Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 20 15:37:58 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6knf_0730/04_2023/6knf_0730.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6knf_0730/04_2023/6knf_0730.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6knf_0730/04_2023/6knf_0730.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6knf_0730/04_2023/6knf_0730.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6knf_0730/04_2023/6knf_0730.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6knf_0730/04_2023/6knf_0730.pdb" } resolution = 2.99 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 ------------------------------------------------------------------------------- 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= 0.002 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: 5 Type Number sf(0) Gaussians Cu 6 5.60 5 S 30 5.16 5 C 4935 2.51 5 N 1326 2.21 5 O 1452 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 8": "OD1" <-> "OD2" Residue "A ASP 18": "OD1" <-> "OD2" Residue "A PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 46": "OE1" <-> "OE2" Residue "A GLU 58": "OE1" <-> "OE2" Residue "A ASP 79": "OD1" <-> "OD2" Residue "A PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 119": "OE1" <-> "OE2" Residue "A PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 139": "OE1" <-> "OE2" Residue "A TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 197": "OE1" <-> "OE2" Residue "A ASP 205": "OD1" <-> "OD2" Residue "A ASP 230": "OD1" <-> "OD2" Residue "A ASP 275": "OD1" <-> "OD2" Residue "A ASP 277": "OD1" <-> "OD2" Residue "A PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 310": "OE1" <-> "OE2" Residue "A GLU 325": "OE1" <-> "OE2" Residue "A ASP 328": "OD1" <-> "OD2" Residue "B ASP 8": "OD1" <-> "OD2" Residue "B ASP 18": "OD1" <-> "OD2" Residue "B PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 46": "OE1" <-> "OE2" Residue "B GLU 58": "OE1" <-> "OE2" Residue "B ASP 79": "OD1" <-> "OD2" Residue "B PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 119": "OE1" <-> "OE2" Residue "B PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 139": "OE1" <-> "OE2" Residue "B TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 197": "OE1" <-> "OE2" Residue "B ASP 205": "OD1" <-> "OD2" Residue "B ASP 230": "OD1" <-> "OD2" Residue "B ASP 275": "OD1" <-> "OD2" Residue "B ASP 277": "OD1" <-> "OD2" Residue "B GLU 310": "OE1" <-> "OE2" Residue "B GLU 325": "OE1" <-> "OE2" Residue "B ASP 328": "OD1" <-> "OD2" Residue "C ASP 8": "OD1" <-> "OD2" Residue "C ASP 18": "OD1" <-> "OD2" Residue "C PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 46": "OE1" <-> "OE2" Residue "C GLU 58": "OE1" <-> "OE2" Residue "C ASP 79": "OD1" <-> "OD2" Residue "C PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 119": "OE1" <-> "OE2" Residue "C PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 139": "OE1" <-> "OE2" Residue "C TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 197": "OE1" <-> "OE2" Residue "C ASP 205": "OD1" <-> "OD2" Residue "C ASP 230": "OD1" <-> "OD2" Residue "C ASP 275": "OD1" <-> "OD2" Residue "C ASP 277": "OD1" <-> "OD2" Residue "C GLU 310": "OE1" <-> "OE2" Residue "C GLU 325": "OE1" <-> "OE2" Residue "C ASP 328": "OD1" <-> "OD2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 7749 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2581 Classifications: {'peptide': 334} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 311} Chain: "B" Number of atoms: 2581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2581 Classifications: {'peptide': 334} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 311} Chain: "C" Number of atoms: 2581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2581 Classifications: {'peptide': 334} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 311} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CU': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CU': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CU': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1005 SG CYS A 136 25.198 25.320 32.458 1.00 57.62 S ATOM 3586 SG CYS B 136 40.865 66.428 32.465 1.00 58.29 S ATOM 6167 SG CYS C 136 68.598 32.343 32.554 1.00 57.18 S Time building chain proxies: 4.59, per 1000 atoms: 0.59 Number of scatterers: 7749 At special positions: 0 Unit cell: (94.16, 94.16, 75.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cu 6 28.99 S 30 16.00 O 1452 8.00 N 1326 7.00 C 4935 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.93 Conformation dependent library (CDL) restraints added in 1.2 seconds 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1806 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 15 sheets defined 14.4% alpha, 41.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing helix chain 'A' and resid 8 through 12 Processing helix chain 'A' and resid 105 through 109 Processing helix chain 'A' and resid 141 through 149 removed outlier: 3.597A pdb=" N GLY A 149 " --> pdb=" O HIS A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 212 removed outlier: 3.775A pdb=" N ALA A 202 " --> pdb=" O THR A 198 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N GLU A 204 " --> pdb=" O GLY A 200 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N ASP A 205 " --> pdb=" O GLU A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 232 removed outlier: 3.930A pdb=" N HIS A 231 " --> pdb=" O THR A 228 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA A 232 " --> pdb=" O GLY A 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 228 through 232' Processing helix chain 'A' and resid 307 through 315 removed outlier: 3.519A pdb=" N GLY A 315 " --> pdb=" O ALA A 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 12 Processing helix chain 'B' and resid 105 through 109 Processing helix chain 'B' and resid 141 through 149 removed outlier: 3.597A pdb=" N GLY B 149 " --> pdb=" O HIS B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 212 removed outlier: 3.775A pdb=" N ALA B 202 " --> pdb=" O THR B 198 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N GLU B 204 " --> pdb=" O GLY B 200 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N ASP B 205 " --> pdb=" O GLU B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 232 removed outlier: 3.931A pdb=" N HIS B 231 " --> pdb=" O THR B 228 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA B 232 " --> pdb=" O GLY B 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 228 through 232' Processing helix chain 'B' and resid 307 through 315 removed outlier: 3.519A pdb=" N GLY B 315 " --> pdb=" O ALA B 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 12 Processing helix chain 'C' and resid 105 through 109 Processing helix chain 'C' and resid 141 through 149 removed outlier: 3.597A pdb=" N GLY C 149 " --> pdb=" O HIS C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 212 removed outlier: 3.775A pdb=" N ALA C 202 " --> pdb=" O THR C 198 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N GLU C 204 " --> pdb=" O GLY C 200 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N ASP C 205 " --> pdb=" O GLU C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 232 removed outlier: 3.930A pdb=" N HIS C 231 " --> pdb=" O THR C 228 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA C 232 " --> pdb=" O GLY C 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 228 through 232' Processing helix chain 'C' and resid 307 through 315 removed outlier: 3.520A pdb=" N GLY C 315 " --> pdb=" O ALA C 311 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 14 through 16 Processing sheet with id=AA2, first strand: chain 'A' and resid 14 through 16 removed outlier: 6.364A pdb=" N VAL A 39 " --> pdb=" O GLU A 82 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N ARG A 84 " --> pdb=" O VAL A 39 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N PHE A 41 " --> pdb=" O ARG A 84 " (cutoff:3.500A) removed outlier: 8.153A pdb=" N ILE A 86 " --> pdb=" O PHE A 41 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N MET A 43 " --> pdb=" O ILE A 86 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ASP A 79 " --> pdb=" O ALA A 126 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N GLU A 119 " --> pdb=" O LYS C 336 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LYS C 336 " --> pdb=" O GLU A 119 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N THR A 121 " --> pdb=" O VAL C 334 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N VAL C 334 " --> pdb=" O THR A 121 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 73 through 76 removed outlier: 6.121A pdb=" N MET A 73 " --> pdb=" O MET A 155 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N LEU A 157 " --> pdb=" O MET A 73 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N VAL A 75 " --> pdb=" O LEU A 157 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 217 through 220 removed outlier: 8.142A pdb=" N THR A 294 " --> pdb=" O GLY A 261 " (cutoff:3.500A) removed outlier: 8.640A pdb=" N GLY A 261 " --> pdb=" O THR A 294 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ASP A 262 " --> pdb=" O ASP A 277 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ASP A 277 " --> pdb=" O ASP A 262 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 233 through 236 removed outlier: 3.824A pdb=" N ALA A 302 " --> pdb=" O ILE A 257 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 331 through 338 removed outlier: 3.843A pdb=" N VAL A 334 " --> pdb=" O THR B 121 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N THR B 121 " --> pdb=" O VAL A 334 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LYS A 336 " --> pdb=" O GLU B 119 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N GLU B 119 " --> pdb=" O LYS A 336 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ASP B 79 " --> pdb=" O ALA B 126 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N VAL B 39 " --> pdb=" O GLU B 82 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N ARG B 84 " --> pdb=" O VAL B 39 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N PHE B 41 " --> pdb=" O ARG B 84 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N ILE B 86 " --> pdb=" O PHE B 41 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N MET B 43 " --> pdb=" O ILE B 86 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 331 through 338 removed outlier: 3.843A pdb=" N VAL A 334 " --> pdb=" O THR B 121 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N THR B 121 " --> pdb=" O VAL A 334 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LYS A 336 " --> pdb=" O GLU B 119 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N GLU B 119 " --> pdb=" O LYS A 336 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ASP B 79 " --> pdb=" O ALA B 126 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N VAL B 39 " --> pdb=" O GLU B 82 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N ARG B 84 " --> pdb=" O VAL B 39 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N PHE B 41 " --> pdb=" O ARG B 84 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N ILE B 86 " --> pdb=" O PHE B 41 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N MET B 43 " --> pdb=" O ILE B 86 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 73 through 76 removed outlier: 6.123A pdb=" N MET B 73 " --> pdb=" O MET B 155 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N LEU B 157 " --> pdb=" O MET B 73 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N VAL B 75 " --> pdb=" O LEU B 157 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 217 through 220 removed outlier: 8.142A pdb=" N THR B 294 " --> pdb=" O GLY B 261 " (cutoff:3.500A) removed outlier: 8.639A pdb=" N GLY B 261 " --> pdb=" O THR B 294 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ASP B 262 " --> pdb=" O ASP B 277 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ASP B 277 " --> pdb=" O ASP B 262 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 233 through 236 removed outlier: 3.823A pdb=" N ALA B 302 " --> pdb=" O ILE B 257 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 331 through 338 removed outlier: 3.779A pdb=" N VAL B 334 " --> pdb=" O THR C 121 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N THR C 121 " --> pdb=" O VAL B 334 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N LYS B 336 " --> pdb=" O GLU C 119 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N GLU C 119 " --> pdb=" O LYS B 336 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ASP C 79 " --> pdb=" O ALA C 126 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N VAL C 39 " --> pdb=" O GLU C 82 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N ARG C 84 " --> pdb=" O VAL C 39 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N PHE C 41 " --> pdb=" O ARG C 84 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N ILE C 86 " --> pdb=" O PHE C 41 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N MET C 43 " --> pdb=" O ILE C 86 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 331 through 338 removed outlier: 3.779A pdb=" N VAL B 334 " --> pdb=" O THR C 121 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N THR C 121 " --> pdb=" O VAL B 334 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N LYS B 336 " --> pdb=" O GLU C 119 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N GLU C 119 " --> pdb=" O LYS B 336 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ASP C 79 " --> pdb=" O ALA C 126 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N VAL C 39 " --> pdb=" O GLU C 82 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N ARG C 84 " --> pdb=" O VAL C 39 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N PHE C 41 " --> pdb=" O ARG C 84 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N ILE C 86 " --> pdb=" O PHE C 41 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N MET C 43 " --> pdb=" O ILE C 86 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 73 through 76 removed outlier: 6.122A pdb=" N MET C 73 " --> pdb=" O MET C 155 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N LEU C 157 " --> pdb=" O MET C 73 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N VAL C 75 " --> pdb=" O LEU C 157 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 217 through 220 removed outlier: 8.142A pdb=" N THR C 294 " --> pdb=" O GLY C 261 " (cutoff:3.500A) removed outlier: 8.639A pdb=" N GLY C 261 " --> pdb=" O THR C 294 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ASP C 262 " --> pdb=" O ASP C 277 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ASP C 277 " --> pdb=" O ASP C 262 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 233 through 236 removed outlier: 3.823A pdb=" N ALA C 302 " --> pdb=" O ILE C 257 " (cutoff:3.500A) 273 hydrogen bonds defined for protein. 705 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: 2.44 Time building geometry restraints manager: 3.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2561 1.34 - 1.45: 1233 1.45 - 1.57: 4102 1.57 - 1.69: 0 1.69 - 1.80: 57 Bond restraints: 7953 Sorted by residual: bond pdb=" CB PRO B 23 " pdb=" CG PRO B 23 " ideal model delta sigma weight residual 1.506 1.455 0.051 3.90e-02 6.57e+02 1.73e+00 bond pdb=" CB PRO C 23 " pdb=" CG PRO C 23 " ideal model delta sigma weight residual 1.506 1.456 0.050 3.90e-02 6.57e+02 1.67e+00 bond pdb=" CB PRO A 23 " pdb=" CG PRO A 23 " ideal model delta sigma weight residual 1.506 1.456 0.050 3.90e-02 6.57e+02 1.66e+00 bond pdb=" CG PRO C 254 " pdb=" CD PRO C 254 " ideal model delta sigma weight residual 1.503 1.467 0.036 3.40e-02 8.65e+02 1.12e+00 bond pdb=" CG PRO A 254 " pdb=" CD PRO A 254 " ideal model delta sigma weight residual 1.503 1.468 0.035 3.40e-02 8.65e+02 1.09e+00 ... (remaining 7948 not shown) Histogram of bond angle deviations from ideal: 98.58 - 105.67: 236 105.67 - 112.75: 4276 112.75 - 119.84: 2512 119.84 - 126.93: 3682 126.93 - 134.02: 139 Bond angle restraints: 10845 Sorted by residual: angle pdb=" C ASN C 305 " pdb=" N HIS C 306 " pdb=" CA HIS C 306 " ideal model delta sigma weight residual 122.55 118.75 3.80 2.03e+00 2.43e-01 3.51e+00 angle pdb=" N ASN A 307 " pdb=" CA ASN A 307 " pdb=" C ASN A 307 " ideal model delta sigma weight residual 108.17 104.74 3.43 1.85e+00 2.92e-01 3.44e+00 angle pdb=" N ASN C 307 " pdb=" CA ASN C 307 " pdb=" C ASN C 307 " ideal model delta sigma weight residual 108.17 104.75 3.42 1.85e+00 2.92e-01 3.43e+00 angle pdb=" C ASN A 305 " pdb=" N HIS A 306 " pdb=" CA HIS A 306 " ideal model delta sigma weight residual 122.55 118.81 3.74 2.03e+00 2.43e-01 3.39e+00 angle pdb=" N ASN B 307 " pdb=" CA ASN B 307 " pdb=" C ASN B 307 " ideal model delta sigma weight residual 108.17 104.77 3.40 1.85e+00 2.92e-01 3.39e+00 ... (remaining 10840 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.02: 4144 17.02 - 34.05: 383 34.05 - 51.07: 84 51.07 - 68.10: 39 68.10 - 85.12: 6 Dihedral angle restraints: 4656 sinusoidal: 1812 harmonic: 2844 Sorted by residual: dihedral pdb=" CA HIS B 306 " pdb=" C HIS B 306 " pdb=" N ASN B 307 " pdb=" CA ASN B 307 " ideal model delta harmonic sigma weight residual 180.00 153.84 26.16 0 5.00e+00 4.00e-02 2.74e+01 dihedral pdb=" CA HIS C 306 " pdb=" C HIS C 306 " pdb=" N ASN C 307 " pdb=" CA ASN C 307 " ideal model delta harmonic sigma weight residual 180.00 153.86 26.14 0 5.00e+00 4.00e-02 2.73e+01 dihedral pdb=" CA HIS A 306 " pdb=" C HIS A 306 " pdb=" N ASN A 307 " pdb=" CA ASN A 307 " ideal model delta harmonic sigma weight residual 180.00 153.87 26.13 0 5.00e+00 4.00e-02 2.73e+01 ... (remaining 4653 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 684 0.034 - 0.067: 298 0.067 - 0.101: 166 0.101 - 0.134: 42 0.134 - 0.168: 7 Chirality restraints: 1197 Sorted by residual: chirality pdb=" CA HIS A 306 " pdb=" N HIS A 306 " pdb=" C HIS A 306 " pdb=" CB HIS A 306 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.02e-01 chirality pdb=" CA HIS B 306 " pdb=" N HIS B 306 " pdb=" C HIS B 306 " pdb=" CB HIS B 306 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.85e-01 chirality pdb=" CA HIS C 306 " pdb=" N HIS C 306 " pdb=" C HIS C 306 " pdb=" CB HIS C 306 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.48e-01 ... (remaining 1194 not shown) Planarity restraints: 1422 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS C 336 " 0.024 5.00e-02 4.00e+02 3.70e-02 2.19e+00 pdb=" N PRO C 337 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO C 337 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 337 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 336 " 0.024 5.00e-02 4.00e+02 3.70e-02 2.19e+00 pdb=" N PRO A 337 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO A 337 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 337 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 336 " -0.024 5.00e-02 4.00e+02 3.67e-02 2.15e+00 pdb=" N PRO B 337 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO B 337 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 337 " -0.020 5.00e-02 4.00e+02 ... (remaining 1419 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 122 2.59 - 3.17: 6302 3.17 - 3.75: 11208 3.75 - 4.32: 16624 4.32 - 4.90: 29170 Nonbonded interactions: 63426 Sorted by model distance: nonbonded pdb=" NE2 HIS B 100 " pdb="CU CU B 501 " model vdw 2.015 2.320 nonbonded pdb=" NE2 HIS A 100 " pdb="CU CU A 501 " model vdw 2.016 2.320 nonbonded pdb=" NE2 HIS C 100 " pdb="CU CU C 501 " model vdw 2.016 2.320 nonbonded pdb=" NE2 HIS C 306 " pdb="CU CU A 501 " model vdw 2.053 2.320 nonbonded pdb=" ND1 HIS A 145 " pdb="CU CU A 500 " model vdw 2.054 2.320 ... (remaining 63421 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 6.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 24.700 Check model and map are aligned: 0.110 Set scattering table: 0.060 Process input model: 23.990 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8797 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 : 0.007 0.061 7953 Z= 0.490 Angle : 0.634 5.914 10845 Z= 0.353 Chirality : 0.048 0.168 1197 Planarity : 0.005 0.037 1422 Dihedral : 15.036 85.119 2850 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer Outliers : 8.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.46 (0.23), residues: 996 helix: -1.79 (0.48), residues: 78 sheet: -0.73 (0.29), residues: 288 loop : -2.16 (0.20), residues: 630 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 75 time to evaluate : 0.953 Fit side-chains outliers start: 72 outliers final: 27 residues processed: 140 average time/residue: 0.9437 time to fit residues: 142.2471 Evaluate side-chains 79 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 52 time to evaluate : 0.945 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 27 residues processed: 0 time to fit residues: 1.2405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 83 optimal weight: 0.9990 chunk 75 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 40 optimal weight: 0.7980 chunk 77 optimal weight: 0.9990 chunk 30 optimal weight: 0.1980 chunk 47 optimal weight: 0.9980 chunk 57 optimal weight: 0.7980 chunk 89 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 221 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8772 moved from start: 0.0874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.030 7953 Z= 0.243 Angle : 0.542 5.699 10845 Z= 0.293 Chirality : 0.046 0.141 1197 Planarity : 0.004 0.035 1422 Dihedral : 5.140 25.727 1074 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer Outliers : 7.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.24), residues: 996 helix: -1.36 (0.51), residues: 69 sheet: -0.04 (0.29), residues: 282 loop : -1.46 (0.22), residues: 645 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 57 time to evaluate : 0.947 Fit side-chains outliers start: 65 outliers final: 32 residues processed: 113 average time/residue: 0.8749 time to fit residues: 107.3837 Evaluate side-chains 88 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 56 time to evaluate : 0.941 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 31 residues processed: 2 average time/residue: 0.2173 time to fit residues: 1.8293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 90 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 HIS B 76 HIS ** B 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 HIS C 151 ASN C 297 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8792 moved from start: 0.1120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.050 7953 Z= 0.395 Angle : 0.584 5.860 10845 Z= 0.314 Chirality : 0.048 0.164 1197 Planarity : 0.004 0.037 1422 Dihedral : 5.269 26.744 1074 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer Outliers : 7.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.25), residues: 996 helix: -1.68 (0.45), residues: 90 sheet: 0.12 (0.29), residues: 288 loop : -1.19 (0.23), residues: 618 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 56 time to evaluate : 0.988 Fit side-chains outliers start: 59 outliers final: 42 residues processed: 104 average time/residue: 0.8515 time to fit residues: 96.5073 Evaluate side-chains 95 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 53 time to evaluate : 0.915 Switching outliers to nearest non-outliers outliers start: 42 outliers final: 41 residues processed: 3 average time/residue: 0.7991 time to fit residues: 3.8170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 46 optimal weight: 0.5980 chunk 9 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 60 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 chunk 85 optimal weight: 0.5980 chunk 25 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 297 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8767 moved from start: 0.1276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 7953 Z= 0.260 Angle : 0.528 5.690 10845 Z= 0.285 Chirality : 0.046 0.143 1197 Planarity : 0.004 0.036 1422 Dihedral : 5.045 25.949 1074 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer Outliers : 8.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.25), residues: 996 helix: -1.57 (0.45), residues: 90 sheet: 0.35 (0.29), residues: 288 loop : -0.99 (0.24), residues: 618 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 60 time to evaluate : 0.865 Fit side-chains outliers start: 66 outliers final: 43 residues processed: 117 average time/residue: 0.8297 time to fit residues: 105.8675 Evaluate side-chains 99 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 56 time to evaluate : 0.903 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 42 residues processed: 3 average time/residue: 0.5023 time to fit residues: 2.8511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 79 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 1 optimal weight: 0.0010 chunk 71 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 81 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 48 optimal weight: 0.9980 chunk 85 optimal weight: 0.0060 chunk 24 optimal weight: 3.9990 overall best weight: 0.5604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 ASN B 297 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.1478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 7953 Z= 0.205 Angle : 0.507 5.632 10845 Z= 0.273 Chirality : 0.045 0.132 1197 Planarity : 0.004 0.035 1422 Dihedral : 4.862 24.952 1074 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer Outliers : 7.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.25), residues: 996 helix: -1.87 (0.42), residues: 93 sheet: 0.72 (0.30), residues: 270 loop : -0.99 (0.24), residues: 633 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 63 time to evaluate : 0.924 Fit side-chains outliers start: 65 outliers final: 46 residues processed: 119 average time/residue: 0.8454 time to fit residues: 109.4470 Evaluate side-chains 106 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 60 time to evaluate : 0.920 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 45 residues processed: 1 average time/residue: 0.2292 time to fit residues: 1.5913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 32 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 chunk 7 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 297 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8784 moved from start: 0.1429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.053 7953 Z= 0.391 Angle : 0.580 5.824 10845 Z= 0.313 Chirality : 0.047 0.166 1197 Planarity : 0.004 0.036 1422 Dihedral : 5.174 26.547 1074 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer Outliers : 7.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.25), residues: 996 helix: -1.90 (0.43), residues: 90 sheet: 0.28 (0.27), residues: 312 loop : -0.83 (0.25), residues: 594 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 56 time to evaluate : 0.978 Fit side-chains outliers start: 60 outliers final: 44 residues processed: 108 average time/residue: 0.9525 time to fit residues: 111.2485 Evaluate side-chains 99 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 55 time to evaluate : 1.054 Switching outliers to nearest non-outliers outliers start: 44 outliers final: 42 residues processed: 2 average time/residue: 0.2240 time to fit residues: 1.8138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 92 optimal weight: 0.3980 chunk 10 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 80 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 95 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 0.1529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.032 7953 Z= 0.259 Angle : 0.527 5.688 10845 Z= 0.285 Chirality : 0.046 0.140 1197 Planarity : 0.004 0.036 1422 Dihedral : 4.985 25.908 1074 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer Outliers : 6.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.25), residues: 996 helix: -1.96 (0.42), residues: 93 sheet: 0.61 (0.29), residues: 288 loop : -0.75 (0.25), residues: 615 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 57 time to evaluate : 0.949 Fit side-chains outliers start: 51 outliers final: 45 residues processed: 103 average time/residue: 0.9536 time to fit residues: 106.0946 Evaluate side-chains 102 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 57 time to evaluate : 0.903 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 45 residues processed: 0 time to fit residues: 1.2050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 56 optimal weight: 0.6980 chunk 28 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 83 optimal weight: 0.6980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8772 moved from start: 0.1538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.039 7953 Z= 0.325 Angle : 0.550 5.754 10845 Z= 0.297 Chirality : 0.046 0.152 1197 Planarity : 0.004 0.036 1422 Dihedral : 5.064 26.632 1074 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer Outliers : 6.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.25), residues: 996 helix: -1.87 (0.44), residues: 90 sheet: 0.30 (0.27), residues: 312 loop : -0.72 (0.25), residues: 594 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 55 time to evaluate : 1.000 Fit side-chains outliers start: 51 outliers final: 43 residues processed: 102 average time/residue: 0.9913 time to fit residues: 109.0582 Evaluate side-chains 100 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 57 time to evaluate : 0.834 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 43 residues processed: 0 time to fit residues: 1.1342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 80 optimal weight: 0.7980 chunk 84 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 94 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.038 7953 Z= 0.329 Angle : 0.552 5.750 10845 Z= 0.298 Chirality : 0.046 0.149 1197 Planarity : 0.004 0.037 1422 Dihedral : 5.062 26.500 1074 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer Outliers : 6.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.25), residues: 996 helix: -1.85 (0.44), residues: 90 sheet: 0.58 (0.29), residues: 288 loop : -0.69 (0.25), residues: 618 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 56 time to evaluate : 0.932 Fit side-chains outliers start: 50 outliers final: 43 residues processed: 102 average time/residue: 0.9670 time to fit residues: 107.7243 Evaluate side-chains 96 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 53 time to evaluate : 0.970 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 42 residues processed: 1 average time/residue: 1.2286 time to fit residues: 2.5841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 44 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 78 optimal weight: 0.3980 chunk 8 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 48 optimal weight: 0.6980 chunk 62 optimal weight: 0.9990 chunk 83 optimal weight: 0.6980 chunk 24 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 7953 Z= 0.222 Angle : 0.517 5.637 10845 Z= 0.279 Chirality : 0.045 0.134 1197 Planarity : 0.004 0.036 1422 Dihedral : 4.865 25.337 1074 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer Outliers : 5.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.25), residues: 996 helix: -1.93 (0.43), residues: 93 sheet: 0.61 (0.29), residues: 261 loop : -0.80 (0.24), residues: 642 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 57 time to evaluate : 0.890 Fit side-chains outliers start: 46 outliers final: 42 residues processed: 100 average time/residue: 0.9660 time to fit residues: 104.4033 Evaluate side-chains 100 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 58 time to evaluate : 0.860 Switching outliers to nearest non-outliers outliers start: 42 outliers final: 42 residues processed: 0 time to fit residues: 1.3071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 72 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 78 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 80 optimal weight: 0.7980 chunk 9 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.100056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.079767 restraints weight = 11599.280| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 2.33 r_work: 0.2803 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2667 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8968 moved from start: 0.1610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.040 7953 Z= 0.339 Angle : 0.554 5.771 10845 Z= 0.299 Chirality : 0.046 0.154 1197 Planarity : 0.004 0.037 1422 Dihedral : 5.009 26.031 1074 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer Outliers : 5.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.25), residues: 996 helix: -1.82 (0.44), residues: 90 sheet: 0.34 (0.27), residues: 312 loop : -0.66 (0.25), residues: 594 =============================================================================== Job complete usr+sys time: 2843.05 seconds wall clock time: 51 minutes 13.50 seconds (3073.50 seconds total)