Starting phenix.real_space_refine on Sat Mar 7 09:04:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6uks_20811/03_2026/6uks_20811_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/6uks_20811/03_2026/6uks_20811.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/6uks_20811/03_2026/6uks_20811.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6uks_20811/03_2026/6uks_20811.map" model { file = "/net/cci-nas-00/data/ceres_data/6uks_20811/03_2026/6uks_20811_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6uks_20811/03_2026/6uks_20811_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= 0.003 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: 7 Type Number sf(0) Gaussians P 21 5.49 5 Mg 7 5.21 5 S 77 5.16 5 C 13132 2.51 5 N 3612 2.21 5 O 3829 1.98 5 H 20160 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 40838 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 5802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 5802 Classifications: {'peptide': 362} Link IDs: {'PTRANS': 18, 'TRANS': 343} Chain breaks: 1 Chain: "B" Number of atoms: 5802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 5802 Classifications: {'peptide': 362} Link IDs: {'PTRANS': 18, 'TRANS': 343} Chain breaks: 1 Chain: "C" Number of atoms: 5802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 5802 Classifications: {'peptide': 362} Link IDs: {'PTRANS': 18, 'TRANS': 343} Chain breaks: 1 Chain: "D" Number of atoms: 5802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 5802 Classifications: {'peptide': 362} Link IDs: {'PTRANS': 18, 'TRANS': 343} Chain breaks: 1 Chain: "E" Number of atoms: 5802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 5802 Classifications: {'peptide': 362} Link IDs: {'PTRANS': 18, 'TRANS': 343} Chain breaks: 1 Chain: "F" Number of atoms: 5802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 5802 Classifications: {'peptide': 362} Link IDs: {'PTRANS': 18, 'TRANS': 343} Chain breaks: 1 Chain: "G" Number of atoms: 5802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 5802 Classifications: {'peptide': 362} Link IDs: {'PTRANS': 18, 'TRANS': 343} Chain breaks: 1 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.83, per 1000 atoms: 0.19 Number of scatterers: 40838 At special positions: 0 Unit cell: (144.48, 143.62, 92.02, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 77 16.00 P 21 15.00 Mg 7 11.99 O 3829 8.00 N 3612 7.00 C 13132 6.00 H 20160 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=7, symmetry=0 Number of additional bonds: simple=7, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.53 Conformation dependent library (CDL) restraints added in 1.2 seconds 5012 Ramachandran restraints generated. 2506 Oldfield, 0 Emsley, 2506 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4732 Finding SS restraints... Secondary structure from input PDB file: 105 helices and 28 sheets defined 42.3% alpha, 15.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.12 Creating SS restraints... Processing helix chain 'A' and resid 59 through 71 removed outlier: 3.678A pdb=" N SER A 71 " --> pdb=" O LEU A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 90 removed outlier: 3.599A pdb=" N GLY A 89 " --> pdb=" O HIS A 86 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ARG A 90 " --> pdb=" O GLU A 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 86 through 90' Processing helix chain 'A' and resid 144 through 162 removed outlier: 3.845A pdb=" N PHE A 148 " --> pdb=" O ARG A 144 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N GLU A 162 " --> pdb=" O ALA A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 191 removed outlier: 3.515A pdb=" N SER A 190 " --> pdb=" O PRO A 187 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL A 191 " --> pdb=" O LEU A 188 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 187 through 191' Processing helix chain 'A' and resid 197 through 210 Processing helix chain 'A' and resid 212 through 217 Processing helix chain 'A' and resid 235 through 247 Processing helix chain 'A' and resid 262 through 270 Processing helix chain 'A' and resid 284 through 288 removed outlier: 3.698A pdb=" N ALA A 287 " --> pdb=" O VAL A 284 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE A 288 " --> pdb=" O ASP A 285 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 284 through 288' Processing helix chain 'A' and resid 308 through 317 removed outlier: 3.573A pdb=" N LEU A 312 " --> pdb=" O THR A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 369 Processing helix chain 'A' and resid 373 through 388 removed outlier: 3.813A pdb=" N ALA A 377 " --> pdb=" O ALA A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 403 removed outlier: 3.651A pdb=" N TYR A 403 " --> pdb=" O TYR A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 413 Processing helix chain 'A' and resid 414 through 418 removed outlier: 3.580A pdb=" N ARG A 418 " --> pdb=" O GLU A 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 71 removed outlier: 3.678A pdb=" N SER B 71 " --> pdb=" O LEU B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 90 removed outlier: 3.599A pdb=" N GLY B 89 " --> pdb=" O HIS B 86 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ARG B 90 " --> pdb=" O GLU B 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 86 through 90' Processing helix chain 'B' and resid 144 through 162 removed outlier: 3.845A pdb=" N PHE B 148 " --> pdb=" O ARG B 144 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N GLU B 162 " --> pdb=" O ALA B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 191 removed outlier: 3.514A pdb=" N SER B 190 " --> pdb=" O PRO B 187 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL B 191 " --> pdb=" O LEU B 188 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 187 through 191' Processing helix chain 'B' and resid 197 through 210 Processing helix chain 'B' and resid 212 through 217 Processing helix chain 'B' and resid 235 through 247 Processing helix chain 'B' and resid 262 through 270 Processing helix chain 'B' and resid 284 through 288 removed outlier: 3.697A pdb=" N ALA B 287 " --> pdb=" O VAL B 284 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE B 288 " --> pdb=" O ASP B 285 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 284 through 288' Processing helix chain 'B' and resid 308 through 317 removed outlier: 3.572A pdb=" N LEU B 312 " --> pdb=" O THR B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 369 Processing helix chain 'B' and resid 373 through 388 removed outlier: 3.813A pdb=" N ALA B 377 " --> pdb=" O ALA B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 403 removed outlier: 3.651A pdb=" N TYR B 403 " --> pdb=" O TYR B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 413 Processing helix chain 'B' and resid 414 through 418 removed outlier: 3.581A pdb=" N ARG B 418 " --> pdb=" O GLU B 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 71 removed outlier: 3.678A pdb=" N SER C 71 " --> pdb=" O LEU C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 90 removed outlier: 3.599A pdb=" N GLY C 89 " --> pdb=" O HIS C 86 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ARG C 90 " --> pdb=" O GLU C 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 86 through 90' Processing helix chain 'C' and resid 144 through 162 removed outlier: 3.845A pdb=" N PHE C 148 " --> pdb=" O ARG C 144 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N GLU C 162 " --> pdb=" O ALA C 158 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 191 removed outlier: 3.514A pdb=" N SER C 190 " --> pdb=" O PRO C 187 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL C 191 " --> pdb=" O LEU C 188 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 187 through 191' Processing helix chain 'C' and resid 197 through 210 Processing helix chain 'C' and resid 212 through 217 Processing helix chain 'C' and resid 235 through 247 Processing helix chain 'C' and resid 262 through 270 Processing helix chain 'C' and resid 284 through 288 removed outlier: 3.697A pdb=" N ALA C 287 " --> pdb=" O VAL C 284 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE C 288 " --> pdb=" O ASP C 285 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 284 through 288' Processing helix chain 'C' and resid 308 through 317 removed outlier: 3.573A pdb=" N LEU C 312 " --> pdb=" O THR C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 369 Processing helix chain 'C' and resid 373 through 388 removed outlier: 3.814A pdb=" N ALA C 377 " --> pdb=" O ALA C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 392 through 403 removed outlier: 3.651A pdb=" N TYR C 403 " --> pdb=" O TYR C 399 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 413 Processing helix chain 'C' and resid 414 through 418 removed outlier: 3.580A pdb=" N ARG C 418 " --> pdb=" O GLU C 415 " (cutoff:3.500A) Processing helix chain 'D' and resid 59 through 71 removed outlier: 3.678A pdb=" N SER D 71 " --> pdb=" O LEU D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 90 removed outlier: 3.599A pdb=" N GLY D 89 " --> pdb=" O HIS D 86 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ARG D 90 " --> pdb=" O GLU D 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 86 through 90' Processing helix chain 'D' and resid 144 through 162 removed outlier: 3.845A pdb=" N PHE D 148 " --> pdb=" O ARG D 144 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N GLU D 162 " --> pdb=" O ALA D 158 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 191 removed outlier: 3.514A pdb=" N SER D 190 " --> pdb=" O PRO D 187 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL D 191 " --> pdb=" O LEU D 188 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 187 through 191' Processing helix chain 'D' and resid 197 through 210 Processing helix chain 'D' and resid 212 through 217 Processing helix chain 'D' and resid 235 through 247 Processing helix chain 'D' and resid 262 through 270 Processing helix chain 'D' and resid 284 through 288 removed outlier: 3.697A pdb=" N ALA D 287 " --> pdb=" O VAL D 284 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE D 288 " --> pdb=" O ASP D 285 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 284 through 288' Processing helix chain 'D' and resid 308 through 317 removed outlier: 3.573A pdb=" N LEU D 312 " --> pdb=" O THR D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 357 through 369 Processing helix chain 'D' and resid 373 through 388 removed outlier: 3.813A pdb=" N ALA D 377 " --> pdb=" O ALA D 373 " (cutoff:3.500A) Processing helix chain 'D' and resid 392 through 403 removed outlier: 3.650A pdb=" N TYR D 403 " --> pdb=" O TYR D 399 " (cutoff:3.500A) Processing helix chain 'D' and resid 406 through 413 Processing helix chain 'D' and resid 414 through 418 removed outlier: 3.581A pdb=" N ARG D 418 " --> pdb=" O GLU D 415 " (cutoff:3.500A) Processing helix chain 'E' and resid 59 through 71 removed outlier: 3.678A pdb=" N SER E 71 " --> pdb=" O LEU E 67 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 90 removed outlier: 3.599A pdb=" N GLY E 89 " --> pdb=" O HIS E 86 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ARG E 90 " --> pdb=" O GLU E 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 86 through 90' Processing helix chain 'E' and resid 144 through 162 removed outlier: 3.844A pdb=" N PHE E 148 " --> pdb=" O ARG E 144 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLU E 162 " --> pdb=" O ALA E 158 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 191 removed outlier: 3.514A pdb=" N SER E 190 " --> pdb=" O PRO E 187 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL E 191 " --> pdb=" O LEU E 188 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 187 through 191' Processing helix chain 'E' and resid 197 through 210 Processing helix chain 'E' and resid 212 through 217 Processing helix chain 'E' and resid 235 through 247 Processing helix chain 'E' and resid 262 through 270 Processing helix chain 'E' and resid 284 through 288 removed outlier: 3.697A pdb=" N ALA E 287 " --> pdb=" O VAL E 284 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE E 288 " --> pdb=" O ASP E 285 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 284 through 288' Processing helix chain 'E' and resid 308 through 317 removed outlier: 3.571A pdb=" N LEU E 312 " --> pdb=" O THR E 308 " (cutoff:3.500A) Processing helix chain 'E' and resid 357 through 369 Processing helix chain 'E' and resid 373 through 388 removed outlier: 3.813A pdb=" N ALA E 377 " --> pdb=" O ALA E 373 " (cutoff:3.500A) Processing helix chain 'E' and resid 392 through 403 removed outlier: 3.650A pdb=" N TYR E 403 " --> pdb=" O TYR E 399 " (cutoff:3.500A) Processing helix chain 'E' and resid 406 through 413 Processing helix chain 'E' and resid 414 through 418 removed outlier: 3.580A pdb=" N ARG E 418 " --> pdb=" O GLU E 415 " (cutoff:3.500A) Processing helix chain 'F' and resid 59 through 71 removed outlier: 3.677A pdb=" N SER F 71 " --> pdb=" O LEU F 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 90 removed outlier: 3.599A pdb=" N GLY F 89 " --> pdb=" O HIS F 86 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ARG F 90 " --> pdb=" O GLU F 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 86 through 90' Processing helix chain 'F' and resid 144 through 162 removed outlier: 3.845A pdb=" N PHE F 148 " --> pdb=" O ARG F 144 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLU F 162 " --> pdb=" O ALA F 158 " (cutoff:3.500A) Processing helix chain 'F' and resid 187 through 191 removed outlier: 3.514A pdb=" N SER F 190 " --> pdb=" O PRO F 187 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL F 191 " --> pdb=" O LEU F 188 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 187 through 191' Processing helix chain 'F' and resid 197 through 210 Processing helix chain 'F' and resid 212 through 217 Processing helix chain 'F' and resid 235 through 247 Processing helix chain 'F' and resid 262 through 270 Processing helix chain 'F' and resid 284 through 288 removed outlier: 3.698A pdb=" N ALA F 287 " --> pdb=" O VAL F 284 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE F 288 " --> pdb=" O ASP F 285 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 284 through 288' Processing helix chain 'F' and resid 308 through 317 removed outlier: 3.572A pdb=" N LEU F 312 " --> pdb=" O THR F 308 " (cutoff:3.500A) Processing helix chain 'F' and resid 357 through 369 Processing helix chain 'F' and resid 373 through 388 removed outlier: 3.812A pdb=" N ALA F 377 " --> pdb=" O ALA F 373 " (cutoff:3.500A) Processing helix chain 'F' and resid 392 through 403 removed outlier: 3.651A pdb=" N TYR F 403 " --> pdb=" O TYR F 399 " (cutoff:3.500A) Processing helix chain 'F' and resid 406 through 413 Processing helix chain 'F' and resid 414 through 418 removed outlier: 3.580A pdb=" N ARG F 418 " --> pdb=" O GLU F 415 " (cutoff:3.500A) Processing helix chain 'G' and resid 59 through 71 removed outlier: 3.678A pdb=" N SER G 71 " --> pdb=" O LEU G 67 " (cutoff:3.500A) Processing helix chain 'G' and resid 86 through 90 removed outlier: 3.598A pdb=" N GLY G 89 " --> pdb=" O HIS G 86 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ARG G 90 " --> pdb=" O GLU G 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 86 through 90' Processing helix chain 'G' and resid 144 through 162 removed outlier: 3.844A pdb=" N PHE G 148 " --> pdb=" O ARG G 144 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLU G 162 " --> pdb=" O ALA G 158 " (cutoff:3.500A) Processing helix chain 'G' and resid 187 through 191 removed outlier: 3.514A pdb=" N SER G 190 " --> pdb=" O PRO G 187 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL G 191 " --> pdb=" O LEU G 188 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 187 through 191' Processing helix chain 'G' and resid 197 through 210 Processing helix chain 'G' and resid 212 through 217 Processing helix chain 'G' and resid 235 through 247 Processing helix chain 'G' and resid 262 through 270 Processing helix chain 'G' and resid 284 through 288 removed outlier: 3.697A pdb=" N ALA G 287 " --> pdb=" O VAL G 284 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE G 288 " --> pdb=" O ASP G 285 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 284 through 288' Processing helix chain 'G' and resid 308 through 317 removed outlier: 3.573A pdb=" N LEU G 312 " --> pdb=" O THR G 308 " (cutoff:3.500A) Processing helix chain 'G' and resid 357 through 369 Processing helix chain 'G' and resid 373 through 388 removed outlier: 3.814A pdb=" N ALA G 377 " --> pdb=" O ALA G 373 " (cutoff:3.500A) Processing helix chain 'G' and resid 392 through 403 removed outlier: 3.651A pdb=" N TYR G 403 " --> pdb=" O TYR G 399 " (cutoff:3.500A) Processing helix chain 'G' and resid 406 through 413 Processing helix chain 'G' and resid 414 through 418 removed outlier: 3.581A pdb=" N ARG G 418 " --> pdb=" O GLU G 415 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 50 through 52 removed outlier: 3.766A pdb=" N ARG A 117 " --> pdb=" O GLY A 102 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLY A 102 " --> pdb=" O ARG A 117 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 80 through 84 Processing sheet with id=AA3, first strand: chain 'A' and resid 165 through 166 Processing sheet with id=AA4, first strand: chain 'A' and resid 175 through 178 removed outlier: 3.637A pdb=" N LEU A 253 " --> pdb=" O TYR A 169 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ALA A 171 " --> pdb=" O LEU A 253 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N SER A 250 " --> pdb=" O LEU A 278 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N LEU A 280 " --> pdb=" O SER A 250 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N CYS A 252 " --> pdb=" O LEU A 280 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N GLU A 282 " --> pdb=" O CYS A 252 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N LEU A 254 " --> pdb=" O GLU A 282 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N ILE A 326 " --> pdb=" O SER A 277 " (cutoff:3.500A) removed outlier: 8.672A pdb=" N GLU A 351 " --> pdb=" O GLY A 225 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LEU A 227 " --> pdb=" O GLU A 351 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 50 through 52 removed outlier: 3.767A pdb=" N ARG B 117 " --> pdb=" O GLY B 102 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLY B 102 " --> pdb=" O ARG B 117 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 80 through 84 Processing sheet with id=AA7, first strand: chain 'B' and resid 165 through 166 Processing sheet with id=AA8, first strand: chain 'B' and resid 175 through 178 removed outlier: 3.637A pdb=" N LEU B 253 " --> pdb=" O TYR B 169 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ALA B 171 " --> pdb=" O LEU B 253 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N SER B 250 " --> pdb=" O LEU B 278 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N LEU B 280 " --> pdb=" O SER B 250 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N CYS B 252 " --> pdb=" O LEU B 280 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N GLU B 282 " --> pdb=" O CYS B 252 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N LEU B 254 " --> pdb=" O GLU B 282 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N ILE B 326 " --> pdb=" O SER B 277 " (cutoff:3.500A) removed outlier: 8.672A pdb=" N GLU B 351 " --> pdb=" O GLY B 225 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LEU B 227 " --> pdb=" O GLU B 351 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 50 through 52 removed outlier: 3.766A pdb=" N ARG C 117 " --> pdb=" O GLY C 102 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLY C 102 " --> pdb=" O ARG C 117 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 80 through 84 Processing sheet with id=AB2, first strand: chain 'C' and resid 165 through 166 Processing sheet with id=AB3, first strand: chain 'C' and resid 175 through 178 removed outlier: 3.637A pdb=" N LEU C 253 " --> pdb=" O TYR C 169 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ALA C 171 " --> pdb=" O LEU C 253 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N SER C 250 " --> pdb=" O LEU C 278 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N LEU C 280 " --> pdb=" O SER C 250 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N CYS C 252 " --> pdb=" O LEU C 280 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N GLU C 282 " --> pdb=" O CYS C 252 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N LEU C 254 " --> pdb=" O GLU C 282 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N ILE C 326 " --> pdb=" O SER C 277 " (cutoff:3.500A) removed outlier: 8.672A pdb=" N GLU C 351 " --> pdb=" O GLY C 225 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LEU C 227 " --> pdb=" O GLU C 351 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 50 through 52 removed outlier: 3.766A pdb=" N ARG D 117 " --> pdb=" O GLY D 102 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLY D 102 " --> pdb=" O ARG D 117 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 80 through 84 Processing sheet with id=AB6, first strand: chain 'D' and resid 165 through 166 Processing sheet with id=AB7, first strand: chain 'D' and resid 175 through 178 removed outlier: 3.637A pdb=" N LEU D 253 " --> pdb=" O TYR D 169 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ALA D 171 " --> pdb=" O LEU D 253 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N SER D 250 " --> pdb=" O LEU D 278 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N LEU D 280 " --> pdb=" O SER D 250 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N CYS D 252 " --> pdb=" O LEU D 280 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N GLU D 282 " --> pdb=" O CYS D 252 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N LEU D 254 " --> pdb=" O GLU D 282 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N ILE D 326 " --> pdb=" O SER D 277 " (cutoff:3.500A) removed outlier: 8.672A pdb=" N GLU D 351 " --> pdb=" O GLY D 225 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LEU D 227 " --> pdb=" O GLU D 351 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 50 through 52 removed outlier: 3.767A pdb=" N ARG E 117 " --> pdb=" O GLY E 102 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLY E 102 " --> pdb=" O ARG E 117 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 80 through 84 Processing sheet with id=AC1, first strand: chain 'E' and resid 165 through 166 Processing sheet with id=AC2, first strand: chain 'E' and resid 175 through 178 removed outlier: 3.637A pdb=" N LEU E 253 " --> pdb=" O TYR E 169 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ALA E 171 " --> pdb=" O LEU E 253 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N SER E 250 " --> pdb=" O LEU E 278 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N LEU E 280 " --> pdb=" O SER E 250 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N CYS E 252 " --> pdb=" O LEU E 280 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N GLU E 282 " --> pdb=" O CYS E 252 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N LEU E 254 " --> pdb=" O GLU E 282 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N ILE E 326 " --> pdb=" O SER E 277 " (cutoff:3.500A) removed outlier: 8.672A pdb=" N GLU E 351 " --> pdb=" O GLY E 225 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LEU E 227 " --> pdb=" O GLU E 351 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 50 through 52 removed outlier: 3.766A pdb=" N ARG F 117 " --> pdb=" O GLY F 102 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLY F 102 " --> pdb=" O ARG F 117 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 80 through 84 Processing sheet with id=AC5, first strand: chain 'F' and resid 165 through 166 Processing sheet with id=AC6, first strand: chain 'F' and resid 175 through 178 removed outlier: 3.637A pdb=" N LEU F 253 " --> pdb=" O TYR F 169 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ALA F 171 " --> pdb=" O LEU F 253 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N SER F 250 " --> pdb=" O LEU F 278 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N LEU F 280 " --> pdb=" O SER F 250 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N CYS F 252 " --> pdb=" O LEU F 280 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N GLU F 282 " --> pdb=" O CYS F 252 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N LEU F 254 " --> pdb=" O GLU F 282 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N ILE F 326 " --> pdb=" O SER F 277 " (cutoff:3.500A) removed outlier: 8.672A pdb=" N GLU F 351 " --> pdb=" O GLY F 225 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LEU F 227 " --> pdb=" O GLU F 351 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 50 through 52 removed outlier: 3.766A pdb=" N ARG G 117 " --> pdb=" O GLY G 102 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLY G 102 " --> pdb=" O ARG G 117 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 80 through 84 Processing sheet with id=AC9, first strand: chain 'G' and resid 165 through 166 Processing sheet with id=AD1, first strand: chain 'G' and resid 175 through 178 removed outlier: 3.637A pdb=" N LEU G 253 " --> pdb=" O TYR G 169 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ALA G 171 " --> pdb=" O LEU G 253 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N SER G 250 " --> pdb=" O LEU G 278 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N LEU G 280 " --> pdb=" O SER G 250 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N CYS G 252 " --> pdb=" O LEU G 280 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N GLU G 282 " --> pdb=" O CYS G 252 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N LEU G 254 " --> pdb=" O GLU G 282 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N ILE G 326 " --> pdb=" O SER G 277 " (cutoff:3.500A) removed outlier: 8.672A pdb=" N GLU G 351 " --> pdb=" O GLY G 225 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LEU G 227 " --> pdb=" O GLU G 351 " (cutoff:3.500A) 833 hydrogen bonds defined for protein. 2352 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: 11.01 Time building geometry restraints manager: 4.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.78 - 1.02: 20137 1.02 - 1.25: 3306 1.25 - 1.49: 9477 1.49 - 1.73: 8310 1.73 - 1.96: 126 Bond restraints: 41356 Sorted by residual: bond pdb=" NH2 ARG C 56 " pdb="HH22 ARG C 56 " ideal model delta sigma weight residual 0.860 0.937 -0.077 2.00e-02 2.50e+03 1.50e+01 bond pdb=" OG1 THR G 130 " pdb=" HG1 THR G 130 " ideal model delta sigma weight residual 0.840 0.781 0.059 2.00e-02 2.50e+03 8.60e+00 bond pdb=" CG2 THR E 130 " pdb="HG22 THR E 130 " ideal model delta sigma weight residual 0.970 1.029 -0.059 2.00e-02 2.50e+03 8.57e+00 bond pdb=" OG1 THR E 130 " pdb=" HG1 THR E 130 " ideal model delta sigma weight residual 0.840 0.784 0.056 2.00e-02 2.50e+03 7.85e+00 bond pdb=" NH1 ARG C 56 " pdb="HH12 ARG C 56 " ideal model delta sigma weight residual 0.860 0.911 -0.051 2.00e-02 2.50e+03 6.52e+00 ... (remaining 41351 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.66: 73467 2.66 - 5.32: 846 5.32 - 7.97: 110 7.97 - 10.63: 15 10.63 - 13.29: 7 Bond angle restraints: 74445 Sorted by residual: angle pdb=" OG1 THR E 130 " pdb=" CB THR E 130 " pdb=" HB THR E 130 " ideal model delta sigma weight residual 109.00 95.71 13.29 3.00e+00 1.11e-01 1.96e+01 angle pdb=" C SER A 59 " pdb=" N TYR A 60 " pdb=" CA TYR A 60 " ideal model delta sigma weight residual 120.38 126.28 -5.90 1.37e+00 5.33e-01 1.86e+01 angle pdb=" C SER F 59 " pdb=" N TYR F 60 " pdb=" CA TYR F 60 " ideal model delta sigma weight residual 120.38 126.27 -5.89 1.37e+00 5.33e-01 1.85e+01 angle pdb=" C SER B 59 " pdb=" N TYR B 60 " pdb=" CA TYR B 60 " ideal model delta sigma weight residual 120.38 126.25 -5.87 1.37e+00 5.33e-01 1.84e+01 angle pdb=" C SER D 59 " pdb=" N TYR D 60 " pdb=" CA TYR D 60 " ideal model delta sigma weight residual 120.38 126.23 -5.85 1.37e+00 5.33e-01 1.83e+01 ... (remaining 74440 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.67: 18697 27.67 - 55.35: 762 55.35 - 83.02: 50 83.02 - 110.70: 0 110.70 - 138.37: 7 Dihedral angle restraints: 19516 sinusoidal: 10619 harmonic: 8897 Sorted by residual: dihedral pdb=" O1A AGS C 800 " pdb=" O3A AGS C 800 " pdb=" PA AGS C 800 " pdb=" PB AGS C 800 " ideal model delta sinusoidal sigma weight residual -67.73 70.64 -138.37 1 3.00e+01 1.11e-03 1.86e+01 dihedral pdb=" O1A AGS G 800 " pdb=" O3A AGS G 800 " pdb=" PA AGS G 800 " pdb=" PB AGS G 800 " ideal model delta sinusoidal sigma weight residual -67.73 70.59 -138.32 1 3.00e+01 1.11e-03 1.86e+01 dihedral pdb=" O1A AGS F 800 " pdb=" O3A AGS F 800 " pdb=" PA AGS F 800 " pdb=" PB AGS F 800 " ideal model delta sinusoidal sigma weight residual -67.73 70.59 -138.32 1 3.00e+01 1.11e-03 1.86e+01 ... (remaining 19513 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1938 0.038 - 0.076: 838 0.076 - 0.114: 286 0.114 - 0.152: 59 0.152 - 0.189: 15 Chirality restraints: 3136 Sorted by residual: chirality pdb=" CA PRO B 54 " pdb=" N PRO B 54 " pdb=" C PRO B 54 " pdb=" CB PRO B 54 " both_signs ideal model delta sigma weight residual False 2.72 2.53 0.19 2.00e-01 2.50e+01 8.97e-01 chirality pdb=" CA PRO C 54 " pdb=" N PRO C 54 " pdb=" C PRO C 54 " pdb=" CB PRO C 54 " both_signs ideal model delta sigma weight residual False 2.72 2.53 0.19 2.00e-01 2.50e+01 8.96e-01 chirality pdb=" CA PRO D 54 " pdb=" N PRO D 54 " pdb=" C PRO D 54 " pdb=" CB PRO D 54 " both_signs ideal model delta sigma weight residual False 2.72 2.53 0.19 2.00e-01 2.50e+01 8.84e-01 ... (remaining 3133 not shown) Planarity restraints: 6062 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 56 " -0.001 9.50e-02 1.11e+02 1.83e-02 7.55e+00 pdb=" NE ARG C 56 " -0.001 2.00e-02 2.50e+03 pdb=" CZ ARG C 56 " -0.023 2.00e-02 2.50e+03 pdb=" NH1 ARG C 56 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG C 56 " -0.033 2.00e-02 2.50e+03 pdb="HH11 ARG C 56 " 0.016 2.00e-02 2.50e+03 pdb="HH12 ARG C 56 " -0.002 2.00e-02 2.50e+03 pdb="HH21 ARG C 56 " 0.004 2.00e-02 2.50e+03 pdb="HH22 ARG C 56 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR F 130 " -0.045 5.00e-02 4.00e+02 6.80e-02 7.41e+00 pdb=" N PRO F 131 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO F 131 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO F 131 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR D 130 " 0.045 5.00e-02 4.00e+02 6.80e-02 7.39e+00 pdb=" N PRO D 131 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO D 131 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO D 131 " 0.038 5.00e-02 4.00e+02 ... (remaining 6059 not shown) Histogram of nonbonded interaction distances: 1.64 - 2.23: 3744 2.23 - 2.82: 87158 2.82 - 3.42: 97510 3.42 - 4.01: 134682 4.01 - 4.60: 209422 Nonbonded interactions: 532516 Sorted by model distance: nonbonded pdb="HH21 ARG B 223 " pdb=" OD1 ASP B 317 " model vdw 1.638 2.450 nonbonded pdb="HH21 ARG A 223 " pdb=" OD1 ASP A 317 " model vdw 1.638 2.450 nonbonded pdb="HH21 ARG C 223 " pdb=" OD1 ASP C 317 " model vdw 1.639 2.450 nonbonded pdb="HH21 ARG F 223 " pdb=" OD1 ASP F 317 " model vdw 1.639 2.450 nonbonded pdb="HH21 ARG E 223 " pdb=" OD1 ASP E 317 " model vdw 1.639 2.450 ... (remaining 532511 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and resid 49 through 419) selection = (chain 'B' and resid 49 through 419) selection = (chain 'C' and resid 49 through 419) selection = (chain 'D' and resid 49 through 419) selection = (chain 'E' and resid 49 through 419) selection = (chain 'F' and resid 49 through 419) selection = (chain 'G' and resid 49 through 419) } 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: 1.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.270 Extract box with map and model: 0.600 Check model and map are aligned: 0.120 Set scattering table: 0.120 Process input model: 39.930 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 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 : 0.009 0.059 21203 Z= 0.350 Angle : 0.883 8.320 28819 Z= 0.470 Chirality : 0.048 0.189 3136 Planarity : 0.007 0.068 3668 Dihedral : 14.491 138.374 7861 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.38 % Favored : 91.62 % Rotamer: Outliers : 0.32 % Allowed : 1.59 % Favored : 98.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.37 (0.15), residues: 2506 helix: -0.70 (0.16), residues: 917 sheet: -2.56 (0.19), residues: 602 loop : -3.47 (0.17), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 56 TYR 0.018 0.002 TYR D 60 PHE 0.022 0.002 PHE B 148 TRP 0.005 0.001 TRP G 214 HIS 0.007 0.001 HIS D 104 Details of bonding type rmsd covalent geometry : bond 0.00855 (21196) covalent geometry : angle 0.88309 (28819) hydrogen bonds : bond 0.18075 ( 833) hydrogen bonds : angle 6.05639 ( 2352) Misc. bond : bond 0.01319 ( 7) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5012 Ramachandran restraints generated. 2506 Oldfield, 0 Emsley, 2506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5012 Ramachandran restraints generated. 2506 Oldfield, 0 Emsley, 2506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 237 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Evaluate side-chains 516 residues out of total 2205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 509 time to evaluate : 1.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLU cc_start: 0.6868 (mt-10) cc_final: 0.6522 (mt-10) REVERT: A 204 ASP cc_start: 0.7838 (t70) cc_final: 0.7384 (t0) REVERT: A 276 GLN cc_start: 0.8513 (mt0) cc_final: 0.8280 (mt0) REVERT: B 52 GLU cc_start: 0.6897 (mt-10) cc_final: 0.6471 (tt0) REVERT: C 52 GLU cc_start: 0.6524 (mt-10) cc_final: 0.6234 (mt-10) REVERT: C 213 LYS cc_start: 0.8570 (ttpp) cc_final: 0.8235 (ttpt) REVERT: C 276 GLN cc_start: 0.8345 (mt0) cc_final: 0.8112 (mt0) REVERT: D 52 GLU cc_start: 0.6761 (mt-10) cc_final: 0.6474 (mt-10) REVERT: D 213 LYS cc_start: 0.8659 (ttpp) cc_final: 0.8375 (ttpt) REVERT: D 276 GLN cc_start: 0.8348 (mt0) cc_final: 0.8132 (mt0) REVERT: E 213 LYS cc_start: 0.8715 (ttpp) cc_final: 0.8263 (ttmm) REVERT: E 276 GLN cc_start: 0.8408 (mt0) cc_final: 0.8180 (mt0) REVERT: F 52 GLU cc_start: 0.6727 (mt-10) cc_final: 0.6306 (mt-10) REVERT: F 66 TRP cc_start: 0.8699 (t60) cc_final: 0.8328 (t60) REVERT: F 276 GLN cc_start: 0.8478 (mt0) cc_final: 0.8256 (mt0) REVERT: G 52 GLU cc_start: 0.6683 (mt-10) cc_final: 0.6415 (mt-10) REVERT: G 213 LYS cc_start: 0.8686 (ttpp) cc_final: 0.8346 (ttmm) REVERT: G 276 GLN cc_start: 0.8428 (mt0) cc_final: 0.8220 (mt0) outliers start: 7 outliers final: 3 residues processed: 516 average time/residue: 0.3706 time to fit residues: 286.1558 Evaluate side-chains 438 residues out of total 2205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 435 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain F residue 130 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 216 optimal weight: 7.9990 chunk 98 optimal weight: 0.8980 chunk 194 optimal weight: 1.9990 chunk 227 optimal weight: 0.9980 chunk 107 optimal weight: 0.4980 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 2.9990 chunk 247 optimal weight: 4.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 4.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 GLN B 127 GLN B 332 ASN C 127 GLN D 127 GLN D 332 ASN ** E 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 76 HIS ** F 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 332 ASN G 127 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.134555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.100407 restraints weight = 83898.827| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 2.50 r_work: 0.3071 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2917 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 21203 Z= 0.145 Angle : 0.608 5.515 28819 Z= 0.319 Chirality : 0.040 0.131 3136 Planarity : 0.007 0.083 3668 Dihedral : 10.653 147.177 2971 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 0.14 % Allowed : 5.99 % Favored : 93.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.29 (0.16), residues: 2506 helix: 0.45 (0.17), residues: 931 sheet: -2.21 (0.19), residues: 581 loop : -3.00 (0.18), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 58 TYR 0.025 0.001 TYR F 60 PHE 0.014 0.001 PHE G 95 TRP 0.004 0.001 TRP G 62 HIS 0.004 0.001 HIS E 358 Details of bonding type rmsd covalent geometry : bond 0.00324 (21196) covalent geometry : angle 0.60750 (28819) hydrogen bonds : bond 0.05204 ( 833) hydrogen bonds : angle 5.03409 ( 2352) Misc. bond : bond 0.00106 ( 7) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5012 Ramachandran restraints generated. 2506 Oldfield, 0 Emsley, 2506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5012 Ramachandran restraints generated. 2506 Oldfield, 0 Emsley, 2506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 237 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Evaluate side-chains 444 residues out of total 2205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 441 time to evaluate : 0.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLU cc_start: 0.7204 (mt-10) cc_final: 0.6887 (mt-10) REVERT: A 162 GLU cc_start: 0.5896 (mp0) cc_final: 0.5622 (mp0) REVERT: A 276 GLN cc_start: 0.8948 (mt0) cc_final: 0.8719 (mt0) REVERT: B 87 GLU cc_start: 0.8577 (mm-30) cc_final: 0.8344 (mm-30) REVERT: B 204 ASP cc_start: 0.8243 (t70) cc_final: 0.7774 (t0) REVERT: B 282 GLU cc_start: 0.8014 (mm-30) cc_final: 0.7753 (mm-30) REVERT: C 52 GLU cc_start: 0.6937 (mt-10) cc_final: 0.6726 (mt-10) REVERT: C 58 ARG cc_start: 0.8010 (ttt-90) cc_final: 0.7731 (ttt180) REVERT: C 95 PHE cc_start: 0.6122 (m-80) cc_final: 0.5781 (m-10) REVERT: C 213 LYS cc_start: 0.8406 (ttpp) cc_final: 0.8202 (ttpt) REVERT: C 276 GLN cc_start: 0.8815 (mt0) cc_final: 0.8567 (mt0) REVERT: D 97 PHE cc_start: 0.8579 (m-80) cc_final: 0.8193 (m-10) REVERT: D 132 TRP cc_start: 0.7776 (t-100) cc_final: 0.7540 (t-100) REVERT: D 276 GLN cc_start: 0.8731 (mt0) cc_final: 0.8522 (mt0) REVERT: E 204 ASP cc_start: 0.8305 (t70) cc_final: 0.7932 (t70) REVERT: E 276 GLN cc_start: 0.8852 (mt0) cc_final: 0.8599 (mt0) REVERT: F 52 GLU cc_start: 0.7181 (mt-10) cc_final: 0.6959 (mt-10) REVERT: F 85 GLN cc_start: 0.7859 (tt0) cc_final: 0.7649 (tt0) REVERT: F 86 HIS cc_start: 0.8022 (m170) cc_final: 0.7643 (m90) REVERT: F 123 MET cc_start: 0.6369 (ptm) cc_final: 0.6088 (ttp) REVERT: F 189 ASP cc_start: 0.8095 (p0) cc_final: 0.7803 (t0) REVERT: F 276 GLN cc_start: 0.8932 (mt0) cc_final: 0.8711 (mt0) outliers start: 3 outliers final: 3 residues processed: 442 average time/residue: 0.3422 time to fit residues: 233.2563 Evaluate side-chains 429 residues out of total 2205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 426 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain G residue 50 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 232 optimal weight: 0.4980 chunk 246 optimal weight: 3.9990 chunk 54 optimal weight: 0.0870 chunk 224 optimal weight: 7.9990 chunk 199 optimal weight: 0.6980 chunk 95 optimal weight: 2.9990 chunk 133 optimal weight: 0.9980 chunk 17 optimal weight: 3.9990 chunk 110 optimal weight: 9.9990 chunk 210 optimal weight: 3.9990 chunk 131 optimal weight: 2.9990 overall best weight: 1.0560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 127 GLN E 275 GLN F 127 GLN G 332 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.134242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.099952 restraints weight = 84289.636| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 2.49 r_work: 0.3065 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 21203 Z= 0.132 Angle : 0.559 5.223 28819 Z= 0.287 Chirality : 0.039 0.147 3136 Planarity : 0.005 0.055 3668 Dihedral : 10.478 151.574 2968 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 0.18 % Allowed : 7.12 % Favored : 92.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.71 (0.17), residues: 2506 helix: 0.92 (0.17), residues: 945 sheet: -1.91 (0.20), residues: 581 loop : -2.71 (0.18), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG G 144 TYR 0.021 0.001 TYR F 60 PHE 0.009 0.001 PHE E 148 TRP 0.005 0.001 TRP E 66 HIS 0.003 0.001 HIS B 358 Details of bonding type rmsd covalent geometry : bond 0.00307 (21196) covalent geometry : angle 0.55873 (28819) hydrogen bonds : bond 0.04656 ( 833) hydrogen bonds : angle 4.61289 ( 2352) Misc. bond : bond 0.00067 ( 7) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5012 Ramachandran restraints generated. 2506 Oldfield, 0 Emsley, 2506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5012 Ramachandran restraints generated. 2506 Oldfield, 0 Emsley, 2506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 237 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Evaluate side-chains 451 residues out of total 2205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 447 time to evaluate : 1.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 ASP cc_start: 0.8217 (t70) cc_final: 0.7951 (t70) REVERT: A 276 GLN cc_start: 0.8923 (mt0) cc_final: 0.8714 (mt0) REVERT: B 204 ASP cc_start: 0.8227 (t70) cc_final: 0.7735 (t0) REVERT: B 347 VAL cc_start: 0.8856 (t) cc_final: 0.8386 (p) REVERT: C 86 HIS cc_start: 0.7764 (m170) cc_final: 0.7495 (m170) REVERT: C 95 PHE cc_start: 0.6144 (m-80) cc_final: 0.5782 (m-10) REVERT: C 276 GLN cc_start: 0.8797 (mt0) cc_final: 0.8560 (mt0) REVERT: D 95 PHE cc_start: 0.6353 (m-80) cc_final: 0.5917 (m-80) REVERT: D 132 TRP cc_start: 0.7833 (t-100) cc_final: 0.7517 (t-100) REVERT: D 276 GLN cc_start: 0.8762 (mt0) cc_final: 0.8508 (mt0) REVERT: D 415 GLU cc_start: 0.8720 (mp0) cc_final: 0.8470 (mp0) REVERT: E 97 PHE cc_start: 0.8648 (m-80) cc_final: 0.8426 (m-10) REVERT: E 204 ASP cc_start: 0.8294 (t70) cc_final: 0.7932 (t70) REVERT: E 276 GLN cc_start: 0.8845 (mt0) cc_final: 0.8596 (mt0) REVERT: F 52 GLU cc_start: 0.7225 (mt-10) cc_final: 0.7008 (mt-10) REVERT: F 276 GLN cc_start: 0.8937 (mt0) cc_final: 0.8720 (mt0) REVERT: G 123 MET cc_start: 0.5713 (ttp) cc_final: 0.5475 (ttp) outliers start: 4 outliers final: 2 residues processed: 448 average time/residue: 0.3592 time to fit residues: 245.1811 Evaluate side-chains 430 residues out of total 2205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 428 time to evaluate : 1.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain B residue 217 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 24 optimal weight: 5.9990 chunk 228 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 194 optimal weight: 2.9990 chunk 247 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 75 optimal weight: 6.9990 chunk 107 optimal weight: 4.9990 chunk 124 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 45 optimal weight: 10.0000 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 397 GLN B 76 HIS D 397 GLN E 85 GLN E 275 GLN E 397 GLN F 397 GLN G 397 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.131964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.097761 restraints weight = 84360.409| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 2.48 r_work: 0.3029 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 21203 Z= 0.186 Angle : 0.561 5.222 28819 Z= 0.287 Chirality : 0.040 0.138 3136 Planarity : 0.005 0.061 3668 Dihedral : 10.557 152.724 2968 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 0.45 % Allowed : 7.66 % Favored : 91.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.35 (0.17), residues: 2506 helix: 1.23 (0.18), residues: 945 sheet: -1.73 (0.20), residues: 567 loop : -2.50 (0.19), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 346 TYR 0.023 0.001 TYR E 60 PHE 0.009 0.001 PHE G 137 TRP 0.004 0.001 TRP G 66 HIS 0.003 0.001 HIS F 249 Details of bonding type rmsd covalent geometry : bond 0.00448 (21196) covalent geometry : angle 0.56096 (28819) hydrogen bonds : bond 0.04603 ( 833) hydrogen bonds : angle 4.52448 ( 2352) Misc. bond : bond 0.00168 ( 7) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5012 Ramachandran restraints generated. 2506 Oldfield, 0 Emsley, 2506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5012 Ramachandran restraints generated. 2506 Oldfield, 0 Emsley, 2506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 237 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Evaluate side-chains 445 residues out of total 2205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 435 time to evaluate : 1.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 ASP cc_start: 0.8314 (t70) cc_final: 0.8031 (t70) REVERT: A 276 GLN cc_start: 0.8918 (mt0) cc_final: 0.8579 (mt0) REVERT: A 333 TYR cc_start: 0.8418 (m-80) cc_final: 0.8000 (m-80) REVERT: B 52 GLU cc_start: 0.7262 (mt-10) cc_final: 0.6974 (mt-10) REVERT: B 204 ASP cc_start: 0.8262 (t70) cc_final: 0.7768 (t0) REVERT: B 347 VAL cc_start: 0.8903 (t) cc_final: 0.8700 (m) REVERT: C 85 GLN cc_start: 0.8173 (tt0) cc_final: 0.7933 (tt0) REVERT: C 95 PHE cc_start: 0.6403 (m-80) cc_final: 0.6103 (m-10) REVERT: C 276 GLN cc_start: 0.8824 (mt0) cc_final: 0.8601 (mt0) REVERT: C 347 VAL cc_start: 0.8923 (t) cc_final: 0.8661 (m) REVERT: C 415 GLU cc_start: 0.8628 (mp0) cc_final: 0.8356 (mp0) REVERT: D 95 PHE cc_start: 0.6614 (m-80) cc_final: 0.6088 (m-80) REVERT: D 132 TRP cc_start: 0.7917 (t-100) cc_final: 0.7625 (t-100) REVERT: D 276 GLN cc_start: 0.8824 (mt0) cc_final: 0.8567 (mt0) REVERT: D 415 GLU cc_start: 0.8730 (mp0) cc_final: 0.8486 (mp0) REVERT: E 276 GLN cc_start: 0.8831 (mt0) cc_final: 0.8590 (mt0) REVERT: E 415 GLU cc_start: 0.8705 (mp0) cc_final: 0.8461 (mp0) REVERT: F 204 ASP cc_start: 0.8314 (t70) cc_final: 0.7574 (t70) REVERT: F 276 GLN cc_start: 0.8941 (mt0) cc_final: 0.8733 (mt0) REVERT: G 52 GLU cc_start: 0.7274 (mt-10) cc_final: 0.7028 (mt-10) outliers start: 10 outliers final: 5 residues processed: 441 average time/residue: 0.3509 time to fit residues: 235.4923 Evaluate side-chains 427 residues out of total 2205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 422 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain G residue 319 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 78 optimal weight: 8.9990 chunk 31 optimal weight: 3.9990 chunk 176 optimal weight: 4.9990 chunk 164 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 157 optimal weight: 0.7980 chunk 197 optimal weight: 2.9990 chunk 47 optimal weight: 0.0270 chunk 8 optimal weight: 2.9990 chunk 226 optimal weight: 10.0000 chunk 173 optimal weight: 2.9990 overall best weight: 1.9644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN B 397 GLN C 397 GLN E 275 GLN E 397 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.131731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.097824 restraints weight = 84726.594| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 2.49 r_work: 0.3023 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2872 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.2663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 21203 Z= 0.178 Angle : 0.542 4.892 28819 Z= 0.279 Chirality : 0.040 0.161 3136 Planarity : 0.005 0.062 3668 Dihedral : 10.689 153.724 2968 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 0.41 % Allowed : 8.57 % Favored : 91.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.17), residues: 2506 helix: 1.38 (0.18), residues: 945 sheet: -1.63 (0.20), residues: 567 loop : -2.39 (0.20), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 144 TYR 0.019 0.001 TYR E 60 PHE 0.009 0.001 PHE D 137 TRP 0.005 0.001 TRP G 66 HIS 0.005 0.001 HIS B 76 Details of bonding type rmsd covalent geometry : bond 0.00429 (21196) covalent geometry : angle 0.54173 (28819) hydrogen bonds : bond 0.04447 ( 833) hydrogen bonds : angle 4.42691 ( 2352) Misc. bond : bond 0.00112 ( 7) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5012 Ramachandran restraints generated. 2506 Oldfield, 0 Emsley, 2506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5012 Ramachandran restraints generated. 2506 Oldfield, 0 Emsley, 2506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 237 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Evaluate side-chains 427 residues out of total 2205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 418 time to evaluate : 1.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 ASP cc_start: 0.8279 (t70) cc_final: 0.7993 (t70) REVERT: A 276 GLN cc_start: 0.8915 (mt0) cc_final: 0.8606 (mt0) REVERT: A 333 TYR cc_start: 0.8412 (m-80) cc_final: 0.7973 (m-80) REVERT: B 52 GLU cc_start: 0.7243 (mt-10) cc_final: 0.6957 (mt-10) REVERT: B 87 GLU cc_start: 0.8528 (mm-30) cc_final: 0.8320 (mm-30) REVERT: B 123 MET cc_start: 0.5758 (ttp) cc_final: 0.5437 (ttp) REVERT: B 204 ASP cc_start: 0.8267 (t70) cc_final: 0.7985 (t70) REVERT: B 258 ASP cc_start: 0.7659 (t0) cc_final: 0.7430 (t0) REVERT: B 282 GLU cc_start: 0.7987 (mm-30) cc_final: 0.7738 (mm-30) REVERT: B 347 VAL cc_start: 0.8920 (t) cc_final: 0.8713 (m) REVERT: C 95 PHE cc_start: 0.6498 (m-80) cc_final: 0.6292 (m-10) REVERT: C 347 VAL cc_start: 0.8930 (t) cc_final: 0.8690 (m) REVERT: D 95 PHE cc_start: 0.6717 (m-80) cc_final: 0.6209 (m-80) REVERT: D 132 TRP cc_start: 0.7937 (t-100) cc_final: 0.7639 (t-100) REVERT: D 276 GLN cc_start: 0.8834 (mt0) cc_final: 0.8573 (mt0) REVERT: D 415 GLU cc_start: 0.8715 (mp0) cc_final: 0.8471 (mp0) REVERT: E 276 GLN cc_start: 0.8813 (mt0) cc_final: 0.8573 (mt0) REVERT: E 415 GLU cc_start: 0.8714 (mp0) cc_final: 0.8449 (mp0) REVERT: F 86 HIS cc_start: 0.7944 (m170) cc_final: 0.7533 (m90) REVERT: F 258 ASP cc_start: 0.7794 (t0) cc_final: 0.7579 (t0) REVERT: F 276 GLN cc_start: 0.8938 (mt0) cc_final: 0.8735 (mt0) REVERT: G 123 MET cc_start: 0.5648 (ttp) cc_final: 0.5429 (ttp) REVERT: G 277 SER cc_start: 0.8858 (p) cc_final: 0.8540 (t) outliers start: 9 outliers final: 6 residues processed: 424 average time/residue: 0.3643 time to fit residues: 233.6464 Evaluate side-chains 418 residues out of total 2205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 412 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain B residue 217 ASP Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain G residue 319 VAL Chi-restraints excluded: chain G residue 342 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 238 optimal weight: 1.9990 chunk 45 optimal weight: 10.0000 chunk 221 optimal weight: 7.9990 chunk 40 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 218 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 227 optimal weight: 2.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 85 GLN C 76 HIS E 275 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.131387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.097555 restraints weight = 85041.299| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 2.49 r_work: 0.3019 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 21203 Z= 0.182 Angle : 0.543 5.175 28819 Z= 0.278 Chirality : 0.039 0.147 3136 Planarity : 0.005 0.050 3668 Dihedral : 10.751 154.920 2968 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 0.41 % Allowed : 9.30 % Favored : 90.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.17), residues: 2506 helix: 1.47 (0.18), residues: 945 sheet: -1.56 (0.20), residues: 567 loop : -2.36 (0.20), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 58 TYR 0.018 0.001 TYR B 60 PHE 0.009 0.001 PHE C 137 TRP 0.005 0.001 TRP B 66 HIS 0.011 0.001 HIS B 104 Details of bonding type rmsd covalent geometry : bond 0.00441 (21196) covalent geometry : angle 0.54336 (28819) hydrogen bonds : bond 0.04378 ( 833) hydrogen bonds : angle 4.39407 ( 2352) Misc. bond : bond 0.00115 ( 7) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5012 Ramachandran restraints generated. 2506 Oldfield, 0 Emsley, 2506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5012 Ramachandran restraints generated. 2506 Oldfield, 0 Emsley, 2506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 237 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Evaluate side-chains 434 residues out of total 2205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 425 time to evaluate : 1.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 ASP cc_start: 0.8292 (t70) cc_final: 0.8010 (t70) REVERT: A 276 GLN cc_start: 0.8910 (mt0) cc_final: 0.8616 (mt0) REVERT: A 333 TYR cc_start: 0.8423 (m-80) cc_final: 0.7971 (m-80) REVERT: B 52 GLU cc_start: 0.7240 (mt-10) cc_final: 0.6961 (mt-10) REVERT: B 87 GLU cc_start: 0.8549 (mm-30) cc_final: 0.8336 (mm-30) REVERT: B 123 MET cc_start: 0.5730 (ttp) cc_final: 0.5409 (ttp) REVERT: B 204 ASP cc_start: 0.8274 (t70) cc_final: 0.7998 (t70) REVERT: B 282 GLU cc_start: 0.7993 (mm-30) cc_final: 0.7787 (tp30) REVERT: B 347 VAL cc_start: 0.8927 (t) cc_final: 0.8725 (m) REVERT: C 64 LEU cc_start: 0.8087 (mm) cc_final: 0.7867 (mt) REVERT: C 95 PHE cc_start: 0.6605 (m-80) cc_final: 0.6354 (m-80) REVERT: C 204 ASP cc_start: 0.8216 (t70) cc_final: 0.7926 (t0) REVERT: C 347 VAL cc_start: 0.8935 (t) cc_final: 0.8691 (m) REVERT: D 95 PHE cc_start: 0.6713 (m-80) cc_final: 0.6173 (m-10) REVERT: D 132 TRP cc_start: 0.7967 (t-100) cc_final: 0.7674 (t-100) REVERT: D 276 GLN cc_start: 0.8817 (mt0) cc_final: 0.8574 (mt0) REVERT: D 415 GLU cc_start: 0.8735 (mp0) cc_final: 0.8481 (mp0) REVERT: E 213 LYS cc_start: 0.8595 (ttpp) cc_final: 0.8140 (ttmm) REVERT: E 276 GLN cc_start: 0.8812 (mt0) cc_final: 0.8575 (mt0) REVERT: E 347 VAL cc_start: 0.9026 (t) cc_final: 0.8724 (m) REVERT: E 415 GLU cc_start: 0.8720 (mp0) cc_final: 0.8449 (mp0) REVERT: F 58 ARG cc_start: 0.8131 (tpt-90) cc_final: 0.7887 (ttt90) REVERT: F 86 HIS cc_start: 0.7951 (m170) cc_final: 0.7548 (m90) REVERT: F 258 ASP cc_start: 0.7777 (t0) cc_final: 0.7553 (t0) REVERT: F 276 GLN cc_start: 0.8937 (mt0) cc_final: 0.8720 (mt0) REVERT: F 347 VAL cc_start: 0.8981 (t) cc_final: 0.8773 (m) REVERT: G 123 MET cc_start: 0.5611 (ttp) cc_final: 0.5334 (ttp) REVERT: G 277 SER cc_start: 0.8869 (p) cc_final: 0.8545 (t) outliers start: 9 outliers final: 7 residues processed: 429 average time/residue: 0.3640 time to fit residues: 235.0729 Evaluate side-chains 428 residues out of total 2205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 421 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain F residue 331 THR Chi-restraints excluded: chain F residue 385 LEU Chi-restraints excluded: chain G residue 319 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 219 optimal weight: 4.9990 chunk 44 optimal weight: 10.0000 chunk 244 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 67 optimal weight: 3.9990 chunk 1 optimal weight: 6.9990 chunk 77 optimal weight: 2.9990 chunk 145 optimal weight: 0.6980 chunk 114 optimal weight: 6.9990 chunk 245 optimal weight: 1.9990 chunk 42 optimal weight: 6.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 85 GLN C 76 HIS E 275 GLN F 76 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.131094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.097361 restraints weight = 84745.260| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 2.48 r_work: 0.3016 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 21203 Z= 0.175 Angle : 0.534 5.128 28819 Z= 0.274 Chirality : 0.039 0.155 3136 Planarity : 0.005 0.066 3668 Dihedral : 10.799 156.403 2968 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 0.41 % Allowed : 9.71 % Favored : 89.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.18), residues: 2506 helix: 1.58 (0.18), residues: 945 sheet: -1.47 (0.21), residues: 567 loop : -2.29 (0.20), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 144 TYR 0.018 0.001 TYR B 60 PHE 0.008 0.001 PHE B 148 TRP 0.005 0.001 TRP B 66 HIS 0.007 0.001 HIS B 104 Details of bonding type rmsd covalent geometry : bond 0.00425 (21196) covalent geometry : angle 0.53371 (28819) hydrogen bonds : bond 0.04225 ( 833) hydrogen bonds : angle 4.30781 ( 2352) Misc. bond : bond 0.00113 ( 7) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5012 Ramachandran restraints generated. 2506 Oldfield, 0 Emsley, 2506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5012 Ramachandran restraints generated. 2506 Oldfield, 0 Emsley, 2506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 237 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Evaluate side-chains 435 residues out of total 2205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 426 time to evaluate : 1.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 ASP cc_start: 0.8252 (t70) cc_final: 0.7970 (t70) REVERT: A 276 GLN cc_start: 0.8894 (mt0) cc_final: 0.8621 (mt0) REVERT: A 333 TYR cc_start: 0.8431 (m-80) cc_final: 0.7940 (m-80) REVERT: B 52 GLU cc_start: 0.7214 (mt-10) cc_final: 0.6916 (mt-10) REVERT: B 58 ARG cc_start: 0.7951 (tpt-90) cc_final: 0.7685 (ttt-90) REVERT: B 123 MET cc_start: 0.5732 (ttp) cc_final: 0.5446 (ttp) REVERT: B 204 ASP cc_start: 0.8267 (t70) cc_final: 0.7986 (t70) REVERT: B 282 GLU cc_start: 0.8020 (mm-30) cc_final: 0.7741 (mm-30) REVERT: B 347 VAL cc_start: 0.8925 (t) cc_final: 0.8720 (m) REVERT: C 204 ASP cc_start: 0.8213 (t70) cc_final: 0.7849 (t70) REVERT: C 347 VAL cc_start: 0.8939 (t) cc_final: 0.8690 (m) REVERT: D 95 PHE cc_start: 0.6850 (m-80) cc_final: 0.6638 (m-10) REVERT: D 105 PHE cc_start: 0.7832 (m-80) cc_final: 0.7607 (m-80) REVERT: D 132 TRP cc_start: 0.7979 (t-100) cc_final: 0.7688 (t-100) REVERT: D 276 GLN cc_start: 0.8813 (mt0) cc_final: 0.8577 (mt0) REVERT: D 415 GLU cc_start: 0.8738 (mp0) cc_final: 0.8466 (mp0) REVERT: E 86 HIS cc_start: 0.7968 (m170) cc_final: 0.7665 (m90) REVERT: E 213 LYS cc_start: 0.8600 (ttpp) cc_final: 0.8145 (ttmm) REVERT: E 276 GLN cc_start: 0.8819 (mt0) cc_final: 0.8570 (mt0) REVERT: E 347 VAL cc_start: 0.9039 (t) cc_final: 0.8755 (m) REVERT: E 415 GLU cc_start: 0.8733 (mp0) cc_final: 0.8454 (mp0) REVERT: F 86 HIS cc_start: 0.7972 (m170) cc_final: 0.7591 (m90) REVERT: F 123 MET cc_start: 0.5661 (ttp) cc_final: 0.5210 (ttp) REVERT: F 276 GLN cc_start: 0.8938 (mt0) cc_final: 0.8693 (mt0) REVERT: F 347 VAL cc_start: 0.8990 (t) cc_final: 0.8779 (m) REVERT: G 277 SER cc_start: 0.8869 (p) cc_final: 0.8537 (t) outliers start: 9 outliers final: 9 residues processed: 430 average time/residue: 0.3707 time to fit residues: 240.1061 Evaluate side-chains 429 residues out of total 2205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 420 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain B residue 217 ASP Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain F residue 64 LEU Chi-restraints excluded: chain F residue 331 THR Chi-restraints excluded: chain G residue 319 VAL Chi-restraints excluded: chain G residue 342 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 69 optimal weight: 0.9980 chunk 113 optimal weight: 1.9990 chunk 39 optimal weight: 7.9990 chunk 129 optimal weight: 2.9990 chunk 193 optimal weight: 0.3980 chunk 122 optimal weight: 2.9990 chunk 221 optimal weight: 0.9990 chunk 169 optimal weight: 3.9990 chunk 136 optimal weight: 2.9990 chunk 232 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 HIS C 76 HIS E 275 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.131558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.097773 restraints weight = 84917.311| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 2.50 r_work: 0.3020 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.3076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 21203 Z= 0.144 Angle : 0.520 5.159 28819 Z= 0.266 Chirality : 0.039 0.141 3136 Planarity : 0.005 0.048 3668 Dihedral : 10.728 154.851 2968 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 0.50 % Allowed : 10.20 % Favored : 89.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.18), residues: 2506 helix: 1.68 (0.17), residues: 945 sheet: -1.38 (0.21), residues: 567 loop : -2.20 (0.20), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 58 TYR 0.017 0.001 TYR B 60 PHE 0.007 0.001 PHE C 137 TRP 0.006 0.001 TRP B 66 HIS 0.008 0.001 HIS A 104 Details of bonding type rmsd covalent geometry : bond 0.00349 (21196) covalent geometry : angle 0.51958 (28819) hydrogen bonds : bond 0.03979 ( 833) hydrogen bonds : angle 4.20699 ( 2352) Misc. bond : bond 0.00047 ( 7) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5012 Ramachandran restraints generated. 2506 Oldfield, 0 Emsley, 2506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5012 Ramachandran restraints generated. 2506 Oldfield, 0 Emsley, 2506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 237 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Evaluate side-chains 430 residues out of total 2205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 419 time to evaluate : 1.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 GLU cc_start: 0.5686 (mp0) cc_final: 0.5351 (mp0) REVERT: A 204 ASP cc_start: 0.8248 (t70) cc_final: 0.7969 (t70) REVERT: A 276 GLN cc_start: 0.8899 (mt0) cc_final: 0.8617 (mt0) REVERT: A 333 TYR cc_start: 0.8415 (m-80) cc_final: 0.7919 (m-80) REVERT: B 123 MET cc_start: 0.5688 (ttp) cc_final: 0.5391 (ttp) REVERT: B 204 ASP cc_start: 0.8263 (t70) cc_final: 0.7980 (t70) REVERT: B 282 GLU cc_start: 0.8009 (mm-30) cc_final: 0.7717 (mm-30) REVERT: B 347 VAL cc_start: 0.8922 (t) cc_final: 0.8715 (m) REVERT: C 204 ASP cc_start: 0.8190 (t70) cc_final: 0.7839 (t70) REVERT: C 347 VAL cc_start: 0.8941 (t) cc_final: 0.8688 (m) REVERT: D 95 PHE cc_start: 0.6839 (m-80) cc_final: 0.6286 (m-80) REVERT: D 132 TRP cc_start: 0.7993 (t-100) cc_final: 0.7658 (t-100) REVERT: D 276 GLN cc_start: 0.8832 (mt0) cc_final: 0.8622 (mt0) REVERT: D 415 GLU cc_start: 0.8734 (mp0) cc_final: 0.8470 (mp0) REVERT: E 86 HIS cc_start: 0.7974 (m170) cc_final: 0.7679 (m90) REVERT: E 213 LYS cc_start: 0.8611 (ttpp) cc_final: 0.8156 (ttmm) REVERT: E 276 GLN cc_start: 0.8812 (mt0) cc_final: 0.8580 (mt0) REVERT: E 347 VAL cc_start: 0.9031 (t) cc_final: 0.8748 (m) REVERT: E 415 GLU cc_start: 0.8762 (mp0) cc_final: 0.8480 (mp0) REVERT: F 86 HIS cc_start: 0.7959 (m170) cc_final: 0.7578 (m90) REVERT: F 276 GLN cc_start: 0.8950 (mt0) cc_final: 0.8709 (mt0) REVERT: F 347 VAL cc_start: 0.8979 (t) cc_final: 0.8758 (m) outliers start: 11 outliers final: 9 residues processed: 423 average time/residue: 0.3705 time to fit residues: 236.2575 Evaluate side-chains 426 residues out of total 2205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 417 time to evaluate : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain B residue 217 ASP Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 308 THR Chi-restraints excluded: chain F residue 331 THR Chi-restraints excluded: chain G residue 104 HIS Chi-restraints excluded: chain G residue 342 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 62 optimal weight: 2.9990 chunk 43 optimal weight: 6.9990 chunk 103 optimal weight: 1.9990 chunk 228 optimal weight: 4.9990 chunk 104 optimal weight: 3.9990 chunk 126 optimal weight: 1.9990 chunk 40 optimal weight: 8.9990 chunk 245 optimal weight: 2.9990 chunk 198 optimal weight: 0.9980 chunk 3 optimal weight: 10.0000 chunk 66 optimal weight: 4.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 76 HIS E 275 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.130347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.096700 restraints weight = 85246.901| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 2.49 r_work: 0.3007 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2855 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.3169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 21203 Z= 0.196 Angle : 0.540 5.154 28819 Z= 0.277 Chirality : 0.040 0.142 3136 Planarity : 0.005 0.051 3668 Dihedral : 10.871 158.403 2968 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 0.59 % Allowed : 10.66 % Favored : 88.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.18), residues: 2506 helix: 1.38 (0.17), residues: 987 sheet: -1.34 (0.21), residues: 567 loop : -2.27 (0.20), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 144 TYR 0.009 0.001 TYR D 83 PHE 0.008 0.001 PHE A 137 TRP 0.006 0.001 TRP B 66 HIS 0.007 0.001 HIS F 104 Details of bonding type rmsd covalent geometry : bond 0.00477 (21196) covalent geometry : angle 0.54021 (28819) hydrogen bonds : bond 0.04299 ( 833) hydrogen bonds : angle 4.26913 ( 2352) Misc. bond : bond 0.00066 ( 7) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5012 Ramachandran restraints generated. 2506 Oldfield, 0 Emsley, 2506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5012 Ramachandran restraints generated. 2506 Oldfield, 0 Emsley, 2506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 237 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Evaluate side-chains 433 residues out of total 2205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 420 time to evaluate : 1.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 ASP cc_start: 0.8270 (t70) cc_final: 0.7992 (t70) REVERT: A 276 GLN cc_start: 0.8901 (mt0) cc_final: 0.8616 (mt0) REVERT: B 123 MET cc_start: 0.5673 (ttp) cc_final: 0.5364 (ttp) REVERT: B 204 ASP cc_start: 0.8268 (t70) cc_final: 0.7987 (t70) REVERT: B 282 GLU cc_start: 0.7986 (mm-30) cc_final: 0.7661 (mm-30) REVERT: B 347 VAL cc_start: 0.8938 (t) cc_final: 0.8730 (m) REVERT: C 87 GLU cc_start: 0.8489 (mm-30) cc_final: 0.8261 (mm-30) REVERT: C 204 ASP cc_start: 0.8208 (t70) cc_final: 0.7749 (t0) REVERT: C 347 VAL cc_start: 0.8947 (t) cc_final: 0.8699 (m) REVERT: D 132 TRP cc_start: 0.8012 (t-100) cc_final: 0.7725 (t-100) REVERT: D 189 ASP cc_start: 0.8282 (p0) cc_final: 0.7881 (t0) REVERT: D 276 GLN cc_start: 0.8815 (mt0) cc_final: 0.8601 (mt0) REVERT: D 415 GLU cc_start: 0.8731 (mp0) cc_final: 0.8486 (mp0) REVERT: E 86 HIS cc_start: 0.7917 (m170) cc_final: 0.7625 (m90) REVERT: E 213 LYS cc_start: 0.8616 (ttpp) cc_final: 0.8166 (ttmm) REVERT: E 276 GLN cc_start: 0.8854 (mt0) cc_final: 0.8617 (mt0) REVERT: E 347 VAL cc_start: 0.9044 (t) cc_final: 0.8762 (m) REVERT: E 415 GLU cc_start: 0.8779 (mp0) cc_final: 0.8492 (mp0) REVERT: F 86 HIS cc_start: 0.7987 (m170) cc_final: 0.7635 (m90) REVERT: F 123 MET cc_start: 0.5755 (ttp) cc_final: 0.5184 (ttp) REVERT: F 276 GLN cc_start: 0.8936 (mt0) cc_final: 0.8694 (mt0) REVERT: F 347 VAL cc_start: 0.9000 (t) cc_final: 0.8790 (m) REVERT: G 123 MET cc_start: 0.5336 (ttp) cc_final: 0.5115 (ttp) outliers start: 13 outliers final: 12 residues processed: 426 average time/residue: 0.3808 time to fit residues: 242.7090 Evaluate side-chains 434 residues out of total 2205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 422 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain B residue 217 ASP Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 308 THR Chi-restraints excluded: chain F residue 52 GLU Chi-restraints excluded: chain F residue 331 THR Chi-restraints excluded: chain G residue 104 HIS Chi-restraints excluded: chain G residue 319 VAL Chi-restraints excluded: chain G residue 342 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 47 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 chunk 211 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 173 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 10 optimal weight: 8.9990 chunk 180 optimal weight: 6.9990 chunk 183 optimal weight: 7.9990 chunk 135 optimal weight: 0.6980 chunk 127 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 76 HIS E 275 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.132082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.098302 restraints weight = 84313.093| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 2.48 r_work: 0.3029 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2876 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.3293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 21203 Z= 0.109 Angle : 0.516 5.693 28819 Z= 0.263 Chirality : 0.038 0.147 3136 Planarity : 0.005 0.083 3668 Dihedral : 10.645 153.931 2968 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 0.41 % Allowed : 11.16 % Favored : 88.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.18), residues: 2506 helix: 1.86 (0.17), residues: 945 sheet: -1.25 (0.21), residues: 567 loop : -2.08 (0.20), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 58 TYR 0.011 0.001 TYR C 60 PHE 0.006 0.001 PHE B 148 TRP 0.007 0.000 TRP B 66 HIS 0.007 0.001 HIS F 104 Details of bonding type rmsd covalent geometry : bond 0.00257 (21196) covalent geometry : angle 0.51571 (28819) hydrogen bonds : bond 0.03655 ( 833) hydrogen bonds : angle 4.06090 ( 2352) Misc. bond : bond 0.00039 ( 7) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5012 Ramachandran restraints generated. 2506 Oldfield, 0 Emsley, 2506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5012 Ramachandran restraints generated. 2506 Oldfield, 0 Emsley, 2506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 237 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Evaluate side-chains 434 residues out of total 2205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 425 time to evaluate : 1.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 ASP cc_start: 0.8218 (t70) cc_final: 0.7937 (t70) REVERT: A 276 GLN cc_start: 0.8882 (mt0) cc_final: 0.8597 (mt0) REVERT: B 123 MET cc_start: 0.5676 (ttp) cc_final: 0.5358 (ttp) REVERT: B 204 ASP cc_start: 0.8240 (t70) cc_final: 0.7954 (t70) REVERT: B 282 GLU cc_start: 0.7938 (mm-30) cc_final: 0.7623 (mm-30) REVERT: B 347 VAL cc_start: 0.8915 (t) cc_final: 0.8692 (m) REVERT: C 87 GLU cc_start: 0.8521 (mm-30) cc_final: 0.8294 (mm-30) REVERT: C 204 ASP cc_start: 0.8161 (t70) cc_final: 0.7813 (t70) REVERT: C 347 VAL cc_start: 0.8929 (t) cc_final: 0.8660 (m) REVERT: D 95 PHE cc_start: 0.6817 (m-80) cc_final: 0.6188 (m-10) REVERT: D 132 TRP cc_start: 0.7996 (t-100) cc_final: 0.7691 (t-100) REVERT: D 189 ASP cc_start: 0.8261 (p0) cc_final: 0.7838 (t0) REVERT: D 276 GLN cc_start: 0.8811 (mt0) cc_final: 0.8481 (mt0) REVERT: D 415 GLU cc_start: 0.8769 (mp0) cc_final: 0.8487 (mp0) REVERT: E 86 HIS cc_start: 0.7926 (m170) cc_final: 0.7643 (m90) REVERT: E 213 LYS cc_start: 0.8598 (ttpp) cc_final: 0.8148 (ttmm) REVERT: E 276 GLN cc_start: 0.8811 (mt0) cc_final: 0.8555 (mt0) REVERT: E 347 VAL cc_start: 0.9022 (t) cc_final: 0.8739 (m) REVERT: E 415 GLU cc_start: 0.8766 (mp0) cc_final: 0.8474 (mp0) REVERT: F 58 ARG cc_start: 0.8038 (tpt-90) cc_final: 0.7703 (ttt90) REVERT: F 86 HIS cc_start: 0.7968 (m170) cc_final: 0.7594 (m90) REVERT: F 123 MET cc_start: 0.5691 (ttp) cc_final: 0.5264 (ttp) REVERT: F 204 ASP cc_start: 0.8258 (t70) cc_final: 0.7515 (t0) REVERT: F 276 GLN cc_start: 0.8925 (mt0) cc_final: 0.8695 (mt0) REVERT: F 347 VAL cc_start: 0.8978 (t) cc_final: 0.8734 (m) REVERT: G 282 GLU cc_start: 0.8092 (mm-30) cc_final: 0.7856 (mm-30) outliers start: 9 outliers final: 9 residues processed: 428 average time/residue: 0.3771 time to fit residues: 242.1768 Evaluate side-chains 433 residues out of total 2205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 424 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain F residue 331 THR Chi-restraints excluded: chain F residue 385 LEU Chi-restraints excluded: chain G residue 104 HIS Chi-restraints excluded: chain G residue 319 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 41 optimal weight: 6.9990 chunk 79 optimal weight: 8.9990 chunk 81 optimal weight: 0.3980 chunk 220 optimal weight: 7.9990 chunk 33 optimal weight: 1.9990 chunk 169 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 109 optimal weight: 6.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 76 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.131443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.097783 restraints weight = 85346.628| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 2.49 r_work: 0.3019 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2867 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.3340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 21203 Z= 0.145 Angle : 0.522 5.033 28819 Z= 0.266 Chirality : 0.039 0.145 3136 Planarity : 0.005 0.076 3668 Dihedral : 10.722 156.243 2968 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 0.45 % Allowed : 11.29 % Favored : 88.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.18), residues: 2506 helix: 1.63 (0.17), residues: 987 sheet: -1.23 (0.21), residues: 567 loop : -2.10 (0.21), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 117 TYR 0.011 0.001 TYR C 60 PHE 0.006 0.001 PHE B 137 TRP 0.006 0.001 TRP B 66 HIS 0.007 0.001 HIS F 104 Details of bonding type rmsd covalent geometry : bond 0.00352 (21196) covalent geometry : angle 0.52176 (28819) hydrogen bonds : bond 0.03847 ( 833) hydrogen bonds : angle 4.07240 ( 2352) Misc. bond : bond 0.00048 ( 7) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11307.40 seconds wall clock time: 192 minutes 10.32 seconds (11530.32 seconds total)