Starting phenix.real_space_refine on Tue Sep 15 14:39:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6uks_20811/09_2026/6uks_20811_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/6uks_20811/09_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_20811/09_2026/6uks_20811.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6uks_20811/09_2026/6uks_20811.map" model { file = "/net/cci-nas-00/data/ceres_data/6uks_20811/09_2026/6uks_20811_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6uks_20811/09_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/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: 7.19, per 1000 atoms: 0.18 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: 3.84 Conformation dependent library (CDL) restraints added in 1.1 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: 0.98 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: 11.19 Time building geometry restraints manager: 5.33 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=" O3B AGS D 800 " pdb=" PB AGS D 800 " ideal model delta sigma weight residual 1.673 1.585 0.088 2.00e-02 2.50e+03 1.94e+01 bond pdb=" O3B AGS C 800 " pdb=" PB AGS C 800 " ideal model delta sigma weight residual 1.673 1.585 0.088 2.00e-02 2.50e+03 1.93e+01 bond pdb=" O3B AGS F 800 " pdb=" PB AGS F 800 " ideal model delta sigma weight residual 1.673 1.586 0.087 2.00e-02 2.50e+03 1.91e+01 bond pdb=" O3B AGS G 800 " pdb=" PB AGS G 800 " ideal model delta sigma weight residual 1.673 1.586 0.087 2.00e-02 2.50e+03 1.91e+01 bond pdb=" O3B AGS A 802 " pdb=" PB AGS A 802 " ideal model delta sigma weight residual 1.673 1.586 0.087 2.00e-02 2.50e+03 1.90e+01 ... (remaining 41351 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.66: 73343 2.66 - 5.32: 921 5.32 - 7.97: 131 7.97 - 10.63: 43 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 - 15.24: 17211 15.24 - 30.48: 1655 30.48 - 45.72: 489 45.72 - 60.96: 224 60.96 - 76.20: 63 Dihedral angle restraints: 19642 sinusoidal: 10745 harmonic: 8897 Sorted by residual: dihedral pdb=" CA GLN B 122 " pdb=" C GLN B 122 " pdb=" N MET B 123 " pdb=" CA MET B 123 " ideal model delta harmonic sigma weight residual -180.00 -158.55 -21.45 0 5.00e+00 4.00e-02 1.84e+01 dihedral pdb=" CA GLN F 122 " pdb=" C GLN F 122 " pdb=" N MET F 123 " pdb=" CA MET F 123 " ideal model delta harmonic sigma weight residual -180.00 -158.56 -21.44 0 5.00e+00 4.00e-02 1.84e+01 dihedral pdb=" CA GLN D 122 " pdb=" C GLN D 122 " pdb=" N MET D 123 " pdb=" CA MET D 123 " ideal model delta harmonic sigma weight residual -180.00 -158.58 -21.42 0 5.00e+00 4.00e-02 1.84e+01 ... (remaining 19639 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 2217 0.046 - 0.092: 687 0.092 - 0.138: 181 0.138 - 0.184: 23 0.184 - 0.230: 14 Chirality restraints: 3122 Sorted by residual: chirality pdb=" C3' AGS D 800 " pdb=" C2' AGS D 800 " pdb=" C4' AGS D 800 " pdb=" O3' AGS D 800 " both_signs ideal model delta sigma weight residual False -2.37 -2.60 0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" C3' AGS F 800 " pdb=" C2' AGS F 800 " pdb=" C4' AGS F 800 " pdb=" O3' AGS F 800 " both_signs ideal model delta sigma weight residual False -2.37 -2.60 0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" C3' AGS E 800 " pdb=" C2' AGS E 800 " pdb=" C4' AGS E 800 " pdb=" O3' AGS E 800 " both_signs ideal model delta sigma weight residual False -2.37 -2.60 0.23 2.00e-01 2.50e+01 1.32e+00 ... (remaining 3119 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: 1.460 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: 0.310 Extract box with map and model: 0.640 Check model and map are aligned: 0.120 Set scattering table: 0.100 Process input model: 39.760 Find NCS groups from input model: 0.870 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 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 0.088 21203 Z= 0.383 Angle : 0.964 9.985 28819 Z= 0.485 Chirality : 0.049 0.230 3122 Planarity : 0.007 0.068 3668 Dihedral : 15.157 76.202 7987 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/Z covalent geometry : bond 0.00911 / 0.38 (21196) covalent geometry : angle 0.96413 / 0.49 (28819) hydrogen bonds : bond 0.18075 / 12.02 ( 833) hydrogen bonds : angle 6.05639 / 4.17 ( 2352) Misc. bond : bond 0.01319 / 0.59 ( 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 : 1.111 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: 0.3510 time to fit residues: 275.4397 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 : 1.091 ------------------------------------------------------------------------------- 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... ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 127 GLN D 127 GLN D 332 ASN ** D 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 127 GLN ** E 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 127 GLN F 332 ASN ** G 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.134647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.100945 restraints weight = 84366.185| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 2.47 r_work: 0.3079 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21203 Z= 0.135 Angle : 0.592 5.629 28819 Z= 0.301 Chirality : 0.040 0.129 3122 Planarity : 0.006 0.072 3668 Dihedral : 8.472 54.701 3097 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.08 (0.16), residues: 2506 helix: 0.69 (0.17), residues: 945 sheet: -2.13 (0.19), residues: 581 loop : -2.99 (0.18), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 58 TYR 0.021 0.001 TYR F 60 PHE 0.013 0.001 PHE G 95 TRP 0.005 0.001 TRP G 66 HIS 0.003 0.001 HIS C 70 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 (21196) covalent geometry : angle 0.59201 / 0.30 (28819) hydrogen bonds : bond 0.04433 / 2.98 ( 833) hydrogen bonds : angle 4.74447 / 3.28 ( 2352) Misc. bond : bond 0.00020 / 0.01 ( 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 463 residues out of total 2205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 463 time to evaluate : 1.121 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 162 GLU cc_start: 0.5773 (mp0) cc_final: 0.5455 (mp0) REVERT: A 204 ASP cc_start: 0.8319 (t70) cc_final: 0.7969 (t70) REVERT: A 276 GLN cc_start: 0.8960 (mt0) cc_final: 0.8733 (mt0) REVERT: B 87 GLU cc_start: 0.8533 (mm-30) cc_final: 0.8316 (mm-30) REVERT: B 192 VAL cc_start: 0.8793 (t) cc_final: 0.8586 (m) REVERT: B 204 ASP cc_start: 0.8274 (t70) cc_final: 0.7731 (t0) REVERT: B 282 GLU cc_start: 0.8001 (mm-30) cc_final: 0.7776 (tp30) REVERT: B 347 VAL cc_start: 0.8830 (t) cc_final: 0.8582 (m) REVERT: C 58 ARG cc_start: 0.7931 (ttt-90) cc_final: 0.7722 (ttt180) REVERT: C 95 PHE cc_start: 0.6194 (m-80) cc_final: 0.5911 (m-10) REVERT: C 276 GLN cc_start: 0.8821 (mt0) cc_final: 0.8587 (mt0) REVERT: C 347 VAL cc_start: 0.8862 (t) cc_final: 0.8568 (m) REVERT: C 378 GLU cc_start: 0.8540 (mm-30) cc_final: 0.8202 (mm-30) REVERT: C 415 GLU cc_start: 0.8609 (mp0) cc_final: 0.8363 (mp0) REVERT: D 95 PHE cc_start: 0.6486 (m-80) cc_final: 0.5983 (m-80) REVERT: D 97 PHE cc_start: 0.8622 (m-80) cc_final: 0.8227 (m-80) REVERT: D 132 TRP cc_start: 0.7797 (t-100) cc_final: 0.7524 (t-100) REVERT: D 276 GLN cc_start: 0.8778 (mt0) cc_final: 0.8513 (mt0) REVERT: D 415 GLU cc_start: 0.8710 (mp0) cc_final: 0.8462 (mp0) REVERT: E 97 PHE cc_start: 0.8663 (m-80) cc_final: 0.8384 (m-10) REVERT: E 204 ASP cc_start: 0.8337 (t70) cc_final: 0.7988 (t70) REVERT: E 276 GLN cc_start: 0.8875 (mt0) cc_final: 0.8635 (mt0) REVERT: F 52 GLU cc_start: 0.7220 (mt-10) cc_final: 0.7002 (mt-10) REVERT: F 86 HIS cc_start: 0.7942 (m170) cc_final: 0.7567 (m90) REVERT: F 95 PHE cc_start: 0.6581 (m-80) cc_final: 0.6291 (m-80) REVERT: F 276 GLN cc_start: 0.8942 (mt0) cc_final: 0.8725 (mt0) REVERT: F 347 VAL cc_start: 0.8906 (t) cc_final: 0.8677 (m) REVERT: F 415 GLU cc_start: 0.8619 (mp0) cc_final: 0.8389 (mp0) REVERT: G 347 VAL cc_start: 0.8887 (t) cc_final: 0.8578 (m) outliers start: 0 outliers final: 0 residues processed: 463 average time/residue: 0.3323 time to fit residues: 237.6463 Evaluate side-chains 426 residues out of total 2205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 426 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 232 optimal weight: 2.9990 chunk 246 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 224 optimal weight: 8.9990 chunk 199 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 133 optimal weight: 0.7980 chunk 17 optimal weight: 3.9990 chunk 110 optimal weight: 10.0000 chunk 210 optimal weight: 3.9990 chunk 131 optimal weight: 3.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 85 GLN ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 85 GLN ** B 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 332 ASN ** B 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 397 GLN D 397 GLN E 85 GLN E 397 GLN ** F 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 85 GLN G 127 GLN ** G 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.130574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.096466 restraints weight = 84772.954| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 2.50 r_work: 0.3004 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2852 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.2590 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= 0.220 Angle : 0.599 4.955 28819 Z= 0.302 Chirality : 0.041 0.139 3122 Planarity : 0.005 0.047 3668 Dihedral : 7.256 59.995 3094 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 0.68 % Allowed : 7.39 % Favored : 91.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.58 (0.17), residues: 2506 helix: 1.04 (0.18), residues: 945 sheet: -1.89 (0.20), residues: 567 loop : -2.61 (0.19), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 343 TYR 0.023 0.001 TYR F 60 PHE 0.011 0.002 PHE F 97 TRP 0.005 0.001 TRP G 66 HIS 0.004 0.001 HIS B 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00535 / 0.22 (21196) covalent geometry : angle 0.59889 / 0.30 (28819) hydrogen bonds : bond 0.05028 / 3.41 ( 833) hydrogen bonds : angle 4.58516 / 3.18 ( 2352) Misc. bond : bond 0.00251 / 0.13 ( 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 436 residues out of total 2205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 421 time to evaluate : 1.006 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: 0.8267 (t70) cc_final: 0.7899 (t70) REVERT: A 276 GLN cc_start: 0.8923 (mt0) cc_final: 0.8578 (mt0) REVERT: B 204 ASP cc_start: 0.8270 (t70) cc_final: 0.7989 (t70) REVERT: C 276 GLN cc_start: 0.8870 (mt0) cc_final: 0.8669 (mt0) REVERT: C 347 VAL cc_start: 0.8948 (t) cc_final: 0.8713 (m) REVERT: D 105 PHE cc_start: 0.7825 (m-80) cc_final: 0.7606 (m-80) REVERT: D 132 TRP cc_start: 0.7935 (t-100) cc_final: 0.7667 (t-100) REVERT: D 276 GLN cc_start: 0.8822 (mt0) cc_final: 0.8452 (mt0) REVERT: D 397 GLN cc_start: 0.7834 (OUTLIER) cc_final: 0.7555 (tt0) REVERT: D 415 GLU cc_start: 0.8730 (mp0) cc_final: 0.8499 (mp0) REVERT: E 86 HIS cc_start: 0.7869 (m170) cc_final: 0.7566 (m90) REVERT: E 117 ARG cc_start: 0.6575 (ttm110) cc_final: 0.6280 (ttm-80) REVERT: E 276 GLN cc_start: 0.8857 (mt0) cc_final: 0.8618 (mt0) REVERT: E 347 VAL cc_start: 0.9039 (t) cc_final: 0.8746 (m) REVERT: E 397 GLN cc_start: 0.7701 (OUTLIER) cc_final: 0.7373 (tt0) REVERT: F 52 GLU cc_start: 0.7207 (mt-10) cc_final: 0.6862 (mt-10) REVERT: F 64 LEU cc_start: 0.8187 (mm) cc_final: 0.7947 (mp) REVERT: F 97 PHE cc_start: 0.8670 (m-80) cc_final: 0.8315 (m-10) REVERT: F 276 GLN cc_start: 0.8933 (mt0) cc_final: 0.8718 (mt0) outliers start: 15 outliers final: 7 residues processed: 430 average time/residue: 0.3358 time to fit residues: 222.5223 Evaluate side-chains 413 residues out of total 2205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 404 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 ASP Chi-restraints excluded: chain B residue 217 ASP Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 397 GLN Chi-restraints excluded: chain E residue 397 GLN 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 24 optimal weight: 4.9990 chunk 228 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 194 optimal weight: 2.9990 chunk 247 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 124 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 45 optimal weight: 7.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 397 GLN B 85 GLN ** B 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 397 GLN D 397 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 = 0.3628 r_free = 0.3628 target = 0.130646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.097066 restraints weight = 84389.426| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 2.48 r_work: 0.3007 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2855 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.2906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 21203 Z= 0.194 Angle : 0.561 5.516 28819 Z= 0.284 Chirality : 0.040 0.157 3122 Planarity : 0.005 0.046 3668 Dihedral : 7.039 58.749 3094 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 0.50 % Allowed : 9.66 % Favored : 89.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.34 (0.17), residues: 2506 helix: 1.18 (0.18), residues: 945 sheet: -1.77 (0.20), residues: 567 loop : -2.40 (0.20), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 58 TYR 0.026 0.001 TYR E 60 PHE 0.008 0.001 PHE G 137 TRP 0.005 0.001 TRP G 66 HIS 0.006 0.001 HIS A 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00467 / 0.19 (21196) covalent geometry : angle 0.56061 / 0.28 (28819) hydrogen bonds : bond 0.04451 / 3.02 ( 833) hydrogen bonds : angle 4.43803 / 3.08 ( 2352) Misc. bond : bond 0.00019 / 0.01 ( 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 428 residues out of total 2205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 417 time to evaluate : 1.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 276 GLN cc_start: 0.8898 (mt0) cc_final: 0.8582 (mt0) REVERT: B 204 ASP cc_start: 0.8258 (t70) cc_final: 0.7968 (t70) REVERT: C 189 ASP cc_start: 0.8210 (p0) cc_final: 0.7718 (t0) REVERT: C 204 ASP cc_start: 0.8277 (t70) cc_final: 0.7839 (t0) REVERT: C 347 VAL cc_start: 0.8922 (t) cc_final: 0.8661 (m) REVERT: D 132 TRP cc_start: 0.7978 (t-100) cc_final: 0.7734 (t-100) REVERT: D 276 GLN cc_start: 0.8828 (mt0) cc_final: 0.8575 (mt0) REVERT: D 415 GLU cc_start: 0.8775 (mp0) cc_final: 0.8514 (mp0) REVERT: E 58 ARG cc_start: 0.7727 (ttt90) cc_final: 0.7460 (ttt90) REVERT: E 64 LEU cc_start: 0.8193 (mm) cc_final: 0.7958 (mp) REVERT: E 276 GLN cc_start: 0.8825 (mt0) cc_final: 0.8593 (mt0) REVERT: E 347 VAL cc_start: 0.9055 (t) cc_final: 0.8746 (m) REVERT: E 397 GLN cc_start: 0.7339 (OUTLIER) cc_final: 0.7105 (tt0) REVERT: F 50 THR cc_start: 0.6696 (p) cc_final: 0.6458 (p) REVERT: F 86 HIS cc_start: 0.7965 (m90) cc_final: 0.7588 (m90) REVERT: F 97 PHE cc_start: 0.8627 (m-80) cc_final: 0.8246 (m-10) REVERT: F 276 GLN cc_start: 0.8925 (mt0) cc_final: 0.8687 (mt0) outliers start: 11 outliers final: 7 residues processed: 423 average time/residue: 0.3371 time to fit residues: 218.8407 Evaluate side-chains 418 residues out of total 2205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 410 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain B residue 217 ASP Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 397 GLN Chi-restraints excluded: chain F residue 331 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: 9.9990 chunk 31 optimal weight: 5.9990 chunk 176 optimal weight: 4.9990 chunk 164 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 157 optimal weight: 0.8980 chunk 197 optimal weight: 2.9990 chunk 47 optimal weight: 0.2980 chunk 8 optimal weight: 2.9990 chunk 226 optimal weight: 10.0000 chunk 173 optimal weight: 3.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 397 GLN E 76 HIS E 275 GLN E 397 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.129820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.096328 restraints weight = 84775.236| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 2.49 r_work: 0.3001 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2850 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.3128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 21203 Z= 0.203 Angle : 0.557 5.688 28819 Z= 0.284 Chirality : 0.040 0.131 3122 Planarity : 0.005 0.045 3668 Dihedral : 7.046 59.833 3094 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 0.63 % Allowed : 10.39 % Favored : 88.98 % 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: -1.14 (0.17), residues: 2506 helix: 1.36 (0.18), residues: 945 sheet: -1.63 (0.20), residues: 567 loop : -2.33 (0.20), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 58 TYR 0.019 0.001 TYR E 60 PHE 0.008 0.001 PHE F 179 TRP 0.006 0.001 TRP B 66 HIS 0.006 0.001 HIS E 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00492 / 0.20 (21196) covalent geometry : angle 0.55750 / 0.28 (28819) hydrogen bonds : bond 0.04463 / 3.03 ( 833) hydrogen bonds : angle 4.35643 / 3.02 ( 2352) Misc. bond : bond 0.00034 / 0.02 ( 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 431 residues out of total 2205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 417 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: A 276 GLN cc_start: 0.8909 (mt0) cc_final: 0.8599 (mt0) REVERT: B 50 THR cc_start: 0.6844 (p) cc_final: 0.6610 (p) REVERT: B 87 GLU cc_start: 0.8523 (mm-30) cc_final: 0.8236 (mm-30) REVERT: B 204 ASP cc_start: 0.8273 (t70) cc_final: 0.7984 (t70) REVERT: C 121 MET cc_start: 0.4491 (tmm) cc_final: 0.4163 (tmm) REVERT: C 189 ASP cc_start: 0.8186 (p0) cc_final: 0.7750 (t0) REVERT: C 204 ASP cc_start: 0.8285 (t70) cc_final: 0.7831 (t0) REVERT: C 347 VAL cc_start: 0.8925 (t) cc_final: 0.8669 (m) REVERT: D 132 TRP cc_start: 0.8011 (t-100) cc_final: 0.7765 (t-100) REVERT: D 276 GLN cc_start: 0.8827 (mt0) cc_final: 0.8585 (mt0) REVERT: D 415 GLU cc_start: 0.8765 (mp0) cc_final: 0.8515 (mp0) REVERT: E 58 ARG cc_start: 0.7749 (ttt90) cc_final: 0.7537 (ttt90) REVERT: E 64 LEU cc_start: 0.8203 (mm) cc_final: 0.7923 (mp) REVERT: E 86 HIS cc_start: 0.7919 (m170) cc_final: 0.7645 (m90) REVERT: E 117 ARG cc_start: 0.6580 (ttm110) cc_final: 0.6275 (ttm-80) REVERT: E 276 GLN cc_start: 0.8861 (mt0) cc_final: 0.8626 (mt0) REVERT: F 50 THR cc_start: 0.6832 (p) cc_final: 0.6583 (p) REVERT: F 86 HIS cc_start: 0.7922 (m90) cc_final: 0.7568 (m90) REVERT: F 123 MET cc_start: 0.5876 (ttp) cc_final: 0.5392 (ttp) REVERT: F 276 GLN cc_start: 0.8935 (mt0) cc_final: 0.8692 (mt0) REVERT: F 415 GLU cc_start: 0.8739 (mp0) cc_final: 0.8491 (mp0) outliers start: 14 outliers final: 11 residues processed: 423 average time/residue: 0.3371 time to fit residues: 219.2804 Evaluate side-chains 425 residues out of total 2205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 414 time to evaluate : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain B residue 217 ASP Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain D residue 104 HIS 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 50 THR Chi-restraints excluded: chain G residue 104 HIS 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: 5.9990 chunk 40 optimal weight: 7.9990 chunk 26 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 chunk 218 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 227 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 HIS A 127 GLN ** B 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 HIS E 76 HIS E 275 GLN F 76 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.129719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.096270 restraints weight = 85113.438| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 2.50 r_work: 0.3000 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2856 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.3331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 21203 Z= 0.198 Angle : 0.551 5.297 28819 Z= 0.280 Chirality : 0.040 0.133 3122 Planarity : 0.005 0.044 3668 Dihedral : 6.903 57.096 3094 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 0.86 % Allowed : 10.84 % Favored : 88.30 % 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: -1.08 (0.17), residues: 2506 helix: 1.19 (0.17), residues: 987 sheet: -1.33 (0.21), residues: 553 loop : -2.39 (0.20), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 58 TYR 0.020 0.001 TYR F 60 PHE 0.008 0.001 PHE A 179 TRP 0.006 0.001 TRP B 66 HIS 0.006 0.001 HIS E 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00479 / 0.20 (21196) covalent geometry : angle 0.55130 / 0.28 (28819) hydrogen bonds : bond 0.04342 / 2.96 ( 833) hydrogen bonds : angle 4.28342 / 2.97 ( 2352) Misc. bond : bond 0.00032 / 0.02 ( 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 439 residues out of total 2205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 420 time to evaluate : 1.095 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 276 GLN cc_start: 0.8908 (mt0) cc_final: 0.8620 (mt0) REVERT: B 50 THR cc_start: 0.6935 (p) cc_final: 0.6694 (p) REVERT: B 204 ASP cc_start: 0.8278 (t70) cc_final: 0.7987 (t70) REVERT: C 189 ASP cc_start: 0.8163 (p0) cc_final: 0.7738 (t0) REVERT: C 204 ASP cc_start: 0.8285 (t70) cc_final: 0.7955 (t70) REVERT: C 282 GLU cc_start: 0.8040 (mm-30) cc_final: 0.7810 (mm-30) REVERT: C 347 VAL cc_start: 0.8922 (t) cc_final: 0.8673 (m) REVERT: D 132 TRP cc_start: 0.8042 (t-100) cc_final: 0.7808 (t-100) REVERT: D 276 GLN cc_start: 0.8832 (mt0) cc_final: 0.8620 (mt0) REVERT: D 415 GLU cc_start: 0.8743 (mp0) cc_final: 0.8483 (mp0) REVERT: E 58 ARG cc_start: 0.7671 (ttt90) cc_final: 0.7453 (ttt90) REVERT: E 64 LEU cc_start: 0.8203 (mm) cc_final: 0.7895 (mp) REVERT: E 86 HIS cc_start: 0.7966 (m170) cc_final: 0.7712 (m90) REVERT: E 117 ARG cc_start: 0.6719 (ttm110) cc_final: 0.6431 (ttm-80) REVERT: E 213 LYS cc_start: 0.8597 (ttpp) cc_final: 0.8142 (ttmm) REVERT: E 276 GLN cc_start: 0.8854 (mt0) cc_final: 0.8637 (mt0) REVERT: F 50 THR cc_start: 0.6978 (p) cc_final: 0.6743 (p) REVERT: F 86 HIS cc_start: 0.7960 (m90) cc_final: 0.7665 (m90) REVERT: F 123 MET cc_start: 0.5741 (ttp) cc_final: 0.5540 (ttp) REVERT: F 276 GLN cc_start: 0.8933 (mt0) cc_final: 0.8696 (mt0) REVERT: F 415 GLU cc_start: 0.8740 (mp0) cc_final: 0.8485 (mp0) outliers start: 19 outliers final: 15 residues processed: 425 average time/residue: 0.3380 time to fit residues: 219.6127 Evaluate side-chains 433 residues out of total 2205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 418 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain B residue 217 ASP Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 285 ASP 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 F residue 385 LEU Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 104 HIS Chi-restraints excluded: chain G residue 342 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 219 optimal weight: 7.9990 chunk 44 optimal weight: 10.0000 chunk 244 optimal weight: 0.7980 chunk 63 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 chunk 1 optimal weight: 6.9990 chunk 77 optimal weight: 0.9980 chunk 145 optimal weight: 7.9990 chunk 114 optimal weight: 9.9990 chunk 245 optimal weight: 0.6980 chunk 42 optimal weight: 4.9990 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 HIS ** B 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3608 r_free = 0.3608 target = 0.129427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.095991 restraints weight = 84826.367| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 2.50 r_work: 0.2997 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.3478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 21203 Z= 0.190 Angle : 0.545 4.990 28819 Z= 0.277 Chirality : 0.040 0.145 3122 Planarity : 0.005 0.054 3668 Dihedral : 6.874 55.548 3094 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 0.95 % Allowed : 10.93 % Favored : 88.12 % 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: -0.95 (0.18), residues: 2506 helix: 1.31 (0.17), residues: 987 sheet: -1.23 (0.21), residues: 553 loop : -2.35 (0.20), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 58 TYR 0.015 0.001 TYR E 60 PHE 0.008 0.001 PHE A 137 TRP 0.006 0.001 TRP B 66 HIS 0.006 0.001 HIS A 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.19 (21196) covalent geometry : angle 0.54469 / 0.28 (28819) hydrogen bonds : bond 0.04233 / 2.89 ( 833) hydrogen bonds : angle 4.23526 / 2.93 ( 2352) Misc. bond : bond 0.00028 / 0.01 ( 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 445 residues out of total 2205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 424 time to evaluate : 0.970 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 276 GLN cc_start: 0.8911 (mt0) cc_final: 0.8623 (mt0) REVERT: B 50 THR cc_start: 0.6994 (p) cc_final: 0.6594 (p) REVERT: B 204 ASP cc_start: 0.8270 (t70) cc_final: 0.7997 (t70) REVERT: C 189 ASP cc_start: 0.8163 (p0) cc_final: 0.7757 (t0) REVERT: C 204 ASP cc_start: 0.8285 (t70) cc_final: 0.7947 (t70) REVERT: C 282 GLU cc_start: 0.8016 (mm-30) cc_final: 0.7757 (mm-30) REVERT: C 347 VAL cc_start: 0.8924 (t) cc_final: 0.8677 (m) REVERT: D 58 ARG cc_start: 0.7831 (tpt-90) cc_final: 0.7423 (ttt-90) REVERT: D 189 ASP cc_start: 0.8323 (p0) cc_final: 0.7822 (t0) REVERT: D 253 LEU cc_start: 0.8944 (mp) cc_final: 0.8739 (mt) REVERT: D 276 GLN cc_start: 0.8823 (mt0) cc_final: 0.8614 (mt0) REVERT: D 415 GLU cc_start: 0.8765 (mp0) cc_final: 0.8519 (mp0) REVERT: E 58 ARG cc_start: 0.7641 (ttt90) cc_final: 0.7433 (ttt90) REVERT: E 64 LEU cc_start: 0.8207 (mm) cc_final: 0.7957 (mp) REVERT: E 86 HIS cc_start: 0.7968 (m170) cc_final: 0.7723 (m90) REVERT: E 276 GLN cc_start: 0.8848 (mt0) cc_final: 0.8633 (mt0) REVERT: E 347 VAL cc_start: 0.9042 (t) cc_final: 0.8752 (m) REVERT: F 50 THR cc_start: 0.7015 (p) cc_final: 0.6775 (p) REVERT: F 86 HIS cc_start: 0.7970 (m90) cc_final: 0.7666 (m90) REVERT: F 123 MET cc_start: 0.5618 (ttp) cc_final: 0.5281 (ttp) REVERT: F 276 GLN cc_start: 0.8942 (mt0) cc_final: 0.8711 (mt0) REVERT: F 415 GLU cc_start: 0.8767 (mp0) cc_final: 0.8504 (mp0) outliers start: 21 outliers final: 18 residues processed: 431 average time/residue: 0.3561 time to fit residues: 234.0684 Evaluate side-chains 436 residues out of total 2205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 418 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 217 ASP Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain E 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 166 THR Chi-restraints excluded: chain F residue 331 THR Chi-restraints excluded: chain F residue 385 LEU Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 104 HIS 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: 0.6980 chunk 113 optimal weight: 1.9990 chunk 39 optimal weight: 8.9990 chunk 129 optimal weight: 4.9990 chunk 193 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 221 optimal weight: 2.9990 chunk 169 optimal weight: 0.0010 chunk 136 optimal weight: 1.9990 chunk 232 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 overall best weight: 1.3392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 HIS B 127 GLN C 76 HIS E 275 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.130843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.097320 restraints weight = 84750.087| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 2.51 r_work: 0.3017 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.3617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 21203 Z= 0.133 Angle : 0.514 5.305 28819 Z= 0.261 Chirality : 0.038 0.142 3122 Planarity : 0.004 0.044 3668 Dihedral : 6.622 54.093 3094 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 0.91 % Allowed : 11.34 % Favored : 87.76 % 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: -0.70 (0.18), residues: 2506 helix: 1.53 (0.17), residues: 987 sheet: -1.10 (0.21), residues: 553 loop : -2.23 (0.21), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 58 TYR 0.015 0.001 TYR E 60 PHE 0.007 0.001 PHE E 97 TRP 0.007 0.000 TRP B 66 HIS 0.005 0.001 HIS B 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.13 (21196) covalent geometry : angle 0.51390 / 0.26 (28819) hydrogen bonds : bond 0.03675 / 2.50 ( 833) hydrogen bonds : angle 4.03707 / 2.79 ( 2352) Misc. bond : bond 0.00019 / 0.01 ( 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 444 residues out of total 2205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 424 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: symmetry clash revert: symmetry clash REVERT: A 276 GLN cc_start: 0.8887 (mt0) cc_final: 0.8623 (mt0) REVERT: B 50 THR cc_start: 0.6880 (p) cc_final: 0.6626 (p) REVERT: B 204 ASP cc_start: 0.8254 (t70) cc_final: 0.7961 (t70) REVERT: C 189 ASP cc_start: 0.8117 (p0) cc_final: 0.7725 (t0) REVERT: C 204 ASP cc_start: 0.8282 (t70) cc_final: 0.7944 (t70) REVERT: C 282 GLU cc_start: 0.7993 (mm-30) cc_final: 0.7762 (mm-30) REVERT: C 347 VAL cc_start: 0.8906 (t) cc_final: 0.8649 (m) REVERT: D 189 ASP cc_start: 0.8305 (p0) cc_final: 0.7831 (t0) REVERT: D 253 LEU cc_start: 0.8932 (mp) cc_final: 0.8634 (mm) REVERT: D 276 GLN cc_start: 0.8823 (mt0) cc_final: 0.8600 (mt0) REVERT: D 415 GLU cc_start: 0.8739 (mp0) cc_final: 0.8463 (mp0) REVERT: E 58 ARG cc_start: 0.7627 (ttt90) cc_final: 0.7418 (ttt90) REVERT: E 64 LEU cc_start: 0.8195 (mm) cc_final: 0.7932 (mp) REVERT: E 86 HIS cc_start: 0.7911 (m170) cc_final: 0.7654 (m90) REVERT: E 276 GLN cc_start: 0.8834 (mt0) cc_final: 0.8580 (mt0) REVERT: E 347 VAL cc_start: 0.9026 (t) cc_final: 0.8744 (m) REVERT: F 50 THR cc_start: 0.6992 (p) cc_final: 0.6748 (p) REVERT: F 86 HIS cc_start: 0.7922 (m90) cc_final: 0.7634 (m90) REVERT: F 123 MET cc_start: 0.5519 (ttp) cc_final: 0.5171 (ttp) REVERT: F 276 GLN cc_start: 0.8939 (mt0) cc_final: 0.8706 (mt0) REVERT: F 415 GLU cc_start: 0.8749 (mp0) cc_final: 0.8478 (mp0) REVERT: G 76 HIS cc_start: 0.7241 (m90) cc_final: 0.7036 (m90) outliers start: 20 outliers final: 19 residues processed: 430 average time/residue: 0.3615 time to fit residues: 238.2032 Evaluate side-chains 437 residues out of total 2205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 418 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 217 ASP Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 285 ASP Chi-restraints excluded: chain E residue 308 THR Chi-restraints excluded: chain E residue 322 THR Chi-restraints excluded: chain F residue 331 THR Chi-restraints excluded: chain F residue 385 LEU Chi-restraints excluded: chain G residue 50 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: 3.9990 chunk 43 optimal weight: 7.9990 chunk 103 optimal weight: 0.7980 chunk 228 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 chunk 126 optimal weight: 1.9990 chunk 40 optimal weight: 8.9990 chunk 245 optimal weight: 2.9990 chunk 198 optimal weight: 1.9990 chunk 3 optimal weight: 10.0000 chunk 66 optimal weight: 2.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 HIS B 397 GLN C 76 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.129446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.096198 restraints weight = 85107.444| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 2.48 r_work: 0.2997 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2845 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.3685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 21203 Z= 0.180 Angle : 0.536 4.798 28819 Z= 0.271 Chirality : 0.039 0.150 3122 Planarity : 0.005 0.054 3668 Dihedral : 6.718 55.112 3094 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 1.00 % Allowed : 11.43 % Favored : 87.57 % 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: -0.68 (0.18), residues: 2506 helix: 1.50 (0.17), residues: 994 sheet: -1.06 (0.21), residues: 553 loop : -2.21 (0.21), residues: 959 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 58 TYR 0.013 0.001 TYR E 60 PHE 0.008 0.001 PHE A 179 TRP 0.005 0.001 TRP B 66 HIS 0.006 0.001 HIS B 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.18 (21196) covalent geometry : angle 0.53579 / 0.27 (28819) hydrogen bonds : bond 0.04117 / 2.81 ( 833) hydrogen bonds : angle 4.14178 / 2.87 ( 2352) Misc. bond : bond 0.00027 / 0.01 ( 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 432 residues out of total 2205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 410 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: 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 276 GLN cc_start: 0.8898 (mt0) cc_final: 0.8632 (mt0) REVERT: B 50 THR cc_start: 0.6908 (p) cc_final: 0.6648 (p) REVERT: B 204 ASP cc_start: 0.8242 (t70) cc_final: 0.7947 (t70) REVERT: C 52 GLU cc_start: 0.7360 (mt-10) cc_final: 0.7085 (tt0) REVERT: C 58 ARG cc_start: 0.7703 (ttt-90) cc_final: 0.7482 (ttt-90) REVERT: C 189 ASP cc_start: 0.8101 (p0) cc_final: 0.7706 (t0) REVERT: C 204 ASP cc_start: 0.8270 (t70) cc_final: 0.7914 (t70) REVERT: C 347 VAL cc_start: 0.8926 (t) cc_final: 0.8666 (m) REVERT: D 189 ASP cc_start: 0.8320 (p0) cc_final: 0.7808 (t0) REVERT: D 276 GLN cc_start: 0.8816 (mt0) cc_final: 0.8604 (mt0) REVERT: D 415 GLU cc_start: 0.8766 (mp0) cc_final: 0.8480 (mp0) REVERT: E 64 LEU cc_start: 0.8197 (mm) cc_final: 0.7921 (mp) REVERT: E 86 HIS cc_start: 0.7926 (m170) cc_final: 0.7679 (m90) REVERT: E 213 LYS cc_start: 0.8565 (ttpp) cc_final: 0.8131 (ttmm) REVERT: E 276 GLN cc_start: 0.8849 (mt0) cc_final: 0.8593 (mt0) REVERT: E 347 VAL cc_start: 0.9039 (t) cc_final: 0.8749 (m) REVERT: F 86 HIS cc_start: 0.7940 (m90) cc_final: 0.7619 (m90) REVERT: F 123 MET cc_start: 0.5558 (ttp) cc_final: 0.5176 (ttp) REVERT: F 276 GLN cc_start: 0.8944 (mt0) cc_final: 0.8696 (mt0) REVERT: F 415 GLU cc_start: 0.8753 (mp0) cc_final: 0.8482 (mp0) REVERT: G 76 HIS cc_start: 0.7299 (m90) cc_final: 0.6996 (m90) outliers start: 22 outliers final: 21 residues processed: 416 average time/residue: 0.3575 time to fit residues: 228.1059 Evaluate side-chains 432 residues out of total 2205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 411 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 217 ASP Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 397 GLN Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 285 ASP Chi-restraints excluded: chain E residue 308 THR Chi-restraints excluded: chain E residue 322 THR Chi-restraints excluded: chain E residue 385 LEU 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 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: 1.9990 chunk 211 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 chunk 173 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 10 optimal weight: 7.9990 chunk 180 optimal weight: 6.9990 chunk 183 optimal weight: 9.9990 chunk 135 optimal weight: 0.5980 chunk 127 optimal weight: 1.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 HIS C 76 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.129548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.096393 restraints weight = 84639.330| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 2.47 r_work: 0.3002 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.3693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 21203 Z= 0.177 Angle : 0.688 59.128 28819 Z= 0.378 Chirality : 0.040 0.463 3122 Planarity : 0.005 0.052 3668 Dihedral : 6.719 55.079 3094 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 0.91 % Allowed : 11.66 % Favored : 87.44 % Cbeta Deviations : 0.04 % 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: -0.68 (0.18), residues: 2506 helix: 1.50 (0.17), residues: 994 sheet: -1.05 (0.21), residues: 553 loop : -2.21 (0.21), residues: 959 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 58 TYR 0.018 0.001 TYR E 83 PHE 0.007 0.001 PHE A 179 TRP 0.005 0.001 TRP B 66 HIS 0.006 0.001 HIS B 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.18 (21196) covalent geometry : angle 0.68767 / 0.38 (28819) hydrogen bonds : bond 0.04096 / 2.79 ( 833) hydrogen bonds : angle 4.14301 / 2.87 ( 2352) Misc. bond : bond 0.00022 / 0.01 ( 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 431 residues out of total 2205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 411 time to evaluate : 1.143 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 276 GLN cc_start: 0.8900 (mt0) cc_final: 0.8636 (mt0) REVERT: B 50 THR cc_start: 0.6927 (p) cc_final: 0.6673 (p) REVERT: B 58 ARG cc_start: 0.7731 (tpt-90) cc_final: 0.7332 (ttt180) REVERT: B 204 ASP cc_start: 0.8230 (t70) cc_final: 0.7930 (t70) REVERT: C 58 ARG cc_start: 0.7702 (ttt-90) cc_final: 0.7456 (ttt-90) REVERT: C 189 ASP cc_start: 0.8114 (p0) cc_final: 0.7712 (t0) REVERT: C 204 ASP cc_start: 0.8255 (t70) cc_final: 0.7895 (t70) REVERT: C 347 VAL cc_start: 0.8928 (t) cc_final: 0.8666 (m) REVERT: D 189 ASP cc_start: 0.8310 (p0) cc_final: 0.7800 (t0) REVERT: D 276 GLN cc_start: 0.8812 (mt0) cc_final: 0.8599 (mt0) REVERT: D 415 GLU cc_start: 0.8770 (mp0) cc_final: 0.8484 (mp0) REVERT: E 64 LEU cc_start: 0.8184 (mm) cc_final: 0.7913 (mp) REVERT: E 86 HIS cc_start: 0.7923 (m170) cc_final: 0.7678 (m90) REVERT: E 213 LYS cc_start: 0.8551 (ttpp) cc_final: 0.8117 (ttmm) REVERT: E 276 GLN cc_start: 0.8841 (mt0) cc_final: 0.8588 (mt0) REVERT: E 347 VAL cc_start: 0.9041 (t) cc_final: 0.8747 (m) REVERT: F 86 HIS cc_start: 0.7939 (m90) cc_final: 0.7616 (m90) REVERT: F 123 MET cc_start: 0.5555 (ttp) cc_final: 0.5174 (ttp) REVERT: F 276 GLN cc_start: 0.8942 (mt0) cc_final: 0.8695 (mt0) REVERT: G 76 HIS cc_start: 0.7293 (m90) cc_final: 0.6991 (m90) REVERT: G 123 MET cc_start: 0.5602 (ttp) cc_final: 0.5248 (ttp) outliers start: 20 outliers final: 20 residues processed: 416 average time/residue: 0.3634 time to fit residues: 231.9059 Evaluate side-chains 430 residues out of total 2205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 410 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 217 ASP Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 285 ASP Chi-restraints excluded: chain E residue 308 THR Chi-restraints excluded: chain E residue 322 THR Chi-restraints excluded: chain E residue 385 LEU 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 342 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 41 optimal weight: 0.0980 chunk 79 optimal weight: 0.3980 chunk 81 optimal weight: 6.9990 chunk 220 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 169 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 109 optimal weight: 6.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 HIS C 76 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.129559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.096351 restraints weight = 85416.056| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 2.48 r_work: 0.2998 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.3687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 21203 Z= 0.177 Angle : 0.688 59.128 28819 Z= 0.378 Chirality : 0.040 0.463 3122 Planarity : 0.005 0.052 3668 Dihedral : 6.719 55.079 3094 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 0.91 % Allowed : 11.56 % Favored : 87.53 % Cbeta Deviations : 0.04 % 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: -0.68 (0.18), residues: 2506 helix: 1.50 (0.17), residues: 994 sheet: -1.05 (0.21), residues: 553 loop : -2.21 (0.21), residues: 959 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 58 TYR 0.018 0.001 TYR E 83 PHE 0.007 0.001 PHE A 179 TRP 0.005 0.001 TRP B 66 HIS 0.006 0.001 HIS B 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.18 (21196) covalent geometry : angle 0.68767 / 0.38 (28819) hydrogen bonds : bond 0.04096 / 2.79 ( 833) hydrogen bonds : angle 4.14301 / 2.87 ( 2352) Misc. bond : bond 0.00022 / 0.01 ( 7) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10639.91 seconds wall clock time: 180 minutes 43.69 seconds (10843.69 seconds total)