_final: 0.8701 (tmm160) REVERT: M 173 GLU cc_start: 0.9606 (OUTLIER) cc_final: 0.9296 (mp0) REVERT: N 127 MET cc_start: 0.7574 (tpt) cc_final: 0.7249 (tpp) REVERT: N 130 ILE cc_start: 0.9241 (mm) cc_final: 0.8859 (tt) REVERT: N 153 HIS cc_start: 0.9506 (OUTLIER) cc_final: 0.9266 (p-80) REVERT: N 190 CYS cc_start: 0.7938 (OUTLIER) cc_final: 0.7675 (p) outliers start: 67 outliers final: 48 residues processed: 216 average time/residue: 0.1387 time to fit residues: 49.2460 Evaluate side-chains 224 residues out of total 2308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 166 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 113 LYS Chi-restraints excluded: chain C residue 217 CYS Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 123 MET Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain E residue 338 SER Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 71 ILE Chi-restraints excluded: chain F residue 132 MET Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 217 CYS Chi-restraints excluded: chain F residue 236 LEU Chi-restraints excluded: chain F residue 324 THR Chi-restraints excluded: chain F residue 351 THR Chi-restraints excluded: chain M residue 133 ARG Chi-restraints excluded: chain M residue 173 GLU Chi-restraints excluded: chain N residue 153 HIS Chi-restraints excluded: chain N residue 174 SER Chi-restraints excluded: chain N residue 190 CYS Chi-restraints excluded: chain O residue 133 ARG Chi-restraints excluded: chain O residue 144 GLN Chi-restraints excluded: chain O residue 190 CYS Chi-restraints excluded: chain P residue 162 TYR Chi-restraints excluded: chain P residue 197 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 262 optimal weight: 20.0000 chunk 111 optimal weight: 7.9990 chunk 99 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 142 optimal weight: 0.9990 chunk 168 optimal weight: 0.5980 chunk 97 optimal weight: 0.9980 chunk 113 optimal weight: 0.3980 chunk 62 optimal weight: 0.6980 chunk 208 optimal weight: 5.9990 chunk 121 optimal weight: 4.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.093459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2679 r_free = 0.2679 target = 0.058795 restraints weight = 51044.971| |-----------------------------------------------------------------------------| r_work (start): 0.2596 rms_B_bonded: 2.79 r_work: 0.2420 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.0853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 21966 Z= 0.104 Angle : 0.522 9.208 29716 Z= 0.257 Chirality : 0.041 0.201 3294 Planarity : 0.003 0.045 3844 Dihedral : 5.185 53.247 3046 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.47 % Allowed : 26.30 % Favored : 71.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.36 (0.17), residues: 2702 helix: 2.13 (0.14), residues: 1354 sheet: 0.70 (0.27), residues: 390 loop : 1.31 (0.22), residues: 958 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG P 160 TYR 0.041 0.001 TYR O 221 PHE 0.009 0.001 PHE E 127 TRP 0.008 0.001 TRP A 79 HIS 0.007 0.001 HIS P 153 Details of bonding type rmsd covalent geometry : bond 0.00208 (21966) covalent geometry : angle 0.52239 (29716) hydrogen bonds : bond 0.03975 ( 1357) hydrogen bonds : angle 4.00221 ( 3687) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5404 Ramachandran restraints generated. 2702 Oldfield, 0 Emsley, 2702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5404 Ramachandran restraints generated. 2702 Oldfield, 0 Emsley, 2702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 177 time to evaluate : 0.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8687 (pp) REVERT: A 162 ASN cc_start: 0.8595 (t0) cc_final: 0.8353 (t0) REVERT: B 64 ILE cc_start: 0.9709 (OUTLIER) cc_final: 0.9436 (pp) REVERT: B 180 LEU cc_start: 0.9417 (OUTLIER) cc_final: 0.9188 (pt) REVERT: B 192 ILE cc_start: 0.9022 (tp) cc_final: 0.8798 (pt) REVERT: B 225 ASN cc_start: 0.9279 (t0) cc_final: 0.8993 (t0) REVERT: C 113 LYS cc_start: 0.8563 (OUTLIER) cc_final: 0.8118 (mmtp) REVERT: C 244 ASP cc_start: 0.9188 (t0) cc_final: 0.8892 (t0) REVERT: D 64 ILE cc_start: 0.9682 (OUTLIER) cc_final: 0.9448 (pp) REVERT: F 64 ILE cc_start: 0.9538 (OUTLIER) cc_final: 0.9324 (pp) REVERT: F 225 ASN cc_start: 0.9301 (t0) cc_final: 0.8990 (t0) REVERT: F 297 ASN cc_start: 0.9154 (t0) cc_final: 0.8849 (t0) REVERT: M 127 MET cc_start: 0.6921 (tpp) cc_final: 0.6614 (mmm) REVERT: M 133 ARG cc_start: 0.8996 (OUTLIER) cc_final: 0.8754 (tmm160) REVERT: M 148 LEU cc_start: 0.7890 (OUTLIER) cc_final: 0.7679 (mt) REVERT: M 173 GLU cc_start: 0.9597 (OUTLIER) cc_final: 0.9277 (mp0) REVERT: N 127 MET cc_start: 0.7571 (tpt) cc_final: 0.7246 (tpp) REVERT: N 130 ILE cc_start: 0.9237 (mm) cc_final: 0.8852 (tt) REVERT: N 153 HIS cc_start: 0.9507 (OUTLIER) cc_final: 0.9229 (p-80) REVERT: N 190 CYS cc_start: 0.7926 (OUTLIER) cc_final: 0.7661 (p) REVERT: P 141 MET cc_start: 0.8681 (tpt) cc_final: 0.8360 (mmm) outliers start: 57 outliers final: 36 residues processed: 216 average time/residue: 0.1441 time to fit residues: 51.5994 Evaluate side-chains 221 residues out of total 2308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 174 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 113 LYS Chi-restraints excluded: chain C residue 217 CYS Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 123 MET Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 71 ILE Chi-restraints excluded: chain F residue 132 MET Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 217 CYS Chi-restraints excluded: chain F residue 236 LEU Chi-restraints excluded: chain F residue 324 THR Chi-restraints excluded: chain M residue 133 ARG Chi-restraints excluded: chain M residue 148 LEU Chi-restraints excluded: chain M residue 173 GLU Chi-restraints excluded: chain N residue 153 HIS Chi-restraints excluded: chain N residue 174 SER Chi-restraints excluded: chain N residue 190 CYS Chi-restraints excluded: chain N residue 221 TYR Chi-restraints excluded: chain O residue 190 CYS Chi-restraints excluded: chain P residue 162 TYR Chi-restraints excluded: chain P residue 197 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 23 optimal weight: 5.9990 chunk 56 optimal weight: 2.9990 chunk 134 optimal weight: 0.9990 chunk 237 optimal weight: 20.0000 chunk 79 optimal weight: 2.9990 chunk 113 optimal weight: 0.9980 chunk 154 optimal weight: 3.9990 chunk 208 optimal weight: 5.9990 chunk 57 optimal weight: 1.9990 chunk 70 optimal weight: 8.9990 chunk 116 optimal weight: 0.4980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.093065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2648 r_free = 0.2648 target = 0.057650 restraints weight = 51593.711| |-----------------------------------------------------------------------------| r_work (start): 0.2577 rms_B_bonded: 2.82 r_work: 0.2401 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.0859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 21966 Z= 0.133 Angle : 0.530 8.779 29716 Z= 0.260 Chirality : 0.042 0.204 3294 Planarity : 0.003 0.044 3844 Dihedral : 5.209 55.192 3046 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.77 % Allowed : 25.74 % Favored : 71.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.38 (0.17), residues: 2702 helix: 2.18 (0.14), residues: 1348 sheet: 0.70 (0.27), residues: 390 loop : 1.29 (0.22), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG P 160 TYR 0.039 0.001 TYR O 221 PHE 0.008 0.001 PHE E 127 TRP 0.009 0.001 TRP C 79 HIS 0.007 0.001 HIS P 153 Details of bonding type rmsd covalent geometry : bond 0.00289 (21966) covalent geometry : angle 0.52967 (29716) hydrogen bonds : bond 0.04031 ( 1357) hydrogen bonds : angle 4.01084 ( 3687) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5404 Ramachandran restraints generated. 2702 Oldfield, 0 Emsley, 2702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5404 Ramachandran restraints generated. 2702 Oldfield, 0 Emsley, 2702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 168 time to evaluate : 0.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 LEU cc_start: 0.9043 (OUTLIER) cc_final: 0.8763 (pp) REVERT: A 162 ASN cc_start: 0.8626 (t0) cc_final: 0.8388 (t0) REVERT: B 64 ILE cc_start: 0.9705 (OUTLIER) cc_final: 0.9346 (pp) REVERT: B 180 LEU cc_start: 0.9429 (OUTLIER) cc_final: 0.9183 (pt) REVERT: B 192 ILE cc_start: 0.9030 (tp) cc_final: 0.8813 (pt) REVERT: C 113 LYS cc_start: 0.8617 (OUTLIER) cc_final: 0.8153 (mmtp) REVERT: D 64 ILE cc_start: 0.9686 (OUTLIER) cc_final: 0.9445 (pp) REVERT: F 64 ILE cc_start: 0.9558 (OUTLIER) cc_final: 0.9340 (pp) REVERT: F 297 ASN cc_start: 0.9179 (t0) cc_final: 0.8876 (t0) REVERT: M 127 MET cc_start: 0.6927 (tpp) cc_final: 0.6620 (mmm) REVERT: M 133 ARG cc_start: 0.9000 (OUTLIER) cc_final: 0.8765 (tmm160) REVERT: M 173 GLU cc_start: 0.9621 (OUTLIER) cc_final: 0.9299 (mp0) REVERT: N 127 MET cc_start: 0.7556 (tpt) cc_final: 0.7229 (tpp) REVERT: N 130 ILE cc_start: 0.9220 (mm) cc_final: 0.8823 (tt) REVERT: N 153 HIS cc_start: 0.9531 (OUTLIER) cc_final: 0.9292 (p-80) REVERT: N 190 CYS cc_start: 0.7939 (OUTLIER) cc_final: 0.7675 (p) outliers start: 64 outliers final: 47 residues processed: 213 average time/residue: 0.1302 time to fit residues: 45.5123 Evaluate side-chains 222 residues out of total 2308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 165 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 113 LYS Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain C residue 217 CYS Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 123 MET Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 338 SER Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 71 ILE Chi-restraints excluded: chain F residue 132 MET Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 217 CYS Chi-restraints excluded: chain F residue 236 LEU Chi-restraints excluded: chain F residue 324 THR Chi-restraints excluded: chain M residue 133 ARG Chi-restraints excluded: chain M residue 173 GLU Chi-restraints excluded: chain N residue 153 HIS Chi-restraints excluded: chain N residue 174 SER Chi-restraints excluded: chain N residue 190 CYS Chi-restraints excluded: chain O residue 127 MET Chi-restraints excluded: chain O residue 144 GLN Chi-restraints excluded: chain O residue 190 CYS Chi-restraints excluded: chain P residue 162 TYR Chi-restraints excluded: chain P residue 197 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 189 optimal weight: 0.2980 chunk 89 optimal weight: 0.9990 chunk 121 optimal weight: 0.0970 chunk 101 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 29 optimal weight: 0.5980 chunk 107 optimal weight: 5.9990 chunk 169 optimal weight: 0.5980 chunk 265 optimal weight: 7.9990 chunk 61 optimal weight: 2.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 ASN ** D 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 173 HIS ** F 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.094980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2696 r_free = 0.2696 target = 0.059733 restraints weight = 51834.815| |-----------------------------------------------------------------------------| r_work (start): 0.2600 rms_B_bonded: 2.82 r_work: 0.2428 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.0967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 21966 Z= 0.101 Angle : 0.535 8.747 29716 Z= 0.263 Chirality : 0.042 0.213 3294 Planarity : 0.003 0.078 3844 Dihedral : 5.164 53.003 3046 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.34 % Allowed : 26.69 % Favored : 70.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.40 (0.17), residues: 2702 helix: 2.17 (0.14), residues: 1346 sheet: 0.91 (0.27), residues: 360 loop : 1.24 (0.21), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG P 160 TYR 0.037 0.001 TYR O 221 PHE 0.009 0.001 PHE E 127 TRP 0.008 0.001 TRP D 79 HIS 0.007 0.001 HIS P 153 Details of bonding type rmsd covalent geometry : bond 0.00196 (21966) covalent geometry : angle 0.53506 (29716) hydrogen bonds : bond 0.03964 ( 1357) hydrogen bonds : angle 3.98064 ( 3687) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5404 Ramachandran restraints generated. 2702 Oldfield, 0 Emsley, 2702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5404 Ramachandran restraints generated. 2702 Oldfield, 0 Emsley, 2702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 172 time to evaluate : 0.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8748 (pp) REVERT: A 162 ASN cc_start: 0.8561 (t0) cc_final: 0.8313 (t0) REVERT: B 64 ILE cc_start: 0.9717 (OUTLIER) cc_final: 0.9448 (pp) REVERT: B 180 LEU cc_start: 0.9432 (OUTLIER) cc_final: 0.9188 (pt) REVERT: B 225 ASN cc_start: 0.9310 (t0) cc_final: 0.9013 (t0) REVERT: C 113 LYS cc_start: 0.8604 (OUTLIER) cc_final: 0.8116 (mmtp) REVERT: C 244 ASP cc_start: 0.9251 (t0) cc_final: 0.8915 (t0) REVERT: D 34 ILE cc_start: 0.9427 (mt) cc_final: 0.9092 (pt) REVERT: D 64 ILE cc_start: 0.9689 (OUTLIER) cc_final: 0.9455 (pp) REVERT: F 64 ILE cc_start: 0.9548 (OUTLIER) cc_final: 0.9333 (pp) REVERT: F 132 MET cc_start: 0.9309 (OUTLIER) cc_final: 0.8910 (tmm) REVERT: F 297 ASN cc_start: 0.9188 (t0) cc_final: 0.8897 (t0) REVERT: M 127 MET cc_start: 0.6809 (tpp) cc_final: 0.6498 (mmm) REVERT: M 133 ARG cc_start: 0.9012 (OUTLIER) cc_final: 0.8800 (tmm160) REVERT: M 173 GLU cc_start: 0.9653 (OUTLIER) cc_final: 0.9329 (mp0) REVERT: N 127 MET cc_start: 0.7564 (tpt) cc_final: 0.7261 (tpp) REVERT: N 130 ILE cc_start: 0.9218 (mm) cc_final: 0.8828 (tt) REVERT: N 141 MET cc_start: 0.8761 (tpt) cc_final: 0.8290 (mmm) REVERT: N 153 HIS cc_start: 0.9507 (OUTLIER) cc_final: 0.9230 (p-80) REVERT: N 190 CYS cc_start: 0.7855 (OUTLIER) cc_final: 0.7594 (p) REVERT: P 141 MET cc_start: 0.9008 (tpt) cc_final: 0.8628 (mmm) outliers start: 54 outliers final: 34 residues processed: 210 average time/residue: 0.1393 time to fit residues: 48.6883 Evaluate side-chains 216 residues out of total 2308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 171 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 113 LYS Chi-restraints excluded: chain C residue 217 CYS Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 123 MET Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 71 ILE Chi-restraints excluded: chain F residue 132 MET Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 217 CYS Chi-restraints excluded: chain F residue 236 LEU Chi-restraints excluded: chain M residue 133 ARG Chi-restraints excluded: chain M residue 173 GLU Chi-restraints excluded: chain N residue 153 HIS Chi-restraints excluded: chain N residue 174 SER Chi-restraints excluded: chain N residue 190 CYS Chi-restraints excluded: chain N residue 221 TYR Chi-restraints excluded: chain O residue 144 GLN Chi-restraints excluded: chain O residue 190 CYS Chi-restraints excluded: chain P residue 162 TYR Chi-restraints excluded: chain P residue 197 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 122 optimal weight: 2.9990 chunk 221 optimal weight: 0.0570 chunk 139 optimal weight: 0.4980 chunk 210 optimal weight: 6.9990 chunk 88 optimal weight: 4.9990 chunk 169 optimal weight: 0.1980 chunk 117 optimal weight: 0.7980 chunk 3 optimal weight: 9.9990 chunk 175 optimal weight: 0.7980 chunk 220 optimal weight: 0.7980 chunk 66 optimal weight: 7.9990 overall best weight: 0.4698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.094295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2702 r_free = 0.2702 target = 0.060246 restraints weight = 50882.055| |-----------------------------------------------------------------------------| r_work (start): 0.2621 rms_B_bonded: 2.79 r_work: 0.2439 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.1054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 21966 Z= 0.102 Angle : 0.538 12.774 29716 Z= 0.266 Chirality : 0.042 0.218 3294 Planarity : 0.003 0.047 3844 Dihedral : 5.156 53.304 3043 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.12 % Allowed : 26.95 % Favored : 70.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.42 (0.17), residues: 2702 helix: 2.15 (0.14), residues: 1348 sheet: 0.94 (0.27), residues: 360 loop : 1.30 (0.21), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.000 ARG P 160 TYR 0.035 0.001 TYR O 221 PHE 0.008 0.001 PHE E 127 TRP 0.008 0.001 TRP D 79 HIS 0.008 0.001 HIS P 153 Details of bonding type rmsd covalent geometry : bond 0.00201 (21966) covalent geometry : angle 0.53826 (29716) hydrogen bonds : bond 0.03951 ( 1357) hydrogen bonds : angle 3.97580 ( 3687) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5404 Ramachandran restraints generated. 2702 Oldfield, 0 Emsley, 2702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5404 Ramachandran restraints generated. 2702 Oldfield, 0 Emsley, 2702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 175 time to evaluate : 0.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8744 (pp) REVERT: A 162 ASN cc_start: 0.8565 (t0) cc_final: 0.8348 (t0) REVERT: B 64 ILE cc_start: 0.9698 (OUTLIER) cc_final: 0.9425 (pp) REVERT: B 180 LEU cc_start: 0.9412 (OUTLIER) cc_final: 0.9154 (pt) REVERT: B 225 ASN cc_start: 0.9308 (t0) cc_final: 0.9015 (t0) REVERT: C 78 ASN cc_start: 0.8418 (t0) cc_final: 0.8193 (t0) REVERT: C 113 LYS cc_start: 0.8574 (OUTLIER) cc_final: 0.8080 (mmtp) REVERT: C 128 ASN cc_start: 0.9132 (t0) cc_final: 0.8915 (t0) REVERT: D 34 ILE cc_start: 0.9409 (mt) cc_final: 0.9092 (pt) REVERT: D 64 ILE cc_start: 0.9674 (OUTLIER) cc_final: 0.9446 (pp) REVERT: F 64 ILE cc_start: 0.9545 (OUTLIER) cc_final: 0.9330 (pp) REVERT: F 132 MET cc_start: 0.9309 (OUTLIER) cc_final: 0.8904 (tmm) REVERT: F 297 ASN cc_start: 0.9186 (t0) cc_final: 0.8896 (t0) REVERT: M 127 MET cc_start: 0.6972 (tpp) cc_final: 0.6619 (mmm) REVERT: M 133 ARG cc_start: 0.9011 (OUTLIER) cc_final: 0.8755 (tmm160) REVERT: M 173 GLU cc_start: 0.9642 (OUTLIER) cc_final: 0.9321 (mp0) REVERT: N 127 MET cc_start: 0.7672 (tpt) cc_final: 0.7355 (tpp) REVERT: N 130 ILE cc_start: 0.9229 (mm) cc_final: 0.8872 (tt) REVERT: N 153 HIS cc_start: 0.9540 (OUTLIER) cc_final: 0.9270 (p-80) REVERT: N 190 CYS cc_start: 0.8000 (OUTLIER) cc_final: 0.7739 (p) REVERT: P 141 MET cc_start: 0.8937 (tpt) cc_final: 0.8560 (mmm) outliers start: 49 outliers final: 32 residues processed: 211 average time/residue: 0.1381 time to fit residues: 48.1080 Evaluate side-chains 212 residues out of total 2308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 169 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 113 LYS Chi-restraints excluded: chain C residue 217 CYS Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 123 MET Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 71 ILE Chi-restraints excluded: chain F residue 132 MET Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 217 CYS Chi-restraints excluded: chain F residue 236 LEU Chi-restraints excluded: chain M residue 133 ARG Chi-restraints excluded: chain M residue 173 GLU Chi-restraints excluded: chain N residue 153 HIS Chi-restraints excluded: chain N residue 174 SER Chi-restraints excluded: chain N residue 190 CYS Chi-restraints excluded: chain N residue 221 TYR Chi-restraints excluded: chain O residue 144 GLN Chi-restraints excluded: chain O residue 190 CYS Chi-restraints excluded: chain P residue 162 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 40 optimal weight: 7.9990 chunk 43 optimal weight: 1.9990 chunk 258 optimal weight: 4.9990 chunk 60 optimal weight: 0.9990 chunk 217 optimal weight: 0.0050 chunk 81 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 54 optimal weight: 7.9990 chunk 108 optimal weight: 5.9990 chunk 263 optimal weight: 6.9990 chunk 178 optimal weight: 0.9980 overall best weight: 1.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.093305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2661 r_free = 0.2661 target = 0.058222 restraints weight = 51823.826| |-----------------------------------------------------------------------------| r_work (start): 0.2579 rms_B_bonded: 2.84 r_work: 0.2407 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.1029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 21966 Z= 0.142 Angle : 0.556 11.763 29716 Z= 0.275 Chirality : 0.043 0.215 3294 Planarity : 0.003 0.044 3844 Dihedral : 5.202 55.713 3043 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.99 % Allowed : 27.08 % Favored : 70.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.41 (0.17), residues: 2702 helix: 2.18 (0.14), residues: 1368 sheet: 0.78 (0.27), residues: 390 loop : 1.30 (0.22), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG P 160 TYR 0.033 0.001 TYR O 221 PHE 0.008 0.001 PHE E 127 TRP 0.009 0.001 TRP D 79 HIS 0.008 0.001 HIS P 153 Details of bonding type rmsd covalent geometry : bond 0.00312 (21966) covalent geometry : angle 0.55568 (29716) hydrogen bonds : bond 0.04052 ( 1357) hydrogen bonds : angle 4.01568 ( 3687) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5325.76 seconds wall clock time: 92 minutes 10.96 seconds (5530.96 seconds total)