Starting phenix.real_space_refine on Mon Jul 6 13:00:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wiz_32541/07_2026/7wiz_32541_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wiz_32541/07_2026/7wiz_32541.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wiz_32541/07_2026/7wiz_32541.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wiz_32541/07_2026/7wiz_32541.map" model { file = "/net/cci-nas-00/data/ceres_data/7wiz_32541/07_2026/7wiz_32541_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wiz_32541/07_2026/7wiz_32541_trim.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.009 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 24 5.49 5 S 88 5.16 5 C 11216 2.51 5 N 3116 2.21 5 O 3372 1.98 5 H 17752 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 120 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 35568 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 8815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 556, 8815 Classifications: {'peptide': 556} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 527} Chain: "B" Number of atoms: 8815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 556, 8815 Classifications: {'peptide': 556} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 527} Chain: "C" Number of atoms: 8815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 556, 8815 Classifications: {'peptide': 556} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 527} Chain: "D" Number of atoms: 8815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 556, 8815 Classifications: {'peptide': 556} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 527} Chain: "A" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 17 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "A" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 60 Unusual residues: {'ACP': 1, 'UTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 77 Unusual residues: {'ACP': 1, 'UTP': 1} Inner-chain residues flagged as termini: ['pdbres="GLN B 702 "'] Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1} Link IDs: {None: 2} Chain: "C" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 17 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "C" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 60 Unusual residues: {'ACP': 1, 'UTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 77 Unusual residues: {'ACP': 1, 'UTP': 1} Inner-chain residues flagged as termini: ['pdbres="GLN D 702 "'] Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1} Link IDs: {None: 2} Time building chain proxies: 6.36, per 1000 atoms: 0.18 Number of scatterers: 35568 At special positions: 0 Unit cell: (132.5, 98.58, 126.14, 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 88 16.00 P 24 15.00 O 3372 8.00 N 3116 7.00 C 11216 6.00 H 17752 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.54 Conformation dependent library (CDL) restraints added in 1.1 seconds 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4096 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 16 sheets defined 45.6% alpha, 13.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing helix chain 'A' and resid 15 through 30 Processing helix chain 'A' and resid 51 through 56 removed outlier: 3.885A pdb=" N HIS A 55 " --> pdb=" O SER A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 79 Processing helix chain 'A' and resid 83 through 85 No H-bonds generated for 'chain 'A' and resid 83 through 85' Processing helix chain 'A' and resid 90 through 104 Processing helix chain 'A' and resid 112 through 129 removed outlier: 7.242A pdb=" N THR A 118 " --> pdb=" O VAL A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 169 removed outlier: 4.108A pdb=" N PHE A 167 " --> pdb=" O ARG A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 172 No H-bonds generated for 'chain 'A' and resid 170 through 172' Processing helix chain 'A' and resid 193 through 205 Processing helix chain 'A' and resid 222 through 234 Processing helix chain 'A' and resid 251 through 258 Processing helix chain 'A' and resid 260 through 269 Processing helix chain 'A' and resid 274 through 278 Processing helix chain 'A' and resid 282 through 292 Processing helix chain 'A' and resid 314 through 329 Processing helix chain 'A' and resid 340 through 342 No H-bonds generated for 'chain 'A' and resid 340 through 342' Processing helix chain 'A' and resid 343 through 348 removed outlier: 3.752A pdb=" N LEU A 347 " --> pdb=" O GLU A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 363 Processing helix chain 'A' and resid 377 through 390 removed outlier: 3.980A pdb=" N LYS A 381 " --> pdb=" O GLY A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 414 Processing helix chain 'A' and resid 462 through 468 Processing helix chain 'A' and resid 488 through 494 Processing helix chain 'A' and resid 526 through 531 removed outlier: 3.615A pdb=" N TYR A 529 " --> pdb=" O HIS A 526 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU A 530 " --> pdb=" O PRO A 527 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER A 531 " --> pdb=" O GLU A 528 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 526 through 531' Processing helix chain 'A' and resid 537 through 548 Processing helix chain 'A' and resid 550 through 556 Processing helix chain 'B' and resid 15 through 30 Processing helix chain 'B' and resid 51 through 56 removed outlier: 3.885A pdb=" N HIS B 55 " --> pdb=" O SER B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 79 Processing helix chain 'B' and resid 83 through 85 No H-bonds generated for 'chain 'B' and resid 83 through 85' Processing helix chain 'B' and resid 90 through 104 Processing helix chain 'B' and resid 112 through 129 removed outlier: 7.242A pdb=" N THR B 118 " --> pdb=" O VAL B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 169 removed outlier: 4.107A pdb=" N PHE B 167 " --> pdb=" O ARG B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 172 No H-bonds generated for 'chain 'B' and resid 170 through 172' Processing helix chain 'B' and resid 193 through 205 Processing helix chain 'B' and resid 222 through 234 Processing helix chain 'B' and resid 251 through 258 Processing helix chain 'B' and resid 260 through 269 Processing helix chain 'B' and resid 274 through 278 Processing helix chain 'B' and resid 282 through 292 Processing helix chain 'B' and resid 314 through 329 Processing helix chain 'B' and resid 340 through 342 No H-bonds generated for 'chain 'B' and resid 340 through 342' Processing helix chain 'B' and resid 343 through 348 removed outlier: 3.752A pdb=" N LEU B 347 " --> pdb=" O GLU B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 363 Processing helix chain 'B' and resid 377 through 390 removed outlier: 3.980A pdb=" N LYS B 381 " --> pdb=" O GLY B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 414 Processing helix chain 'B' and resid 462 through 468 Processing helix chain 'B' and resid 488 through 494 Processing helix chain 'B' and resid 526 through 531 removed outlier: 3.614A pdb=" N TYR B 529 " --> pdb=" O HIS B 526 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU B 530 " --> pdb=" O PRO B 527 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER B 531 " --> pdb=" O GLU B 528 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 526 through 531' Processing helix chain 'B' and resid 537 through 548 Processing helix chain 'B' and resid 550 through 556 Processing helix chain 'C' and resid 15 through 30 Processing helix chain 'C' and resid 51 through 56 removed outlier: 3.885A pdb=" N HIS C 55 " --> pdb=" O SER C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 79 Processing helix chain 'C' and resid 83 through 85 No H-bonds generated for 'chain 'C' and resid 83 through 85' Processing helix chain 'C' and resid 90 through 104 Processing helix chain 'C' and resid 112 through 129 removed outlier: 7.242A pdb=" N THR C 118 " --> pdb=" O VAL C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 169 removed outlier: 4.108A pdb=" N PHE C 167 " --> pdb=" O ARG C 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 172 No H-bonds generated for 'chain 'C' and resid 170 through 172' Processing helix chain 'C' and resid 193 through 205 Processing helix chain 'C' and resid 222 through 234 Processing helix chain 'C' and resid 251 through 258 Processing helix chain 'C' and resid 260 through 269 Processing helix chain 'C' and resid 274 through 278 Processing helix chain 'C' and resid 282 through 292 Processing helix chain 'C' and resid 314 through 329 Processing helix chain 'C' and resid 340 through 342 No H-bonds generated for 'chain 'C' and resid 340 through 342' Processing helix chain 'C' and resid 343 through 348 removed outlier: 3.752A pdb=" N LEU C 347 " --> pdb=" O GLU C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 363 Processing helix chain 'C' and resid 377 through 390 removed outlier: 3.980A pdb=" N LYS C 381 " --> pdb=" O GLY C 377 " (cutoff:3.500A) Processing helix chain 'C' and resid 400 through 414 Processing helix chain 'C' and resid 462 through 468 Processing helix chain 'C' and resid 488 through 494 Processing helix chain 'C' and resid 526 through 531 removed outlier: 3.615A pdb=" N TYR C 529 " --> pdb=" O HIS C 526 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU C 530 " --> pdb=" O PRO C 527 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER C 531 " --> pdb=" O GLU C 528 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 526 through 531' Processing helix chain 'C' and resid 537 through 548 Processing helix chain 'C' and resid 550 through 556 Processing helix chain 'D' and resid 15 through 30 Processing helix chain 'D' and resid 51 through 56 removed outlier: 3.884A pdb=" N HIS D 55 " --> pdb=" O SER D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 69 through 79 Processing helix chain 'D' and resid 83 through 85 No H-bonds generated for 'chain 'D' and resid 83 through 85' Processing helix chain 'D' and resid 90 through 104 Processing helix chain 'D' and resid 112 through 129 removed outlier: 7.242A pdb=" N THR D 118 " --> pdb=" O VAL D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 169 removed outlier: 4.108A pdb=" N PHE D 167 " --> pdb=" O ARG D 163 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 172 No H-bonds generated for 'chain 'D' and resid 170 through 172' Processing helix chain 'D' and resid 193 through 205 Processing helix chain 'D' and resid 222 through 234 Processing helix chain 'D' and resid 251 through 258 Processing helix chain 'D' and resid 260 through 269 Processing helix chain 'D' and resid 274 through 278 Processing helix chain 'D' and resid 282 through 292 Processing helix chain 'D' and resid 314 through 329 Processing helix chain 'D' and resid 340 through 342 No H-bonds generated for 'chain 'D' and resid 340 through 342' Processing helix chain 'D' and resid 343 through 348 removed outlier: 3.752A pdb=" N LEU D 347 " --> pdb=" O GLU D 343 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 363 Processing helix chain 'D' and resid 377 through 390 removed outlier: 3.980A pdb=" N LYS D 381 " --> pdb=" O GLY D 377 " (cutoff:3.500A) Processing helix chain 'D' and resid 400 through 414 Processing helix chain 'D' and resid 462 through 468 Processing helix chain 'D' and resid 488 through 494 Processing helix chain 'D' and resid 526 through 531 removed outlier: 3.615A pdb=" N TYR D 529 " --> pdb=" O HIS D 526 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU D 530 " --> pdb=" O PRO D 527 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER D 531 " --> pdb=" O GLU D 528 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 526 through 531' Processing helix chain 'D' and resid 537 through 548 Processing helix chain 'D' and resid 550 through 556 Processing sheet with id=AA1, first strand: chain 'A' and resid 87 through 89 removed outlier: 4.534A pdb=" N GLY A 8 " --> pdb=" O LEU A 146 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N TYR A 3 " --> pdb=" O CYS A 175 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N ALA A 177 " --> pdb=" O TYR A 3 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N LEU A 5 " --> pdb=" O ALA A 177 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N VAL A 179 " --> pdb=" O LEU A 5 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N THR A 7 " --> pdb=" O VAL A 179 " (cutoff:3.500A) removed outlier: 8.639A pdb=" N LEU A 181 " --> pdb=" O THR A 7 " (cutoff:3.500A) removed outlier: 9.120A pdb=" N LEU A 212 " --> pdb=" O PHE A 174 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N LEU A 176 " --> pdb=" O LEU A 212 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N VAL A 214 " --> pdb=" O LEU A 176 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N HIS A 178 " --> pdb=" O VAL A 214 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N ARG A 216 " --> pdb=" O HIS A 178 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N SER A 180 " --> pdb=" O ARG A 216 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N ILE A 243 " --> pdb=" O ILE A 213 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N CYS A 215 " --> pdb=" O ILE A 243 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 59 through 60 Processing sheet with id=AA3, first strand: chain 'A' and resid 332 through 338 removed outlier: 8.133A pdb=" N LEU A 368 " --> pdb=" O CYS A 300 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N ALA A 302 " --> pdb=" O LEU A 368 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N LEU A 395 " --> pdb=" O VAL A 521 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N THR A 523 " --> pdb=" O LEU A 395 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N GLY A 397 " --> pdb=" O THR A 523 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N GLY A 501 " --> pdb=" O GLU A 510 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ILE A 512 " --> pdb=" O PHE A 499 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N PHE A 499 " --> pdb=" O ILE A 512 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 433 through 435 Processing sheet with id=AA5, first strand: chain 'B' and resid 87 through 89 removed outlier: 4.534A pdb=" N GLY B 8 " --> pdb=" O LEU B 146 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N TYR B 3 " --> pdb=" O CYS B 175 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N ALA B 177 " --> pdb=" O TYR B 3 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N LEU B 5 " --> pdb=" O ALA B 177 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N VAL B 179 " --> pdb=" O LEU B 5 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N THR B 7 " --> pdb=" O VAL B 179 " (cutoff:3.500A) removed outlier: 8.638A pdb=" N LEU B 181 " --> pdb=" O THR B 7 " (cutoff:3.500A) removed outlier: 9.121A pdb=" N LEU B 212 " --> pdb=" O PHE B 174 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N LEU B 176 " --> pdb=" O LEU B 212 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N VAL B 214 " --> pdb=" O LEU B 176 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N HIS B 178 " --> pdb=" O VAL B 214 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N ARG B 216 " --> pdb=" O HIS B 178 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N SER B 180 " --> pdb=" O ARG B 216 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N ILE B 243 " --> pdb=" O ILE B 213 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N CYS B 215 " --> pdb=" O ILE B 243 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 59 through 60 Processing sheet with id=AA7, first strand: chain 'B' and resid 332 through 338 removed outlier: 8.133A pdb=" N LEU B 368 " --> pdb=" O CYS B 300 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N ALA B 302 " --> pdb=" O LEU B 368 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N LEU B 395 " --> pdb=" O VAL B 521 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N THR B 523 " --> pdb=" O LEU B 395 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N GLY B 397 " --> pdb=" O THR B 523 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N GLY B 501 " --> pdb=" O GLU B 510 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ILE B 512 " --> pdb=" O PHE B 499 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N PHE B 499 " --> pdb=" O ILE B 512 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 433 through 435 Processing sheet with id=AA9, first strand: chain 'C' and resid 87 through 89 removed outlier: 4.534A pdb=" N GLY C 8 " --> pdb=" O LEU C 146 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N TYR C 3 " --> pdb=" O CYS C 175 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N ALA C 177 " --> pdb=" O TYR C 3 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N LEU C 5 " --> pdb=" O ALA C 177 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N VAL C 179 " --> pdb=" O LEU C 5 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N THR C 7 " --> pdb=" O VAL C 179 " (cutoff:3.500A) removed outlier: 8.639A pdb=" N LEU C 181 " --> pdb=" O THR C 7 " (cutoff:3.500A) removed outlier: 9.120A pdb=" N LEU C 212 " --> pdb=" O PHE C 174 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N LEU C 176 " --> pdb=" O LEU C 212 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N VAL C 214 " --> pdb=" O LEU C 176 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N HIS C 178 " --> pdb=" O VAL C 214 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N ARG C 216 " --> pdb=" O HIS C 178 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N SER C 180 " --> pdb=" O ARG C 216 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N ILE C 243 " --> pdb=" O ILE C 213 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N CYS C 215 " --> pdb=" O ILE C 243 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 59 through 60 Processing sheet with id=AB2, first strand: chain 'C' and resid 332 through 338 removed outlier: 8.133A pdb=" N LEU C 368 " --> pdb=" O CYS C 300 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N ALA C 302 " --> pdb=" O LEU C 368 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N LEU C 395 " --> pdb=" O VAL C 521 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N THR C 523 " --> pdb=" O LEU C 395 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N GLY C 397 " --> pdb=" O THR C 523 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N GLY C 501 " --> pdb=" O GLU C 510 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ILE C 512 " --> pdb=" O PHE C 499 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N PHE C 499 " --> pdb=" O ILE C 512 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 433 through 435 Processing sheet with id=AB4, first strand: chain 'D' and resid 87 through 89 removed outlier: 4.534A pdb=" N GLY D 8 " --> pdb=" O LEU D 146 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N TYR D 3 " --> pdb=" O CYS D 175 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N ALA D 177 " --> pdb=" O TYR D 3 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N LEU D 5 " --> pdb=" O ALA D 177 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N VAL D 179 " --> pdb=" O LEU D 5 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N THR D 7 " --> pdb=" O VAL D 179 " (cutoff:3.500A) removed outlier: 8.639A pdb=" N LEU D 181 " --> pdb=" O THR D 7 " (cutoff:3.500A) removed outlier: 9.120A pdb=" N LEU D 212 " --> pdb=" O PHE D 174 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N LEU D 176 " --> pdb=" O LEU D 212 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N VAL D 214 " --> pdb=" O LEU D 176 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N HIS D 178 " --> pdb=" O VAL D 214 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N ARG D 216 " --> pdb=" O HIS D 178 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N SER D 180 " --> pdb=" O ARG D 216 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N ILE D 243 " --> pdb=" O ILE D 213 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N CYS D 215 " --> pdb=" O ILE D 243 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 59 through 60 Processing sheet with id=AB6, first strand: chain 'D' and resid 332 through 338 removed outlier: 8.133A pdb=" N LEU D 368 " --> pdb=" O CYS D 300 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N ALA D 302 " --> pdb=" O LEU D 368 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N LEU D 395 " --> pdb=" O VAL D 521 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N THR D 523 " --> pdb=" O LEU D 395 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N GLY D 397 " --> pdb=" O THR D 523 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N GLY D 501 " --> pdb=" O GLU D 510 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ILE D 512 " --> pdb=" O PHE D 499 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N PHE D 499 " --> pdb=" O ILE D 512 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 433 through 435 748 hydrogen bonds defined for protein. 2196 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: 8.94 Time building geometry restraints manager: 4.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 17700 1.04 - 1.24: 2472 1.24 - 1.45: 5244 1.45 - 1.65: 10372 1.65 - 1.86: 144 Bond restraints: 35932 Sorted by residual: bond pdb=" C1' ACP B 703 " pdb=" O4' ACP B 703 " ideal model delta sigma weight residual 1.390 1.619 -0.229 2.00e-02 2.50e+03 1.31e+02 bond pdb=" C1' ACP D 703 " pdb=" O4' ACP D 703 " ideal model delta sigma weight residual 1.390 1.619 -0.229 2.00e-02 2.50e+03 1.31e+02 bond pdb=" C1' ACP A 602 " pdb=" O4' ACP A 602 " ideal model delta sigma weight residual 1.390 1.619 -0.229 2.00e-02 2.50e+03 1.31e+02 bond pdb=" C1' ACP C 602 " pdb=" O4' ACP C 602 " ideal model delta sigma weight residual 1.390 1.619 -0.229 2.00e-02 2.50e+03 1.31e+02 bond pdb=" C1' ACP A 602 " pdb=" C2' ACP A 602 " ideal model delta sigma weight residual 1.527 1.305 0.222 2.00e-02 2.50e+03 1.24e+02 ... (remaining 35927 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.15: 64971 6.15 - 12.31: 97 12.31 - 18.46: 8 18.46 - 24.61: 8 24.61 - 30.76: 16 Bond angle restraints: 65100 Sorted by residual: angle pdb=" SD MET B 156 " pdb=" CE MET B 156 " pdb=" HE3 MET B 156 " ideal model delta sigma weight residual 109.00 78.24 30.76 3.00e+00 1.11e-01 1.05e+02 angle pdb=" SD MET D 156 " pdb=" CE MET D 156 " pdb=" HE3 MET D 156 " ideal model delta sigma weight residual 109.00 78.35 30.65 3.00e+00 1.11e-01 1.04e+02 angle pdb=" SD MET A 156 " pdb=" CE MET A 156 " pdb=" HE3 MET A 156 " ideal model delta sigma weight residual 109.00 78.43 30.57 3.00e+00 1.11e-01 1.04e+02 angle pdb=" SD MET C 156 " pdb=" CE MET C 156 " pdb=" HE3 MET C 156 " ideal model delta sigma weight residual 109.00 78.43 30.57 3.00e+00 1.11e-01 1.04e+02 angle pdb=" HE2 MET D 156 " pdb=" CE MET D 156 " pdb=" HE3 MET D 156 " ideal model delta sigma weight residual 110.00 80.26 29.74 3.00e+00 1.11e-01 9.82e+01 ... (remaining 65095 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 14616 17.77 - 35.54: 1550 35.54 - 53.31: 601 53.31 - 71.08: 137 71.08 - 88.85: 32 Dihedral angle restraints: 16936 sinusoidal: 9588 harmonic: 7348 Sorted by residual: dihedral pdb=" CA VAL C 169 " pdb=" C VAL C 169 " pdb=" N LYS C 170 " pdb=" CA LYS C 170 " ideal model delta harmonic sigma weight residual 180.00 160.94 19.06 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CA VAL D 169 " pdb=" C VAL D 169 " pdb=" N LYS D 170 " pdb=" CA LYS D 170 " ideal model delta harmonic sigma weight residual 180.00 160.94 19.06 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CA VAL A 169 " pdb=" C VAL A 169 " pdb=" N LYS A 170 " pdb=" CA LYS A 170 " ideal model delta harmonic sigma weight residual 180.00 160.94 19.06 0 5.00e+00 4.00e-02 1.45e+01 ... (remaining 16933 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 2473 0.076 - 0.153: 279 0.153 - 0.229: 4 0.229 - 0.305: 4 0.305 - 0.382: 4 Chirality restraints: 2764 Sorted by residual: chirality pdb=" C2' ACP B 703 " pdb=" C1' ACP B 703 " pdb=" C3' ACP B 703 " pdb=" O2' ACP B 703 " both_signs ideal model delta sigma weight residual False -2.75 -2.37 -0.38 2.00e-01 2.50e+01 3.64e+00 chirality pdb=" C2' ACP A 602 " pdb=" C1' ACP A 602 " pdb=" C3' ACP A 602 " pdb=" O2' ACP A 602 " both_signs ideal model delta sigma weight residual False -2.75 -2.37 -0.38 2.00e-01 2.50e+01 3.62e+00 chirality pdb=" C2' ACP D 703 " pdb=" C1' ACP D 703 " pdb=" C3' ACP D 703 " pdb=" O2' ACP D 703 " both_signs ideal model delta sigma weight residual False -2.75 -2.37 -0.38 2.00e-01 2.50e+01 3.62e+00 ... (remaining 2761 not shown) Planarity restraints: 5264 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP D 40 " 0.033 5.00e-02 4.00e+02 4.91e-02 3.85e+00 pdb=" N PRO D 41 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO D 41 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO D 41 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 40 " 0.033 5.00e-02 4.00e+02 4.90e-02 3.85e+00 pdb=" N PRO A 41 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO A 41 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 41 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 40 " -0.033 5.00e-02 4.00e+02 4.90e-02 3.85e+00 pdb=" N PRO C 41 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO C 41 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 41 " -0.027 5.00e-02 4.00e+02 ... (remaining 5261 not shown) Histogram of nonbonded interaction distances: 1.54 - 2.15: 1613 2.15 - 2.76: 69220 2.76 - 3.38: 98441 3.38 - 3.99: 133019 3.99 - 4.60: 210640 Nonbonded interactions: 512933 Sorted by model distance: nonbonded pdb=" OE1 GLU B 160 " pdb=" HE ARG B 163 " model vdw 1.539 2.450 nonbonded pdb=" OE1 GLU D 160 " pdb=" HE ARG D 163 " model vdw 1.545 2.450 nonbonded pdb=" OE1 GLU A 160 " pdb=" HE ARG A 163 " model vdw 1.546 2.450 nonbonded pdb=" OE1 GLU C 160 " pdb=" HE ARG C 163 " model vdw 1.549 2.450 nonbonded pdb=" H THR D 193 " pdb=" O1G UTP D 701 " model vdw 1.559 2.450 ... (remaining 512928 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: 0.02 Found NCS groups: ncs_group { reference = (chain 'A' and resid 1 through 556) selection = (chain 'B' and resid 1 through 556) selection = (chain 'C' and resid 1 through 556) selection = (chain 'D' and resid 1 through 556) } 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: 1.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.230 Extract box with map and model: 0.540 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 34.930 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.060 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:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 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 : 0.011 0.229 18180 Z= 0.496 Angle : 0.916 16.349 24660 Z= 0.410 Chirality : 0.048 0.382 2764 Planarity : 0.003 0.049 3156 Dihedral : 17.800 88.847 7064 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.17 % Favored : 91.65 % Rotamer: Outliers : 1.85 % Allowed : 20.94 % Favored : 77.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -3.90 (0.14), residues: 2216 helix: -2.04 (0.13), residues: 936 sheet: -2.01 (0.24), residues: 380 loop : -3.36 (0.16), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 297 TYR 0.012 0.001 TYR A 42 PHE 0.010 0.001 PHE B 165 TRP 0.009 0.001 TRP B 285 HIS 0.003 0.001 HIS D 478 Details of bonding type rmsd/Z covalent geometry : bond 0.01074 / 0.50 (18180) covalent geometry : angle 0.91615 / 0.41 (24660) hydrogen bonds : bond 0.13314 / 8.53 ( 748) hydrogen bonds : angle 6.83926 / 4.78 ( 2196) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 1948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 311 time to evaluate : 1.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 448 MET cc_start: 0.8298 (ttm) cc_final: 0.8080 (ttm) REVERT: A 452 LYS cc_start: 0.8585 (OUTLIER) cc_final: 0.8214 (ttmt) REVERT: A 490 HIS cc_start: 0.7505 (m-70) cc_final: 0.7194 (m-70) REVERT: A 550 ARG cc_start: 0.7874 (mmt-90) cc_final: 0.7502 (tpp-160) REVERT: B 1 MET cc_start: 0.7666 (ttm) cc_final: 0.7422 (ttm) REVERT: B 190 GLU cc_start: 0.7596 (tt0) cc_final: 0.7306 (tt0) REVERT: B 204 ARG cc_start: 0.7568 (mtt90) cc_final: 0.7097 (mtm110) REVERT: B 490 HIS cc_start: 0.7091 (m-70) cc_final: 0.6846 (m-70) REVERT: B 550 ARG cc_start: 0.7594 (mmt-90) cc_final: 0.7146 (tpp-160) REVERT: C 57 GLU cc_start: 0.7779 (tm-30) cc_final: 0.7497 (tm-30) REVERT: C 448 MET cc_start: 0.8247 (ttm) cc_final: 0.8032 (ttm) REVERT: C 502 THR cc_start: 0.7155 (t) cc_final: 0.6918 (t) REVERT: C 550 ARG cc_start: 0.8029 (mmt-90) cc_final: 0.7744 (tpp-160) REVERT: D 186 LYS cc_start: 0.8179 (tppt) cc_final: 0.7951 (tppt) REVERT: D 353 LYS cc_start: 0.7870 (mmtp) cc_final: 0.7650 (mmtp) REVERT: D 448 MET cc_start: 0.8402 (ttm) cc_final: 0.7962 (ttp) REVERT: D 490 HIS cc_start: 0.7070 (m-70) cc_final: 0.6845 (m-70) outliers start: 36 outliers final: 18 residues processed: 341 average time/residue: 0.3867 time to fit residues: 190.5495 Evaluate side-chains 280 residues out of total 1948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 261 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 CYS Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 443 GLN Chi-restraints excluded: chain A residue 452 LYS Chi-restraints excluded: chain A residue 537 SER Chi-restraints excluded: chain B residue 281 CYS Chi-restraints excluded: chain B residue 435 ASP Chi-restraints excluded: chain B residue 537 SER Chi-restraints excluded: chain C residue 382 ILE Chi-restraints excluded: chain C residue 435 ASP Chi-restraints excluded: chain C residue 443 GLN Chi-restraints excluded: chain C residue 452 LYS Chi-restraints excluded: chain C residue 535 LYS Chi-restraints excluded: chain C residue 537 SER Chi-restraints excluded: chain D residue 281 CYS Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 452 LYS Chi-restraints excluded: chain D residue 535 LYS Chi-restraints excluded: chain D residue 537 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 216 optimal weight: 0.9980 chunk 98 optimal weight: 6.9990 chunk 194 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 5.9990 chunk 200 optimal weight: 2.9990 chunk 212 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.145376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.102561 restraints weight = 57165.870| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 2.00 r_work: 0.2988 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2833 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.1214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 18180 Z= 0.124 Angle : 0.583 5.590 24660 Z= 0.296 Chirality : 0.042 0.133 2764 Planarity : 0.005 0.065 3156 Dihedral : 11.231 86.600 2749 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.05 % Favored : 93.77 % Rotamer: Outliers : 2.52 % Allowed : 19.87 % Favored : 77.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -2.46 (0.16), residues: 2216 helix: -0.58 (0.16), residues: 952 sheet: -1.75 (0.24), residues: 380 loop : -2.71 (0.18), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 383 TYR 0.013 0.001 TYR A 488 PHE 0.008 0.001 PHE B 162 TRP 0.008 0.001 TRP D 285 HIS 0.005 0.001 HIS C 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.12 (18180) covalent geometry : angle 0.58300 / 0.30 (24660) hydrogen bonds : bond 0.03717 / 2.48 ( 748) hydrogen bonds : angle 5.08460 / 3.54 ( 2196) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 271 time to evaluate : 1.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 378 MET cc_start: 0.5807 (tpt) cc_final: 0.5462 (tpt) REVERT: A 448 MET cc_start: 0.8416 (ttm) cc_final: 0.8190 (ttp) REVERT: A 452 LYS cc_start: 0.8414 (OUTLIER) cc_final: 0.7970 (ttmt) REVERT: A 490 HIS cc_start: 0.7998 (m-70) cc_final: 0.7637 (m-70) REVERT: A 550 ARG cc_start: 0.7822 (mmt-90) cc_final: 0.7277 (tpp-160) REVERT: B 1 MET cc_start: 0.8175 (ttm) cc_final: 0.7907 (ttm) REVERT: B 190 GLU cc_start: 0.7701 (tt0) cc_final: 0.7480 (tt0) REVERT: B 204 ARG cc_start: 0.7805 (mtt90) cc_final: 0.6921 (mtm110) REVERT: B 345 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.7587 (mp0) REVERT: B 490 HIS cc_start: 0.7525 (m-70) cc_final: 0.7213 (m-70) REVERT: B 535 LYS cc_start: 0.7809 (ttpp) cc_final: 0.7422 (tppt) REVERT: B 550 ARG cc_start: 0.7559 (mmt-90) cc_final: 0.6920 (tpp-160) REVERT: C 57 GLU cc_start: 0.8014 (tm-30) cc_final: 0.7720 (tm-30) REVERT: C 345 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.7999 (mp0) REVERT: C 448 MET cc_start: 0.8261 (ttm) cc_final: 0.8058 (ttm) REVERT: C 550 ARG cc_start: 0.8011 (mmt-90) cc_final: 0.7490 (tpp-160) REVERT: D 40 ASP cc_start: 0.9135 (m-30) cc_final: 0.8851 (m-30) REVERT: D 186 LYS cc_start: 0.8120 (tppt) cc_final: 0.7787 (tppt) REVERT: D 287 ASP cc_start: 0.7999 (t0) cc_final: 0.7775 (t0) REVERT: D 448 MET cc_start: 0.8439 (ttm) cc_final: 0.7980 (ttp) REVERT: D 483 GLU cc_start: 0.8081 (tp30) cc_final: 0.7832 (tp30) REVERT: D 490 HIS cc_start: 0.7495 (m-70) cc_final: 0.7248 (m-70) outliers start: 49 outliers final: 30 residues processed: 315 average time/residue: 0.3586 time to fit residues: 167.1380 Evaluate side-chains 290 residues out of total 1948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 257 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ASP Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain A residue 281 CYS Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 452 LYS Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 112 GLN Chi-restraints excluded: chain B residue 281 CYS Chi-restraints excluded: chain B residue 345 GLU Chi-restraints excluded: chain B residue 382 ILE Chi-restraints excluded: chain B residue 510 GLU Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 217 SER Chi-restraints excluded: chain C residue 310 PHE Chi-restraints excluded: chain C residue 313 SER Chi-restraints excluded: chain C residue 345 GLU Chi-restraints excluded: chain C residue 382 ILE Chi-restraints excluded: chain C residue 452 LYS Chi-restraints excluded: chain C residue 510 GLU Chi-restraints excluded: chain C residue 535 LYS Chi-restraints excluded: chain D residue 112 GLN Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 217 SER Chi-restraints excluded: chain D residue 281 CYS Chi-restraints excluded: chain D residue 313 SER Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 452 LYS Chi-restraints excluded: chain D residue 510 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 102 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 123 optimal weight: 0.3980 chunk 78 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 131 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 553 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.149100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.108138 restraints weight = 57132.464| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 2.04 r_work: 0.2977 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2826 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18180 Z= 0.143 Angle : 0.559 5.727 24660 Z= 0.284 Chirality : 0.042 0.138 2764 Planarity : 0.004 0.050 3156 Dihedral : 10.037 87.625 2731 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.23 % Favored : 93.59 % Rotamer: Outliers : 2.57 % Allowed : 20.23 % Favored : 77.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -1.65 (0.17), residues: 2216 helix: 0.17 (0.17), residues: 952 sheet: -1.57 (0.25), residues: 380 loop : -2.26 (0.19), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 508 TYR 0.011 0.001 TYR D 42 PHE 0.009 0.001 PHE C 162 TRP 0.009 0.001 TRP D 285 HIS 0.005 0.001 HIS C 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.14 (18180) covalent geometry : angle 0.55877 / 0.28 (24660) hydrogen bonds : bond 0.03486 / 2.31 ( 748) hydrogen bonds : angle 4.71796 / 3.30 ( 2196) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 259 time to evaluate : 1.000 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 378 MET cc_start: 0.5910 (tpt) cc_final: 0.5613 (tpt) REVERT: A 448 MET cc_start: 0.8349 (ttm) cc_final: 0.8116 (ttm) REVERT: A 452 LYS cc_start: 0.8358 (OUTLIER) cc_final: 0.7996 (ttmt) REVERT: A 490 HIS cc_start: 0.8043 (m-70) cc_final: 0.7703 (m-70) REVERT: A 550 ARG cc_start: 0.7828 (mmt-90) cc_final: 0.7265 (tpp-160) REVERT: B 1 MET cc_start: 0.8361 (ttm) cc_final: 0.8070 (ttm) REVERT: B 190 GLU cc_start: 0.7789 (tt0) cc_final: 0.7587 (tt0) REVERT: B 193 THR cc_start: 0.8754 (OUTLIER) cc_final: 0.8551 (m) REVERT: B 345 GLU cc_start: 0.8555 (OUTLIER) cc_final: 0.7777 (mp0) REVERT: B 490 HIS cc_start: 0.7690 (m-70) cc_final: 0.7403 (m-70) REVERT: B 535 LYS cc_start: 0.8178 (ttpp) cc_final: 0.7705 (tppt) REVERT: C 57 GLU cc_start: 0.8077 (tm-30) cc_final: 0.7803 (tm-30) REVERT: C 310 PHE cc_start: 0.4892 (OUTLIER) cc_final: 0.4432 (m-80) REVERT: C 345 GLU cc_start: 0.8528 (OUTLIER) cc_final: 0.7892 (mp0) REVERT: C 509 MET cc_start: 0.8887 (mmp) cc_final: 0.8585 (mmp) REVERT: C 535 LYS cc_start: 0.8364 (OUTLIER) cc_final: 0.8003 (mtpp) REVERT: C 550 ARG cc_start: 0.8002 (mmt-90) cc_final: 0.7482 (tpp-160) REVERT: D 153 ILE cc_start: 0.9211 (tt) cc_final: 0.8978 (tt) REVERT: D 186 LYS cc_start: 0.8120 (tppt) cc_final: 0.7827 (tppt) REVERT: D 278 ARG cc_start: 0.6070 (OUTLIER) cc_final: 0.5574 (ppt90) REVERT: D 448 MET cc_start: 0.8395 (ttm) cc_final: 0.8032 (ttp) REVERT: D 550 ARG cc_start: 0.7897 (tpp-160) cc_final: 0.7602 (tpp-160) outliers start: 50 outliers final: 29 residues processed: 300 average time/residue: 0.3458 time to fit residues: 153.6326 Evaluate side-chains 284 residues out of total 1948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 248 time to evaluate : 1.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ASP Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 281 CYS Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 452 LYS Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 313 SER Chi-restraints excluded: chain B residue 345 GLU Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 510 GLU Chi-restraints excluded: chain C residue 68 ASP Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 217 SER Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 310 PHE Chi-restraints excluded: chain C residue 313 SER Chi-restraints excluded: chain C residue 345 GLU Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 452 LYS Chi-restraints excluded: chain C residue 507 THR Chi-restraints excluded: chain C residue 510 GLU Chi-restraints excluded: chain C residue 535 LYS Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 278 ARG Chi-restraints excluded: chain D residue 281 CYS Chi-restraints excluded: chain D residue 452 LYS Chi-restraints excluded: chain D residue 507 THR Chi-restraints excluded: chain D residue 510 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 0 optimal weight: 2.9990 chunk 153 optimal weight: 10.0000 chunk 110 optimal weight: 2.9990 chunk 142 optimal weight: 2.9990 chunk 66 optimal weight: 0.5980 chunk 182 optimal weight: 1.9990 chunk 215 optimal weight: 3.9990 chunk 111 optimal weight: 1.9990 chunk 203 optimal weight: 6.9990 chunk 93 optimal weight: 6.9990 chunk 117 optimal weight: 2.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 470 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.141598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.096998 restraints weight = 57970.092| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 2.04 r_work: 0.2940 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2790 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.094 18180 Z= 0.196 Angle : 0.583 6.157 24660 Z= 0.297 Chirality : 0.044 0.138 2764 Planarity : 0.004 0.054 3156 Dihedral : 9.463 89.987 2726 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.72 % Favored : 93.10 % Rotamer: Outliers : 3.03 % Allowed : 20.64 % Favored : 76.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -1.65 (0.17), residues: 2216 helix: 0.14 (0.16), residues: 956 sheet: -1.69 (0.27), residues: 324 loop : -2.16 (0.19), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 296 TYR 0.011 0.001 TYR B 42 PHE 0.013 0.001 PHE B 162 TRP 0.011 0.002 TRP D 285 HIS 0.007 0.001 HIS C 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00480 / 0.20 (18180) covalent geometry : angle 0.58264 / 0.30 (24660) hydrogen bonds : bond 0.03704 / 2.47 ( 748) hydrogen bonds : angle 4.76522 / 3.32 ( 2196) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 252 time to evaluate : 0.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 GLU cc_start: 0.8069 (tp30) cc_final: 0.7813 (tp30) REVERT: A 171 ARG cc_start: 0.6882 (OUTLIER) cc_final: 0.6286 (ptt-90) REVERT: A 290 ARG cc_start: 0.7777 (ttm-80) cc_final: 0.7212 (tpt170) REVERT: A 378 MET cc_start: 0.5985 (tpt) cc_final: 0.5710 (tpt) REVERT: A 452 LYS cc_start: 0.8414 (OUTLIER) cc_final: 0.8126 (ttmt) REVERT: A 490 HIS cc_start: 0.8086 (m-70) cc_final: 0.7750 (m-70) REVERT: A 550 ARG cc_start: 0.7924 (mmt-90) cc_final: 0.7361 (tpp-160) REVERT: B 1 MET cc_start: 0.8444 (ttm) cc_final: 0.8182 (ttm) REVERT: B 171 ARG cc_start: 0.7311 (OUTLIER) cc_final: 0.6506 (ptt-90) REVERT: B 333 GLU cc_start: 0.8041 (tt0) cc_final: 0.7811 (tp30) REVERT: B 345 GLU cc_start: 0.8605 (OUTLIER) cc_final: 0.7909 (mp0) REVERT: B 490 HIS cc_start: 0.7766 (m-70) cc_final: 0.7506 (m-70) REVERT: B 535 LYS cc_start: 0.8233 (ttpp) cc_final: 0.7767 (tppt) REVERT: C 170 LYS cc_start: 0.8711 (mttp) cc_final: 0.8279 (mmtm) REVERT: C 171 ARG cc_start: 0.7033 (OUTLIER) cc_final: 0.6630 (ptt-90) REVERT: C 345 GLU cc_start: 0.8570 (OUTLIER) cc_final: 0.7917 (mp0) REVERT: C 509 MET cc_start: 0.8954 (mmp) cc_final: 0.8571 (mmp) REVERT: C 535 LYS cc_start: 0.8373 (mmmm) cc_final: 0.7933 (mtpp) REVERT: C 550 ARG cc_start: 0.8027 (mmt-90) cc_final: 0.7508 (tpp-160) REVERT: D 160 GLU cc_start: 0.8081 (tp30) cc_final: 0.7822 (tp30) REVERT: D 186 LYS cc_start: 0.8183 (tppt) cc_final: 0.7869 (tppt) REVERT: D 278 ARG cc_start: 0.6222 (OUTLIER) cc_final: 0.5713 (ppt90) REVERT: D 312 ASP cc_start: 0.7773 (OUTLIER) cc_final: 0.7488 (t0) REVERT: D 363 ASP cc_start: 0.7634 (p0) cc_final: 0.7315 (p0) REVERT: D 448 MET cc_start: 0.8514 (ttm) cc_final: 0.8230 (ttp) REVERT: D 550 ARG cc_start: 0.7916 (tpp-160) cc_final: 0.7635 (tpp-160) REVERT: B 702 GLN cc_start: 0.7666 (pt0) cc_final: 0.7293 (pt0) REVERT: C 601 GLN cc_start: 0.7697 (pt0) cc_final: 0.7347 (pt0) outliers start: 59 outliers final: 42 residues processed: 298 average time/residue: 0.3556 time to fit residues: 155.7977 Evaluate side-chains 291 residues out of total 1948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 241 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ASP Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 171 ARG Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 312 ASP Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 452 LYS Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain A residue 537 SER Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 112 GLN Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 171 ARG Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 313 SER Chi-restraints excluded: chain B residue 345 GLU Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 510 GLU Chi-restraints excluded: chain B residue 549 ASP Chi-restraints excluded: chain C residue 68 ASP Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 156 MET Chi-restraints excluded: chain C residue 171 ARG Chi-restraints excluded: chain C residue 217 SER Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 313 SER Chi-restraints excluded: chain C residue 345 GLU Chi-restraints excluded: chain C residue 382 ILE Chi-restraints excluded: chain C residue 452 LYS Chi-restraints excluded: chain C residue 507 THR Chi-restraints excluded: chain C residue 510 GLU Chi-restraints excluded: chain C residue 537 SER Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 217 SER Chi-restraints excluded: chain D residue 278 ARG Chi-restraints excluded: chain D residue 312 ASP Chi-restraints excluded: chain D residue 313 SER Chi-restraints excluded: chain D residue 433 VAL Chi-restraints excluded: chain D residue 452 LYS Chi-restraints excluded: chain D residue 507 THR Chi-restraints excluded: chain D residue 510 GLU Chi-restraints excluded: chain D residue 537 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 137 optimal weight: 5.9990 chunk 172 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 211 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 114 optimal weight: 0.6980 chunk 206 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 181 optimal weight: 1.9990 chunk 185 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.151079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.108882 restraints weight = 57327.740| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 1.92 r_work: 0.3019 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18180 Z= 0.107 Angle : 0.527 5.740 24660 Z= 0.269 Chirality : 0.042 0.133 2764 Planarity : 0.004 0.049 3156 Dihedral : 8.860 82.515 2720 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.32 % Favored : 94.49 % Rotamer: Outliers : 2.16 % Allowed : 21.66 % Favored : 76.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -1.32 (0.18), residues: 2216 helix: 0.46 (0.17), residues: 964 sheet: -1.61 (0.27), residues: 324 loop : -2.02 (0.20), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 296 TYR 0.011 0.001 TYR A 488 PHE 0.008 0.001 PHE C 162 TRP 0.008 0.001 TRP D 285 HIS 0.005 0.001 HIS B 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 (18180) covalent geometry : angle 0.52718 / 0.27 (24660) hydrogen bonds : bond 0.03150 / 2.08 ( 748) hydrogen bonds : angle 4.54181 / 3.17 ( 2196) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 250 time to evaluate : 0.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 ARG cc_start: 0.6750 (OUTLIER) cc_final: 0.6267 (ptt-90) REVERT: A 290 ARG cc_start: 0.7833 (ttm-80) cc_final: 0.7369 (tpt170) REVERT: A 378 MET cc_start: 0.5965 (tpt) cc_final: 0.5675 (tpt) REVERT: A 452 LYS cc_start: 0.8411 (OUTLIER) cc_final: 0.8031 (ttmt) REVERT: A 490 HIS cc_start: 0.8004 (m-70) cc_final: 0.7683 (m-70) REVERT: A 502 THR cc_start: 0.8320 (p) cc_final: 0.8098 (p) REVERT: A 509 MET cc_start: 0.8891 (mmp) cc_final: 0.8664 (mmp) REVERT: A 550 ARG cc_start: 0.7930 (mmt-90) cc_final: 0.7378 (tpp-160) REVERT: B 1 MET cc_start: 0.8454 (ttm) cc_final: 0.8239 (ttm) REVERT: B 171 ARG cc_start: 0.6999 (OUTLIER) cc_final: 0.6327 (ptt-90) REVERT: B 345 GLU cc_start: 0.8597 (OUTLIER) cc_final: 0.7903 (mp0) REVERT: B 490 HIS cc_start: 0.7792 (m-70) cc_final: 0.7555 (m-70) REVERT: B 535 LYS cc_start: 0.8267 (ttpp) cc_final: 0.7848 (tppt) REVERT: C 170 LYS cc_start: 0.8741 (mttp) cc_final: 0.8270 (mmtt) REVERT: C 171 ARG cc_start: 0.6920 (OUTLIER) cc_final: 0.6473 (ptt-90) REVERT: C 345 GLU cc_start: 0.8554 (OUTLIER) cc_final: 0.7883 (mp0) REVERT: C 509 MET cc_start: 0.8940 (mmp) cc_final: 0.8580 (mmp) REVERT: C 535 LYS cc_start: 0.8386 (mmmm) cc_final: 0.7930 (mtpp) REVERT: C 550 ARG cc_start: 0.8054 (mmt-90) cc_final: 0.7542 (tpp-160) REVERT: D 171 ARG cc_start: 0.6811 (OUTLIER) cc_final: 0.6401 (ptt-90) REVERT: D 186 LYS cc_start: 0.8208 (tppt) cc_final: 0.7908 (tppt) REVERT: D 278 ARG cc_start: 0.6277 (OUTLIER) cc_final: 0.5758 (ppt90) REVERT: D 448 MET cc_start: 0.8490 (ttm) cc_final: 0.8253 (ttp) REVERT: D 550 ARG cc_start: 0.7911 (tpp-160) cc_final: 0.7623 (tpp-160) REVERT: B 702 GLN cc_start: 0.7565 (pt0) cc_final: 0.7310 (pt0) outliers start: 42 outliers final: 28 residues processed: 285 average time/residue: 0.3595 time to fit residues: 148.5588 Evaluate side-chains 282 residues out of total 1948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 246 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 68 ASP Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 171 ARG Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain A residue 452 LYS Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain A residue 512 ILE Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 171 ARG Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 345 GLU Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 510 GLU Chi-restraints excluded: chain C residue 68 ASP Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 171 ARG Chi-restraints excluded: chain C residue 345 GLU Chi-restraints excluded: chain C residue 382 ILE Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 452 LYS Chi-restraints excluded: chain C residue 507 THR Chi-restraints excluded: chain C residue 510 GLU Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 171 ARG Chi-restraints excluded: chain D residue 172 GLU Chi-restraints excluded: chain D residue 217 SER Chi-restraints excluded: chain D residue 278 ARG Chi-restraints excluded: chain D residue 433 VAL Chi-restraints excluded: chain D residue 452 LYS Chi-restraints excluded: chain D residue 510 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 187 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 163 optimal weight: 2.9990 chunk 199 optimal weight: 5.9990 chunk 144 optimal weight: 6.9990 chunk 16 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 179 optimal weight: 1.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.150324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.107793 restraints weight = 57486.042| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 1.92 r_work: 0.3002 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2856 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 18180 Z= 0.146 Angle : 0.546 5.799 24660 Z= 0.277 Chirality : 0.042 0.136 2764 Planarity : 0.004 0.050 3156 Dihedral : 8.587 82.032 2720 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.14 % Favored : 93.68 % Rotamer: Outliers : 2.72 % Allowed : 21.56 % Favored : 75.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -1.19 (0.18), residues: 2216 helix: 0.57 (0.17), residues: 960 sheet: -1.60 (0.27), residues: 324 loop : -1.91 (0.20), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 296 TYR 0.012 0.001 TYR A 264 PHE 0.009 0.001 PHE A 162 TRP 0.009 0.001 TRP D 285 HIS 0.005 0.001 HIS B 440 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.15 (18180) covalent geometry : angle 0.54555 / 0.28 (24660) hydrogen bonds : bond 0.03291 / 2.19 ( 748) hydrogen bonds : angle 4.53263 / 3.17 ( 2196) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 246 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 ARG cc_start: 0.6853 (OUTLIER) cc_final: 0.6251 (ptt-90) REVERT: A 278 ARG cc_start: 0.6091 (OUTLIER) cc_final: 0.5776 (ppt90) REVERT: A 290 ARG cc_start: 0.7875 (ttm-80) cc_final: 0.7422 (tpt170) REVERT: A 378 MET cc_start: 0.6025 (tpt) cc_final: 0.5744 (tpt) REVERT: A 490 HIS cc_start: 0.8004 (m-70) cc_final: 0.7698 (m-70) REVERT: A 509 MET cc_start: 0.8897 (mmp) cc_final: 0.8692 (mmp) REVERT: A 550 ARG cc_start: 0.7980 (mmt-90) cc_final: 0.7410 (tpp-160) REVERT: B 1 MET cc_start: 0.8524 (ttm) cc_final: 0.8289 (ttm) REVERT: B 171 ARG cc_start: 0.7199 (OUTLIER) cc_final: 0.6433 (ptt-90) REVERT: B 345 GLU cc_start: 0.8611 (OUTLIER) cc_final: 0.7917 (mp0) REVERT: B 490 HIS cc_start: 0.7834 (m-70) cc_final: 0.7618 (m-70) REVERT: B 535 LYS cc_start: 0.8248 (ttpp) cc_final: 0.7824 (tppt) REVERT: C 170 LYS cc_start: 0.8763 (mttp) cc_final: 0.8295 (mmtt) REVERT: C 171 ARG cc_start: 0.7062 (OUTLIER) cc_final: 0.6448 (ptt-90) REVERT: C 345 GLU cc_start: 0.8549 (OUTLIER) cc_final: 0.7874 (mp0) REVERT: C 509 MET cc_start: 0.8950 (mmp) cc_final: 0.8550 (mmp) REVERT: C 535 LYS cc_start: 0.8377 (mmmm) cc_final: 0.7923 (mtpp) REVERT: C 550 ARG cc_start: 0.7978 (mmt-90) cc_final: 0.7463 (tpp-160) REVERT: D 171 ARG cc_start: 0.6984 (OUTLIER) cc_final: 0.6491 (ptt-90) REVERT: D 278 ARG cc_start: 0.6356 (OUTLIER) cc_final: 0.5915 (ppt90) REVERT: D 448 MET cc_start: 0.8511 (ttm) cc_final: 0.8273 (ttp) REVERT: D 550 ARG cc_start: 0.7925 (tpp-160) cc_final: 0.7630 (tpp-160) REVERT: B 702 GLN cc_start: 0.7724 (pt0) cc_final: 0.7335 (pt0) REVERT: C 601 GLN cc_start: 0.7757 (pt0) cc_final: 0.7398 (pt0) outliers start: 53 outliers final: 42 residues processed: 286 average time/residue: 0.3660 time to fit residues: 151.3901 Evaluate side-chains 288 residues out of total 1948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 238 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 68 ASP Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 171 ARG Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 258 GLN Chi-restraints excluded: chain A residue 278 ARG Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 452 LYS Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain A residue 512 ILE Chi-restraints excluded: chain A residue 537 SER Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 112 GLN Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 171 ARG Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 345 GLU Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 502 THR Chi-restraints excluded: chain B residue 510 GLU Chi-restraints excluded: chain B residue 537 SER Chi-restraints excluded: chain C residue 68 ASP Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 171 ARG Chi-restraints excluded: chain C residue 217 SER Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 345 GLU Chi-restraints excluded: chain C residue 382 ILE Chi-restraints excluded: chain C residue 422 THR Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 452 LYS Chi-restraints excluded: chain C residue 507 THR Chi-restraints excluded: chain C residue 510 GLU Chi-restraints excluded: chain C residue 537 SER Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 171 ARG Chi-restraints excluded: chain D residue 172 GLU Chi-restraints excluded: chain D residue 217 SER Chi-restraints excluded: chain D residue 278 ARG Chi-restraints excluded: chain D residue 422 THR Chi-restraints excluded: chain D residue 433 VAL Chi-restraints excluded: chain D residue 452 LYS Chi-restraints excluded: chain D residue 507 THR Chi-restraints excluded: chain D residue 510 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 72 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 199 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 168 optimal weight: 1.9990 chunk 155 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 143 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.150052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.110727 restraints weight = 57553.084| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 1.85 r_work: 0.3025 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2884 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.2706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 18180 Z= 0.152 Angle : 0.547 6.651 24660 Z= 0.278 Chirality : 0.043 0.137 2764 Planarity : 0.004 0.051 3156 Dihedral : 8.433 80.452 2720 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.69 % Favored : 94.13 % Rotamer: Outliers : 2.93 % Allowed : 21.30 % Favored : 75.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -1.10 (0.18), residues: 2216 helix: 0.62 (0.17), residues: 956 sheet: -1.58 (0.27), residues: 324 loop : -1.83 (0.20), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 278 TYR 0.013 0.001 TYR D 488 PHE 0.009 0.001 PHE A 162 TRP 0.009 0.001 TRP D 285 HIS 0.005 0.001 HIS A 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.15 (18180) covalent geometry : angle 0.54675 / 0.28 (24660) hydrogen bonds : bond 0.03308 / 2.20 ( 748) hydrogen bonds : angle 4.53343 / 3.17 ( 2196) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 241 time to evaluate : 0.970 Fit side-chains revert: symmetry clash REVERT: A 171 ARG cc_start: 0.6901 (OUTLIER) cc_final: 0.6301 (ptt-90) REVERT: A 278 ARG cc_start: 0.6118 (OUTLIER) cc_final: 0.5885 (ppt90) REVERT: A 290 ARG cc_start: 0.7900 (ttm-80) cc_final: 0.7462 (tpt170) REVERT: A 378 MET cc_start: 0.6009 (tpt) cc_final: 0.5570 (tpt) REVERT: A 490 HIS cc_start: 0.7939 (m-70) cc_final: 0.7644 (m-70) REVERT: A 550 ARG cc_start: 0.8034 (mmt-90) cc_final: 0.7478 (tpp-160) REVERT: B 1 MET cc_start: 0.8507 (ttm) cc_final: 0.8271 (ttm) REVERT: B 171 ARG cc_start: 0.7083 (OUTLIER) cc_final: 0.6338 (ptt-90) REVERT: B 345 GLU cc_start: 0.8615 (OUTLIER) cc_final: 0.7927 (mp0) REVERT: B 490 HIS cc_start: 0.7849 (m-70) cc_final: 0.7644 (m-70) REVERT: B 535 LYS cc_start: 0.8253 (ttpp) cc_final: 0.7856 (tppt) REVERT: C 170 LYS cc_start: 0.8811 (mttp) cc_final: 0.8368 (mmtt) REVERT: C 171 ARG cc_start: 0.7036 (OUTLIER) cc_final: 0.6387 (ptt-90) REVERT: C 345 GLU cc_start: 0.8542 (OUTLIER) cc_final: 0.7872 (mp0) REVERT: C 535 LYS cc_start: 0.8366 (mmmm) cc_final: 0.7910 (mtpp) REVERT: C 550 ARG cc_start: 0.8026 (mmt-90) cc_final: 0.7525 (tpp-160) REVERT: D 171 ARG cc_start: 0.7057 (OUTLIER) cc_final: 0.6508 (ptt-90) REVERT: D 278 ARG cc_start: 0.6389 (OUTLIER) cc_final: 0.5953 (ppt90) REVERT: D 363 ASP cc_start: 0.7461 (p0) cc_final: 0.7227 (p0) REVERT: D 448 MET cc_start: 0.8549 (ttm) cc_final: 0.8307 (ttp) REVERT: D 550 ARG cc_start: 0.7907 (tpp-160) cc_final: 0.7607 (tpp-160) REVERT: B 702 GLN cc_start: 0.7951 (pt0) cc_final: 0.7598 (pt0) REVERT: C 601 GLN cc_start: 0.7876 (pt0) cc_final: 0.7518 (pt0) REVERT: D 702 GLN cc_start: 0.7982 (pt0) cc_final: 0.7541 (pt0) outliers start: 57 outliers final: 47 residues processed: 284 average time/residue: 0.3853 time to fit residues: 157.4818 Evaluate side-chains 293 residues out of total 1948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 238 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 68 ASP Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 171 ARG Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 258 GLN Chi-restraints excluded: chain A residue 278 ARG Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 452 LYS Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain A residue 512 ILE Chi-restraints excluded: chain A residue 537 SER Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 112 GLN Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 171 ARG Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 313 SER Chi-restraints excluded: chain B residue 345 GLU Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 502 THR Chi-restraints excluded: chain B residue 510 GLU Chi-restraints excluded: chain B residue 537 SER Chi-restraints excluded: chain B residue 549 ASP Chi-restraints excluded: chain C residue 68 ASP Chi-restraints excluded: chain C residue 112 GLN Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 171 ARG Chi-restraints excluded: chain C residue 217 SER Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 345 GLU Chi-restraints excluded: chain C residue 382 ILE Chi-restraints excluded: chain C residue 422 THR Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 452 LYS Chi-restraints excluded: chain C residue 507 THR Chi-restraints excluded: chain C residue 510 GLU Chi-restraints excluded: chain C residue 537 SER Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 171 ARG Chi-restraints excluded: chain D residue 172 GLU Chi-restraints excluded: chain D residue 217 SER Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 278 ARG Chi-restraints excluded: chain D residue 422 THR Chi-restraints excluded: chain D residue 433 VAL Chi-restraints excluded: chain D residue 452 LYS Chi-restraints excluded: chain D residue 507 THR Chi-restraints excluded: chain D residue 510 GLU Chi-restraints excluded: chain D residue 537 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 140 optimal weight: 4.9990 chunk 102 optimal weight: 4.9990 chunk 189 optimal weight: 0.9990 chunk 169 optimal weight: 0.9980 chunk 198 optimal weight: 3.9990 chunk 153 optimal weight: 0.2980 chunk 52 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 210 optimal weight: 3.9990 chunk 154 optimal weight: 0.9980 chunk 212 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 526 HIS ** 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 = 0.3674 r_free = 0.3674 target = 0.151107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.111607 restraints weight = 57193.024| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 1.84 r_work: 0.3038 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.2798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 18180 Z= 0.117 Angle : 0.530 7.141 24660 Z= 0.268 Chirality : 0.042 0.135 2764 Planarity : 0.004 0.049 3156 Dihedral : 8.165 76.530 2720 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.01 % Favored : 94.81 % Rotamer: Outliers : 2.93 % Allowed : 21.05 % Favored : 76.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -0.93 (0.18), residues: 2216 helix: 0.76 (0.17), residues: 960 sheet: -1.55 (0.27), residues: 324 loop : -1.72 (0.20), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 296 TYR 0.013 0.001 TYR D 488 PHE 0.007 0.001 PHE A 162 TRP 0.008 0.001 TRP D 285 HIS 0.004 0.001 HIS B 440 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.12 (18180) covalent geometry : angle 0.53048 / 0.27 (24660) hydrogen bonds : bond 0.03100 / 2.06 ( 748) hydrogen bonds : angle 4.42662 / 3.09 ( 2196) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 248 time to evaluate : 0.947 Fit side-chains revert: symmetry clash REVERT: A 171 ARG cc_start: 0.6818 (OUTLIER) cc_final: 0.6211 (ptt-90) REVERT: A 278 ARG cc_start: 0.6147 (OUTLIER) cc_final: 0.5776 (ppt90) REVERT: A 290 ARG cc_start: 0.7901 (ttm-80) cc_final: 0.7474 (tpt170) REVERT: A 378 MET cc_start: 0.5942 (tpt) cc_final: 0.5509 (tpt) REVERT: A 550 ARG cc_start: 0.8024 (mmt-90) cc_final: 0.7413 (tpp-160) REVERT: B 1 MET cc_start: 0.8485 (ttm) cc_final: 0.8253 (ttm) REVERT: B 171 ARG cc_start: 0.6978 (OUTLIER) cc_final: 0.6259 (ptt-90) REVERT: B 345 GLU cc_start: 0.8627 (OUTLIER) cc_final: 0.7931 (mp0) REVERT: B 535 LYS cc_start: 0.8222 (ttpp) cc_final: 0.7828 (tppt) REVERT: C 170 LYS cc_start: 0.8810 (mttp) cc_final: 0.8373 (mmtt) REVERT: C 171 ARG cc_start: 0.6996 (OUTLIER) cc_final: 0.6355 (ptt-90) REVERT: C 345 GLU cc_start: 0.8542 (OUTLIER) cc_final: 0.7855 (mp0) REVERT: C 509 MET cc_start: 0.9063 (mmp) cc_final: 0.8832 (mmp) REVERT: C 535 LYS cc_start: 0.8359 (mmmm) cc_final: 0.7906 (mtpp) REVERT: C 550 ARG cc_start: 0.8023 (mmt-90) cc_final: 0.7496 (tpp-160) REVERT: D 171 ARG cc_start: 0.6945 (OUTLIER) cc_final: 0.6424 (ptt-90) REVERT: D 363 ASP cc_start: 0.7314 (p0) cc_final: 0.7109 (p0) REVERT: D 452 LYS cc_start: 0.8368 (OUTLIER) cc_final: 0.8034 (ttmt) REVERT: D 550 ARG cc_start: 0.7900 (tpp-160) cc_final: 0.7596 (tpp-160) REVERT: B 702 GLN cc_start: 0.7919 (pt0) cc_final: 0.7441 (pt0) REVERT: C 601 GLN cc_start: 0.7944 (pt0) cc_final: 0.7567 (pt0) REVERT: D 702 GLN cc_start: 0.8014 (pt0) cc_final: 0.7542 (pt0) outliers start: 57 outliers final: 47 residues processed: 292 average time/residue: 0.3947 time to fit residues: 165.8647 Evaluate side-chains 295 residues out of total 1948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 240 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 68 ASP Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 171 ARG Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 258 GLN Chi-restraints excluded: chain A residue 278 ARG Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 452 LYS Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain A residue 512 ILE Chi-restraints excluded: chain A residue 537 SER Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 112 GLN Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 171 ARG Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 313 SER Chi-restraints excluded: chain B residue 345 GLU Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 510 GLU Chi-restraints excluded: chain B residue 537 SER Chi-restraints excluded: chain C residue 68 ASP Chi-restraints excluded: chain C residue 112 GLN Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 171 ARG Chi-restraints excluded: chain C residue 217 SER Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 313 SER Chi-restraints excluded: chain C residue 345 GLU Chi-restraints excluded: chain C residue 382 ILE Chi-restraints excluded: chain C residue 422 THR Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 452 LYS Chi-restraints excluded: chain C residue 507 THR Chi-restraints excluded: chain C residue 510 GLU Chi-restraints excluded: chain C residue 537 SER Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 171 ARG Chi-restraints excluded: chain D residue 172 GLU Chi-restraints excluded: chain D residue 217 SER Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 313 SER Chi-restraints excluded: chain D residue 422 THR Chi-restraints excluded: chain D residue 433 VAL Chi-restraints excluded: chain D residue 452 LYS Chi-restraints excluded: chain D residue 507 THR Chi-restraints excluded: chain D residue 510 GLU Chi-restraints excluded: chain D residue 537 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 115 optimal weight: 0.9980 chunk 140 optimal weight: 4.9990 chunk 11 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 95 optimal weight: 5.9990 chunk 180 optimal weight: 3.9990 chunk 76 optimal weight: 0.9980 chunk 162 optimal weight: 3.9990 chunk 156 optimal weight: 0.8980 chunk 153 optimal weight: 9.9990 chunk 103 optimal weight: 4.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 526 HIS ** 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 = 0.3669 r_free = 0.3669 target = 0.150719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.108202 restraints weight = 57327.305| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 1.93 r_work: 0.3003 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2858 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.2882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 18180 Z= 0.136 Angle : 0.539 6.165 24660 Z= 0.273 Chirality : 0.042 0.135 2764 Planarity : 0.004 0.050 3156 Dihedral : 8.148 77.009 2720 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.73 % Favored : 94.09 % Rotamer: Outliers : 2.98 % Allowed : 21.10 % Favored : 75.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -0.92 (0.18), residues: 2216 helix: 0.75 (0.17), residues: 960 sheet: -1.54 (0.27), residues: 324 loop : -1.68 (0.20), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 383 TYR 0.015 0.001 TYR D 488 PHE 0.008 0.001 PHE A 162 TRP 0.008 0.001 TRP D 285 HIS 0.004 0.001 HIS A 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 (18180) covalent geometry : angle 0.53901 / 0.27 (24660) hydrogen bonds : bond 0.03174 / 2.11 ( 748) hydrogen bonds : angle 4.44015 / 3.10 ( 2196) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 247 time to evaluate : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 171 ARG cc_start: 0.6859 (OUTLIER) cc_final: 0.6206 (ptt-90) REVERT: A 278 ARG cc_start: 0.6136 (OUTLIER) cc_final: 0.5815 (ppt90) REVERT: A 290 ARG cc_start: 0.7908 (ttm-80) cc_final: 0.7457 (tpt90) REVERT: A 378 MET cc_start: 0.5956 (tpt) cc_final: 0.5526 (tpt) REVERT: A 452 LYS cc_start: 0.8311 (OUTLIER) cc_final: 0.8004 (ttmt) REVERT: A 550 ARG cc_start: 0.8037 (mmt-90) cc_final: 0.7421 (tpp-160) REVERT: B 1 MET cc_start: 0.8497 (ttm) cc_final: 0.8262 (ttm) REVERT: B 170 LYS cc_start: 0.8958 (mttp) cc_final: 0.8545 (mmtt) REVERT: B 171 ARG cc_start: 0.6996 (OUTLIER) cc_final: 0.6257 (ptt-90) REVERT: B 294 THR cc_start: 0.8391 (p) cc_final: 0.8175 (p) REVERT: B 345 GLU cc_start: 0.8625 (OUTLIER) cc_final: 0.7925 (mp0) REVERT: B 535 LYS cc_start: 0.8227 (ttpp) cc_final: 0.7821 (tppt) REVERT: C 170 LYS cc_start: 0.8814 (mttp) cc_final: 0.8370 (mmtt) REVERT: C 171 ARG cc_start: 0.7040 (OUTLIER) cc_final: 0.6343 (ptt-90) REVERT: C 296 ARG cc_start: 0.6857 (ptp-110) cc_final: 0.6588 (mtt90) REVERT: C 345 GLU cc_start: 0.8531 (OUTLIER) cc_final: 0.7842 (mp0) REVERT: C 535 LYS cc_start: 0.8354 (mmmm) cc_final: 0.7915 (mtpp) REVERT: C 550 ARG cc_start: 0.7989 (mmt-90) cc_final: 0.7477 (tpp-160) REVERT: D 171 ARG cc_start: 0.6993 (OUTLIER) cc_final: 0.6381 (ptt-90) REVERT: D 278 ARG cc_start: 0.6432 (OUTLIER) cc_final: 0.5923 (ppt90) REVERT: D 312 ASP cc_start: 0.7750 (OUTLIER) cc_final: 0.7523 (t0) REVERT: D 363 ASP cc_start: 0.7335 (p0) cc_final: 0.7105 (p0) REVERT: D 452 LYS cc_start: 0.8341 (OUTLIER) cc_final: 0.8007 (ttmt) REVERT: D 550 ARG cc_start: 0.7889 (tpp-160) cc_final: 0.7552 (tpp-160) REVERT: B 702 GLN cc_start: 0.7987 (pt0) cc_final: 0.7520 (pt0) REVERT: C 601 GLN cc_start: 0.8004 (pt0) cc_final: 0.7574 (pt0) REVERT: D 702 GLN cc_start: 0.8062 (pt0) cc_final: 0.7640 (pt0) outliers start: 58 outliers final: 46 residues processed: 292 average time/residue: 0.3730 time to fit residues: 156.9279 Evaluate side-chains 300 residues out of total 1948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 243 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 68 ASP Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 171 ARG Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 258 GLN Chi-restraints excluded: chain A residue 278 ARG Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 452 LYS Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain A residue 512 ILE Chi-restraints excluded: chain A residue 537 SER Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 112 GLN Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 171 ARG Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 313 SER Chi-restraints excluded: chain B residue 345 GLU Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 510 GLU Chi-restraints excluded: chain B residue 537 SER Chi-restraints excluded: chain C residue 68 ASP Chi-restraints excluded: chain C residue 112 GLN Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 171 ARG Chi-restraints excluded: chain C residue 217 SER Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 313 SER Chi-restraints excluded: chain C residue 345 GLU Chi-restraints excluded: chain C residue 382 ILE Chi-restraints excluded: chain C residue 422 THR Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 452 LYS Chi-restraints excluded: chain C residue 507 THR Chi-restraints excluded: chain C residue 510 GLU Chi-restraints excluded: chain C residue 537 SER Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 171 ARG Chi-restraints excluded: chain D residue 172 GLU Chi-restraints excluded: chain D residue 217 SER Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 278 ARG Chi-restraints excluded: chain D residue 312 ASP Chi-restraints excluded: chain D residue 313 SER Chi-restraints excluded: chain D residue 422 THR Chi-restraints excluded: chain D residue 433 VAL Chi-restraints excluded: chain D residue 452 LYS Chi-restraints excluded: chain D residue 507 THR Chi-restraints excluded: chain D residue 510 GLU Chi-restraints excluded: chain D residue 537 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 188 optimal weight: 0.9990 chunk 117 optimal weight: 1.9990 chunk 82 optimal weight: 0.6980 chunk 48 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 93 optimal weight: 5.9990 chunk 165 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 30 optimal weight: 4.9990 chunk 193 optimal weight: 3.9990 chunk 83 optimal weight: 0.6980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 526 HIS ** 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 = 0.3683 r_free = 0.3683 target = 0.151815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.112500 restraints weight = 57505.938| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 2.03 r_work: 0.3039 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2895 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.2961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 18180 Z= 0.105 Angle : 0.519 6.012 24660 Z= 0.263 Chirality : 0.042 0.133 2764 Planarity : 0.004 0.049 3156 Dihedral : 7.923 72.322 2720 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.87 % Favored : 94.95 % Rotamer: Outliers : 2.72 % Allowed : 21.51 % Favored : 75.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -0.78 (0.18), residues: 2216 helix: 0.86 (0.17), residues: 964 sheet: -1.51 (0.27), residues: 324 loop : -1.60 (0.21), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 465 TYR 0.014 0.001 TYR D 488 PHE 0.006 0.001 PHE A 162 TRP 0.007 0.001 TRP D 285 HIS 0.004 0.001 HIS B 440 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.10 (18180) covalent geometry : angle 0.51855 / 0.26 (24660) hydrogen bonds : bond 0.02974 / 1.97 ( 748) hydrogen bonds : angle 4.34923 / 3.04 ( 2196) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 241 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 ARG cc_start: 0.6752 (OUTLIER) cc_final: 0.6149 (ptt-90) REVERT: A 278 ARG cc_start: 0.6175 (OUTLIER) cc_final: 0.5828 (ppt90) REVERT: A 290 ARG cc_start: 0.7928 (ttm-80) cc_final: 0.7426 (tpt170) REVERT: A 378 MET cc_start: 0.5926 (tpt) cc_final: 0.5496 (tpt) REVERT: A 452 LYS cc_start: 0.8326 (OUTLIER) cc_final: 0.8051 (ttmt) REVERT: A 550 ARG cc_start: 0.8055 (mmt-90) cc_final: 0.7452 (tpp-160) REVERT: B 1 MET cc_start: 0.8466 (ttm) cc_final: 0.8243 (ttm) REVERT: B 170 LYS cc_start: 0.8932 (mttp) cc_final: 0.8538 (mmtt) REVERT: B 171 ARG cc_start: 0.6914 (OUTLIER) cc_final: 0.6242 (ptt-90) REVERT: B 345 GLU cc_start: 0.8625 (OUTLIER) cc_final: 0.7934 (mp0) REVERT: B 535 LYS cc_start: 0.8229 (ttpp) cc_final: 0.7834 (tppt) REVERT: C 170 LYS cc_start: 0.8818 (mttp) cc_final: 0.8425 (mmtt) REVERT: C 171 ARG cc_start: 0.6985 (OUTLIER) cc_final: 0.6331 (ptt-90) REVERT: C 345 GLU cc_start: 0.8554 (OUTLIER) cc_final: 0.7862 (mp0) REVERT: C 535 LYS cc_start: 0.8359 (mmmm) cc_final: 0.7917 (mtpp) REVERT: C 550 ARG cc_start: 0.8002 (mmt-90) cc_final: 0.7497 (tpp-160) REVERT: D 171 ARG cc_start: 0.6825 (OUTLIER) cc_final: 0.6225 (ptt-90) REVERT: D 278 ARG cc_start: 0.6357 (OUTLIER) cc_final: 0.5735 (ppt90) REVERT: D 312 ASP cc_start: 0.7723 (OUTLIER) cc_final: 0.7502 (t0) REVERT: D 363 ASP cc_start: 0.7257 (p0) cc_final: 0.7023 (p0) REVERT: D 452 LYS cc_start: 0.8332 (OUTLIER) cc_final: 0.8004 (ttmt) REVERT: D 550 ARG cc_start: 0.7895 (tpp-160) cc_final: 0.7607 (tpp-160) REVERT: B 702 GLN cc_start: 0.7968 (pt0) cc_final: 0.7511 (pt0) REVERT: C 601 GLN cc_start: 0.7954 (pt0) cc_final: 0.7573 (pt0) REVERT: D 702 GLN cc_start: 0.8044 (pt0) cc_final: 0.7597 (pt0) outliers start: 53 outliers final: 41 residues processed: 283 average time/residue: 0.3792 time to fit residues: 153.3296 Evaluate side-chains 286 residues out of total 1948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 234 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 68 ASP Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 171 ARG Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 258 GLN Chi-restraints excluded: chain A residue 278 ARG Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 452 LYS Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain A residue 512 ILE Chi-restraints excluded: chain A residue 537 SER Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 171 ARG Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 313 SER Chi-restraints excluded: chain B residue 345 GLU Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 510 GLU Chi-restraints excluded: chain B residue 537 SER Chi-restraints excluded: chain C residue 68 ASP Chi-restraints excluded: chain C residue 112 GLN Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 171 ARG Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 313 SER Chi-restraints excluded: chain C residue 345 GLU Chi-restraints excluded: chain C residue 422 THR Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 452 LYS Chi-restraints excluded: chain C residue 510 GLU Chi-restraints excluded: chain C residue 537 SER Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 171 ARG Chi-restraints excluded: chain D residue 172 GLU Chi-restraints excluded: chain D residue 217 SER Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 278 ARG Chi-restraints excluded: chain D residue 312 ASP Chi-restraints excluded: chain D residue 313 SER Chi-restraints excluded: chain D residue 422 THR Chi-restraints excluded: chain D residue 433 VAL Chi-restraints excluded: chain D residue 452 LYS Chi-restraints excluded: chain D residue 507 THR Chi-restraints excluded: chain D residue 510 GLU Chi-restraints excluded: chain D residue 537 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 206 optimal weight: 6.9990 chunk 99 optimal weight: 0.6980 chunk 157 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 165 optimal weight: 2.9990 chunk 191 optimal weight: 0.5980 chunk 172 optimal weight: 0.8980 chunk 134 optimal weight: 2.9990 chunk 139 optimal weight: 4.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 526 HIS ** 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 = 0.3677 r_free = 0.3677 target = 0.151337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.111767 restraints weight = 57443.554| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 1.91 r_work: 0.3032 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.3024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 18180 Z= 0.131 Angle : 0.536 5.790 24660 Z= 0.271 Chirality : 0.042 0.135 2764 Planarity : 0.004 0.049 3156 Dihedral : 7.972 74.360 2720 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.64 % Favored : 94.18 % Rotamer: Outliers : 2.87 % Allowed : 21.30 % Favored : 75.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -0.76 (0.18), residues: 2216 helix: 0.87 (0.17), residues: 960 sheet: -1.50 (0.27), residues: 324 loop : -1.58 (0.21), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 465 TYR 0.013 0.001 TYR A 482 PHE 0.008 0.001 PHE A 162 TRP 0.008 0.001 TRP D 285 HIS 0.005 0.001 HIS A 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.13 (18180) covalent geometry : angle 0.53648 / 0.27 (24660) hydrogen bonds : bond 0.03116 / 2.08 ( 748) hydrogen bonds : angle 4.39355 / 3.07 ( 2196) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8884.55 seconds wall clock time: 151 minutes 17.68 seconds (9077.68 seconds total)