Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 21 19:29:59 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k9l_22754/04_2023/7k9l_22754.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k9l_22754/04_2023/7k9l_22754.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k9l_22754/04_2023/7k9l_22754.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k9l_22754/04_2023/7k9l_22754.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k9l_22754/04_2023/7k9l_22754.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k9l_22754/04_2023/7k9l_22754.pdb" } resolution = 4.9 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= 0.004 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: 4 Type Number sf(0) Gaussians S 44 5.16 5 C 6588 2.51 5 N 1860 2.21 5 O 1980 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ASP 17": "OD1" <-> "OD2" Residue "B GLU 53": "OE1" <-> "OE2" Residue "B ASP 89": "OD1" <-> "OD2" Residue "B PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 165": "OE1" <-> "OE2" Residue "B GLU 189": "OE1" <-> "OE2" Residue "B ASP 218": "OD1" <-> "OD2" Residue "B GLU 224": "OE1" <-> "OE2" Residue "B PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 326": "OE1" <-> "OE2" Residue "A ASP 17": "OD1" <-> "OD2" Residue "A GLU 53": "OE1" <-> "OE2" Residue "A ASP 89": "OD1" <-> "OD2" Residue "A PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 165": "OE1" <-> "OE2" Residue "A GLU 189": "OE1" <-> "OE2" Residue "A ASP 218": "OD1" <-> "OD2" Residue "A GLU 224": "OE1" <-> "OE2" Residue "A PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 326": "OE1" <-> "OE2" Residue "C ASP 17": "OD1" <-> "OD2" Residue "C GLU 53": "OE1" <-> "OE2" Residue "C ASP 89": "OD1" <-> "OD2" Residue "C PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 165": "OE1" <-> "OE2" Residue "C GLU 189": "OE1" <-> "OE2" Residue "C ASP 218": "OD1" <-> "OD2" Residue "C GLU 224": "OE1" <-> "OE2" Residue "C PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 326": "OE1" <-> "OE2" Residue "D ASP 17": "OD1" <-> "OD2" Residue "D GLU 53": "OE1" <-> "OE2" Residue "D ASP 89": "OD1" <-> "OD2" Residue "D PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 165": "OE1" <-> "OE2" Residue "D GLU 189": "OE1" <-> "OE2" Residue "D ASP 218": "OD1" <-> "OD2" Residue "D GLU 224": "OE1" <-> "OE2" Residue "D PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 326": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 10472 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 2618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2618 Classifications: {'peptide': 343} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 324} Chain: "A" Number of atoms: 2618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2618 Classifications: {'peptide': 343} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 324} Chain: "C" Number of atoms: 2618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2618 Classifications: {'peptide': 343} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 324} Chain: "D" Number of atoms: 2618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2618 Classifications: {'peptide': 343} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 324} Time building chain proxies: 5.87, per 1000 atoms: 0.56 Number of scatterers: 10472 At special positions: 0 Unit cell: (97.37, 80.99, 106.47, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 44 16.00 O 1980 8.00 N 1860 7.00 C 6588 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: 4.27 Conformation dependent library (CDL) restraints added in 1.6 seconds 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2520 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 8 sheets defined 56.0% alpha, 13.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'B' and resid 8 through 23 Processing helix chain 'B' and resid 35 through 47 Processing helix chain 'B' and resid 51 through 64 Processing helix chain 'B' and resid 66 through 70 Processing helix chain 'B' and resid 79 through 84 removed outlier: 3.592A pdb=" N LEU B 83 " --> pdb=" O PHE B 79 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N TYR B 84 " --> pdb=" O HIS B 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 79 through 84' Processing helix chain 'B' and resid 92 through 100 removed outlier: 3.866A pdb=" N LYS B 100 " --> pdb=" O VAL B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 140 Processing helix chain 'B' and resid 159 through 181 removed outlier: 3.870A pdb=" N ASN B 180 " --> pdb=" O ILE B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 219 removed outlier: 3.620A pdb=" N CYS B 201 " --> pdb=" O ASP B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 225 Processing helix chain 'B' and resid 244 through 258 Processing helix chain 'B' and resid 275 through 288 removed outlier: 4.094A pdb=" N SER B 280 " --> pdb=" O GLU B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 314 removed outlier: 3.738A pdb=" N GLN B 306 " --> pdb=" O GLY B 302 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N SER B 308 " --> pdb=" O ALA B 304 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N ALA B 309 " --> pdb=" O LEU B 305 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLY B 314 " --> pdb=" O LEU B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 318 No H-bonds generated for 'chain 'B' and resid 316 through 318' Processing helix chain 'B' and resid 319 through 340 Processing helix chain 'A' and resid 8 through 23 Processing helix chain 'A' and resid 35 through 47 Processing helix chain 'A' and resid 51 through 64 Processing helix chain 'A' and resid 66 through 70 Processing helix chain 'A' and resid 79 through 84 removed outlier: 3.593A pdb=" N LEU A 83 " --> pdb=" O PHE A 79 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N TYR A 84 " --> pdb=" O HIS A 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 79 through 84' Processing helix chain 'A' and resid 92 through 100 removed outlier: 3.865A pdb=" N LYS A 100 " --> pdb=" O VAL A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 140 Processing helix chain 'A' and resid 159 through 181 removed outlier: 3.870A pdb=" N ASN A 180 " --> pdb=" O ILE A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 219 removed outlier: 3.619A pdb=" N CYS A 201 " --> pdb=" O ASP A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 225 Processing helix chain 'A' and resid 244 through 258 Processing helix chain 'A' and resid 275 through 288 removed outlier: 4.093A pdb=" N SER A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 314 removed outlier: 3.740A pdb=" N GLN A 306 " --> pdb=" O GLY A 302 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N SER A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N ALA A 309 " --> pdb=" O LEU A 305 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLY A 314 " --> pdb=" O LEU A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 318 No H-bonds generated for 'chain 'A' and resid 316 through 318' Processing helix chain 'A' and resid 319 through 340 Processing helix chain 'C' and resid 8 through 23 Processing helix chain 'C' and resid 35 through 47 Processing helix chain 'C' and resid 51 through 64 Processing helix chain 'C' and resid 66 through 70 Processing helix chain 'C' and resid 79 through 84 removed outlier: 3.593A pdb=" N LEU C 83 " --> pdb=" O PHE C 79 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N TYR C 84 " --> pdb=" O HIS C 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 79 through 84' Processing helix chain 'C' and resid 92 through 100 removed outlier: 3.867A pdb=" N LYS C 100 " --> pdb=" O VAL C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 140 Processing helix chain 'C' and resid 159 through 181 removed outlier: 3.870A pdb=" N ASN C 180 " --> pdb=" O ILE C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 219 removed outlier: 3.620A pdb=" N CYS C 201 " --> pdb=" O ASP C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 225 Processing helix chain 'C' and resid 244 through 258 Processing helix chain 'C' and resid 275 through 288 removed outlier: 4.093A pdb=" N SER C 280 " --> pdb=" O GLU C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 314 removed outlier: 3.738A pdb=" N GLN C 306 " --> pdb=" O GLY C 302 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N SER C 308 " --> pdb=" O ALA C 304 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N ALA C 309 " --> pdb=" O LEU C 305 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLY C 314 " --> pdb=" O LEU C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 318 No H-bonds generated for 'chain 'C' and resid 316 through 318' Processing helix chain 'C' and resid 319 through 340 Processing helix chain 'D' and resid 8 through 23 Processing helix chain 'D' and resid 35 through 47 Processing helix chain 'D' and resid 51 through 64 Processing helix chain 'D' and resid 66 through 70 Processing helix chain 'D' and resid 79 through 84 removed outlier: 3.593A pdb=" N LEU D 83 " --> pdb=" O PHE D 79 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N TYR D 84 " --> pdb=" O HIS D 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 79 through 84' Processing helix chain 'D' and resid 92 through 100 removed outlier: 3.866A pdb=" N LYS D 100 " --> pdb=" O VAL D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 140 Processing helix chain 'D' and resid 159 through 181 removed outlier: 3.870A pdb=" N ASN D 180 " --> pdb=" O ILE D 176 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 219 removed outlier: 3.621A pdb=" N CYS D 201 " --> pdb=" O ASP D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 225 Processing helix chain 'D' and resid 244 through 258 Processing helix chain 'D' and resid 275 through 288 removed outlier: 4.094A pdb=" N SER D 280 " --> pdb=" O GLU D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 314 removed outlier: 3.739A pdb=" N GLN D 306 " --> pdb=" O GLY D 302 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N SER D 308 " --> pdb=" O ALA D 304 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N ALA D 309 " --> pdb=" O LEU D 305 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLY D 314 " --> pdb=" O LEU D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 316 through 318 No H-bonds generated for 'chain 'D' and resid 316 through 318' Processing helix chain 'D' and resid 319 through 340 Processing sheet with id=AA1, first strand: chain 'B' and resid 28 through 32 removed outlier: 6.147A pdb=" N GLY B 28 " --> pdb=" O GLY B 75 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N ILE B 77 " --> pdb=" O GLY B 28 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N LEU B 30 " --> pdb=" O ILE B 77 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N GLY B 74 " --> pdb=" O VAL B 103 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N GLY B 105 " --> pdb=" O GLY B 74 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N VAL B 76 " --> pdb=" O GLY B 105 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N LYS B 107 " --> pdb=" O VAL B 76 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N LEU B 78 " --> pdb=" O LYS B 107 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N VAL B 104 " --> pdb=" O ASP B 143 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N ALA B 145 " --> pdb=" O VAL B 104 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N ILE B 106 " --> pdb=" O ALA B 145 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N TRP B 147 " --> pdb=" O ILE B 106 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N TRP B 147 " --> pdb=" O ILE B 185 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLU B 187 " --> pdb=" O TRP B 147 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N LEU B 228 " --> pdb=" O THR B 268 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA B 31 " --> pdb=" O TYR B 301 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 112 through 114 Processing sheet with id=AA3, first strand: chain 'A' and resid 28 through 32 removed outlier: 6.147A pdb=" N GLY A 28 " --> pdb=" O GLY A 75 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N ILE A 77 " --> pdb=" O GLY A 28 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N LEU A 30 " --> pdb=" O ILE A 77 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N GLY A 74 " --> pdb=" O VAL A 103 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N GLY A 105 " --> pdb=" O GLY A 74 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N VAL A 76 " --> pdb=" O GLY A 105 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N LYS A 107 " --> pdb=" O VAL A 76 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N LEU A 78 " --> pdb=" O LYS A 107 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N VAL A 104 " --> pdb=" O ASP A 143 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N ALA A 145 " --> pdb=" O VAL A 104 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N ILE A 106 " --> pdb=" O ALA A 145 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N TRP A 147 " --> pdb=" O ILE A 106 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N TRP A 147 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLU A 187 " --> pdb=" O TRP A 147 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N LEU A 228 " --> pdb=" O THR A 268 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA A 31 " --> pdb=" O TYR A 301 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 112 through 114 Processing sheet with id=AA5, first strand: chain 'C' and resid 28 through 32 removed outlier: 6.148A pdb=" N GLY C 28 " --> pdb=" O GLY C 75 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N ILE C 77 " --> pdb=" O GLY C 28 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N LEU C 30 " --> pdb=" O ILE C 77 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N GLY C 74 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N GLY C 105 " --> pdb=" O GLY C 74 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N VAL C 76 " --> pdb=" O GLY C 105 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N LYS C 107 " --> pdb=" O VAL C 76 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N LEU C 78 " --> pdb=" O LYS C 107 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N VAL C 104 " --> pdb=" O ASP C 143 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N ALA C 145 " --> pdb=" O VAL C 104 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N ILE C 106 " --> pdb=" O ALA C 145 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N TRP C 147 " --> pdb=" O ILE C 106 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N TRP C 147 " --> pdb=" O ILE C 185 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLU C 187 " --> pdb=" O TRP C 147 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N LEU C 228 " --> pdb=" O THR C 268 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA C 31 " --> pdb=" O TYR C 301 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 112 through 114 Processing sheet with id=AA7, first strand: chain 'D' and resid 28 through 32 removed outlier: 6.148A pdb=" N GLY D 28 " --> pdb=" O GLY D 75 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N ILE D 77 " --> pdb=" O GLY D 28 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N LEU D 30 " --> pdb=" O ILE D 77 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N GLY D 74 " --> pdb=" O VAL D 103 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N GLY D 105 " --> pdb=" O GLY D 74 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N VAL D 76 " --> pdb=" O GLY D 105 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N LYS D 107 " --> pdb=" O VAL D 76 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N LEU D 78 " --> pdb=" O LYS D 107 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N VAL D 104 " --> pdb=" O ASP D 143 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N ALA D 145 " --> pdb=" O VAL D 104 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N ILE D 106 " --> pdb=" O ALA D 145 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N TRP D 147 " --> pdb=" O ILE D 106 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N TRP D 147 " --> pdb=" O ILE D 185 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLU D 187 " --> pdb=" O TRP D 147 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N LEU D 228 " --> pdb=" O THR D 268 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA D 31 " --> pdb=" O TYR D 301 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 112 through 114 564 hydrogen bonds defined for protein. 1632 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: 3.15 Time building geometry restraints manager: 4.63 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: 3395 1.34 - 1.45: 1572 1.45 - 1.57: 5645 1.57 - 1.69: 4 1.69 - 1.81: 56 Bond restraints: 10672 Sorted by residual: bond pdb=" C HIS A 220 " pdb=" N ILE A 221 " ideal model delta sigma weight residual 1.334 1.305 0.029 1.29e-02 6.01e+03 5.11e+00 bond pdb=" C HIS C 220 " pdb=" N ILE C 221 " ideal model delta sigma weight residual 1.334 1.305 0.029 1.29e-02 6.01e+03 4.88e+00 bond pdb=" C HIS B 220 " pdb=" N ILE B 221 " ideal model delta sigma weight residual 1.334 1.306 0.028 1.29e-02 6.01e+03 4.79e+00 bond pdb=" C HIS D 220 " pdb=" N ILE D 221 " ideal model delta sigma weight residual 1.334 1.306 0.028 1.29e-02 6.01e+03 4.67e+00 bond pdb=" CB GLU B 52 " pdb=" CG GLU B 52 " ideal model delta sigma weight residual 1.520 1.580 -0.060 3.00e-02 1.11e+03 4.05e+00 ... (remaining 10667 not shown) Histogram of bond angle deviations from ideal: 98.03 - 105.26: 257 105.26 - 112.50: 5500 112.50 - 119.73: 3748 119.73 - 126.97: 4819 126.97 - 134.20: 140 Bond angle restraints: 14464 Sorted by residual: angle pdb=" CA LEU A 320 " pdb=" CB LEU A 320 " pdb=" CG LEU A 320 " ideal model delta sigma weight residual 116.30 134.20 -17.90 3.50e+00 8.16e-02 2.62e+01 angle pdb=" CA LEU B 320 " pdb=" CB LEU B 320 " pdb=" CG LEU B 320 " ideal model delta sigma weight residual 116.30 134.20 -17.90 3.50e+00 8.16e-02 2.62e+01 angle pdb=" CA LEU C 320 " pdb=" CB LEU C 320 " pdb=" CG LEU C 320 " ideal model delta sigma weight residual 116.30 134.19 -17.89 3.50e+00 8.16e-02 2.61e+01 angle pdb=" CA LEU D 320 " pdb=" CB LEU D 320 " pdb=" CG LEU D 320 " ideal model delta sigma weight residual 116.30 134.18 -17.88 3.50e+00 8.16e-02 2.61e+01 angle pdb=" CA LEU A 78 " pdb=" CB LEU A 78 " pdb=" CG LEU A 78 " ideal model delta sigma weight residual 116.30 132.68 -16.38 3.50e+00 8.16e-02 2.19e+01 ... (remaining 14459 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.34: 5843 17.34 - 34.68: 485 34.68 - 52.03: 112 52.03 - 69.37: 48 69.37 - 86.71: 16 Dihedral angle restraints: 6504 sinusoidal: 2572 harmonic: 3932 Sorted by residual: dihedral pdb=" CA ASN A 319 " pdb=" C ASN A 319 " pdb=" N LEU A 320 " pdb=" CA LEU A 320 " ideal model delta harmonic sigma weight residual -180.00 -150.93 -29.07 0 5.00e+00 4.00e-02 3.38e+01 dihedral pdb=" CA ASN B 319 " pdb=" C ASN B 319 " pdb=" N LEU B 320 " pdb=" CA LEU B 320 " ideal model delta harmonic sigma weight residual -180.00 -150.94 -29.06 0 5.00e+00 4.00e-02 3.38e+01 dihedral pdb=" CA ASN D 319 " pdb=" C ASN D 319 " pdb=" N LEU D 320 " pdb=" CA LEU D 320 " ideal model delta harmonic sigma weight residual -180.00 -150.94 -29.06 0 5.00e+00 4.00e-02 3.38e+01 ... (remaining 6501 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 1372 0.080 - 0.159: 223 0.159 - 0.239: 35 0.239 - 0.318: 10 0.318 - 0.398: 4 Chirality restraints: 1644 Sorted by residual: chirality pdb=" CB THR C 205 " pdb=" CA THR C 205 " pdb=" OG1 THR C 205 " pdb=" CG2 THR C 205 " both_signs ideal model delta sigma weight residual False 2.55 2.15 0.40 2.00e-01 2.50e+01 3.96e+00 chirality pdb=" CB THR D 205 " pdb=" CA THR D 205 " pdb=" OG1 THR D 205 " pdb=" CG2 THR D 205 " both_signs ideal model delta sigma weight residual False 2.55 2.15 0.40 2.00e-01 2.50e+01 3.94e+00 chirality pdb=" CB THR B 205 " pdb=" CA THR B 205 " pdb=" OG1 THR B 205 " pdb=" CG2 THR B 205 " both_signs ideal model delta sigma weight residual False 2.55 2.16 0.40 2.00e-01 2.50e+01 3.92e+00 ... (remaining 1641 not shown) Planarity restraints: 1880 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS B 329 " 0.016 2.00e-02 2.50e+03 3.14e-02 9.84e+00 pdb=" C LYS B 329 " -0.054 2.00e-02 2.50e+03 pdb=" O LYS B 329 " 0.021 2.00e-02 2.50e+03 pdb=" N ARG B 330 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS C 329 " 0.016 2.00e-02 2.50e+03 3.14e-02 9.83e+00 pdb=" C LYS C 329 " -0.054 2.00e-02 2.50e+03 pdb=" O LYS C 329 " 0.021 2.00e-02 2.50e+03 pdb=" N ARG C 330 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS D 329 " -0.016 2.00e-02 2.50e+03 3.13e-02 9.80e+00 pdb=" C LYS D 329 " 0.054 2.00e-02 2.50e+03 pdb=" O LYS D 329 " -0.020 2.00e-02 2.50e+03 pdb=" N ARG D 330 " -0.018 2.00e-02 2.50e+03 ... (remaining 1877 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2647 2.78 - 3.31: 10217 3.31 - 3.84: 18354 3.84 - 4.37: 20655 4.37 - 4.90: 34745 Nonbonded interactions: 86618 Sorted by model distance: nonbonded pdb=" O PHE B 269 " pdb=" OG SER B 300 " model vdw 2.254 2.440 nonbonded pdb=" O PHE D 269 " pdb=" OG SER D 300 " model vdw 2.255 2.440 nonbonded pdb=" O PHE C 269 " pdb=" OG SER C 300 " model vdw 2.255 2.440 nonbonded pdb=" O PHE A 269 " pdb=" OG SER A 300 " model vdw 2.255 2.440 nonbonded pdb=" O GLN A 60 " pdb=" OG1 THR A 64 " model vdw 2.272 2.440 ... (remaining 86613 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' selection = chain 'D' } Set up NCS constraints Number of NCS constrained groups: 1 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set refine NCS operators NCS operators will be refined. 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 group one per residue 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: 1.350 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: 6.610 Check model and map are aligned: 0.150 Set scattering table: 0.080 Process input model: 29.430 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.040 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 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 0.065 10672 Z= 0.482 Angle : 1.189 17.902 14464 Z= 0.639 Chirality : 0.066 0.398 1644 Planarity : 0.008 0.048 1880 Dihedral : 15.276 86.709 3984 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer Outliers : 3.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -1.98 (0.19), residues: 1364 helix: -0.95 (0.16), residues: 652 sheet: -2.05 (0.33), residues: 196 loop : -1.22 (0.24), residues: 516 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 154 time to evaluate : 0.287 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 3 residues processed: 158 average time/residue: 0.1873 time to fit residues: 33.6555 Evaluate side-chains 98 residues out of total 278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 95 time to evaluate : 0.313 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0348 time to fit residues: 0.6376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 114 optimal weight: 5.9990 chunk 103 optimal weight: 6.9990 chunk 57 optimal weight: 9.9990 chunk 35 optimal weight: 6.9990 chunk 69 optimal weight: 6.9990 chunk 55 optimal weight: 3.9990 chunk 106 optimal weight: 9.9990 chunk 41 optimal weight: 6.9990 chunk 64 optimal weight: 4.9990 chunk 79 optimal weight: 4.9990 chunk 123 optimal weight: 3.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 119 ASN D 125 GLN ** D 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 237 HIS ** D 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 324 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.4245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.080 10672 Z= 0.408 Angle : 0.802 7.209 14464 Z= 0.427 Chirality : 0.045 0.165 1644 Planarity : 0.009 0.146 1880 Dihedral : 5.914 27.181 1472 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 27.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer Outliers : 0.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -0.39 (0.21), residues: 1364 helix: 0.54 (0.17), residues: 692 sheet: -1.58 (0.32), residues: 224 loop : -0.57 (0.28), residues: 448 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 116 time to evaluate : 0.334 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 117 average time/residue: 0.1565 time to fit residues: 21.3686 Evaluate side-chains 84 residues out of total 278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 0.327 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 68 optimal weight: 10.0000 chunk 38 optimal weight: 0.5980 chunk 102 optimal weight: 8.9990 chunk 84 optimal weight: 4.9990 chunk 34 optimal weight: 8.9990 chunk 123 optimal weight: 3.9990 chunk 133 optimal weight: 0.0570 chunk 110 optimal weight: 0.8980 chunk 122 optimal weight: 0.9990 chunk 42 optimal weight: 0.8980 chunk 99 optimal weight: 0.0470 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 60 GLN ** D 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 245 HIS D 282 ASN ** D 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.4821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 10672 Z= 0.205 Angle : 0.664 8.071 14464 Z= 0.325 Chirality : 0.043 0.136 1644 Planarity : 0.005 0.051 1880 Dihedral : 4.959 18.337 1472 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 19.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer Outliers : 0.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.29 (0.22), residues: 1364 helix: 1.02 (0.19), residues: 700 sheet: -0.88 (0.38), residues: 172 loop : -0.46 (0.27), residues: 492 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 123 time to evaluate : 0.320 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 123 average time/residue: 0.1467 time to fit residues: 21.2233 Evaluate side-chains 92 residues out of total 278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 0.317 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 0.7980 chunk 93 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 59 optimal weight: 1.9990 chunk 83 optimal weight: 20.0000 chunk 124 optimal weight: 1.9990 chunk 131 optimal weight: 3.9990 chunk 117 optimal weight: 20.0000 chunk 35 optimal weight: 0.0670 chunk 109 optimal weight: 5.9990 overall best weight: 1.1322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 54 ASN ** B 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 324 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.5423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 10672 Z= 0.192 Angle : 0.615 7.077 14464 Z= 0.304 Chirality : 0.041 0.143 1644 Planarity : 0.005 0.037 1880 Dihedral : 4.665 16.711 1472 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 19.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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 (0.23), residues: 1364 helix: 1.23 (0.19), residues: 700 sheet: -0.31 (0.37), residues: 184 loop : -0.34 (0.29), residues: 480 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 122 time to evaluate : 0.279 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 122 average time/residue: 0.1545 time to fit residues: 21.9962 Evaluate side-chains 87 residues out of total 278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 0.297 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 74 optimal weight: 1.9990 chunk 1 optimal weight: 8.9990 chunk 97 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 112 optimal weight: 0.0060 chunk 90 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 chunk 67 optimal weight: 6.9990 chunk 117 optimal weight: 20.0000 chunk 33 optimal weight: 5.9990 chunk 44 optimal weight: 0.0970 overall best weight: 1.4200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN B 85 GLN ** B 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 219 HIS ** B 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 324 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.5811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 10672 Z= 0.202 Angle : 0.615 7.009 14464 Z= 0.306 Chirality : 0.042 0.172 1644 Planarity : 0.004 0.031 1880 Dihedral : 4.677 16.940 1472 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 19.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.71 (0.23), residues: 1364 helix: 1.38 (0.19), residues: 704 sheet: -0.67 (0.35), residues: 212 loop : -0.26 (0.30), residues: 448 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 0.312 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 119 average time/residue: 0.1496 time to fit residues: 20.9955 Evaluate side-chains 85 residues out of total 278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 0.336 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 118 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 77 optimal weight: 6.9990 chunk 32 optimal weight: 5.9990 chunk 131 optimal weight: 0.0070 chunk 109 optimal weight: 3.9990 chunk 60 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 43 optimal weight: 6.9990 chunk 69 optimal weight: 5.9990 chunk 126 optimal weight: 1.9990 overall best weight: 1.7604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 324 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.5918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 10672 Z= 0.214 Angle : 0.609 7.632 14464 Z= 0.305 Chirality : 0.041 0.145 1644 Planarity : 0.004 0.031 1880 Dihedral : 4.585 16.849 1472 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 18.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.62 (0.23), residues: 1364 helix: 1.21 (0.19), residues: 700 sheet: -0.19 (0.37), residues: 176 loop : -0.42 (0.29), residues: 488 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 0.333 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 118 average time/residue: 0.1492 time to fit residues: 20.8363 Evaluate side-chains 79 residues out of total 278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 0.321 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 14 optimal weight: 4.9990 chunk 74 optimal weight: 5.9990 chunk 96 optimal weight: 3.9990 chunk 110 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 131 optimal weight: 0.0870 chunk 82 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 60 optimal weight: 0.5980 chunk 81 optimal weight: 0.3980 chunk 52 optimal weight: 2.9990 overall best weight: 1.2162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 85 GLN ** B 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 219 HIS B 324 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.6207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 10672 Z= 0.194 Angle : 0.627 7.754 14464 Z= 0.310 Chirality : 0.043 0.183 1644 Planarity : 0.004 0.028 1880 Dihedral : 4.467 16.106 1472 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 18.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.47 (0.23), residues: 1364 helix: 1.11 (0.19), residues: 700 sheet: -0.04 (0.40), residues: 132 loop : -0.59 (0.28), residues: 532 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 0.318 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 120 average time/residue: 0.1598 time to fit residues: 22.7332 Evaluate side-chains 90 residues out of total 278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 0.328 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 0.3980 chunk 39 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 83 optimal weight: 20.0000 chunk 89 optimal weight: 3.9990 chunk 64 optimal weight: 0.1980 chunk 12 optimal weight: 0.8980 chunk 103 optimal weight: 5.9990 chunk 119 optimal weight: 3.9990 chunk 125 optimal weight: 9.9990 chunk 114 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 324 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.6466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 10672 Z= 0.190 Angle : 0.619 8.021 14464 Z= 0.307 Chirality : 0.042 0.147 1644 Planarity : 0.004 0.029 1880 Dihedral : 4.297 15.295 1472 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 15.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.43 (0.23), residues: 1364 helix: 1.10 (0.19), residues: 700 sheet: -0.75 (0.32), residues: 220 loop : -0.29 (0.32), residues: 444 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 0.325 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 119 average time/residue: 0.1535 time to fit residues: 21.4682 Evaluate side-chains 88 residues out of total 278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 0.322 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 1.9990 chunk 125 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 53 optimal weight: 0.0370 chunk 95 optimal weight: 2.9990 chunk 37 optimal weight: 7.9990 chunk 110 optimal weight: 0.0970 chunk 115 optimal weight: 1.9990 chunk 121 optimal weight: 0.0170 chunk 80 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 overall best weight: 0.6296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 54 ASN B 85 GLN ** B 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 324 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.6645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 10672 Z= 0.201 Angle : 0.632 7.830 14464 Z= 0.317 Chirality : 0.043 0.213 1644 Planarity : 0.004 0.029 1880 Dihedral : 4.299 14.309 1472 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.58 (0.23), residues: 1364 helix: 1.30 (0.19), residues: 692 sheet: -0.80 (0.32), residues: 216 loop : -0.27 (0.31), residues: 456 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 0.312 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 118 average time/residue: 0.1407 time to fit residues: 19.6925 Evaluate side-chains 92 residues out of total 278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 0.314 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 135 optimal weight: 7.9990 chunk 124 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 83 optimal weight: 10.0000 chunk 66 optimal weight: 7.9990 chunk 85 optimal weight: 0.6980 chunk 114 optimal weight: 6.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 219 HIS ** B 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 324 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.6724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 10672 Z= 0.219 Angle : 0.671 8.358 14464 Z= 0.343 Chirality : 0.044 0.196 1644 Planarity : 0.004 0.033 1880 Dihedral : 4.376 14.376 1472 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 17.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.42 (0.23), residues: 1364 helix: 1.15 (0.19), residues: 692 sheet: -0.58 (0.34), residues: 192 loop : -0.50 (0.30), residues: 480 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 0.322 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 119 average time/residue: 0.1718 time to fit residues: 23.6600 Evaluate side-chains 82 residues out of total 278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 0.309 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 33 optimal weight: 7.9990 chunk 99 optimal weight: 0.0270 chunk 15 optimal weight: 9.9990 chunk 29 optimal weight: 0.2980 chunk 108 optimal weight: 7.9990 chunk 45 optimal weight: 5.9990 chunk 110 optimal weight: 3.9990 chunk 13 optimal weight: 0.6980 chunk 19 optimal weight: 7.9990 chunk 94 optimal weight: 2.9990 chunk 6 optimal weight: 7.9990 overall best weight: 1.6042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 219 HIS ** B 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 324 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.105000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.086548 restraints weight = 5779.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.090086 restraints weight = 3583.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.092788 restraints weight = 2414.716| |-----------------------------------------------------------------------------| r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.6806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 10672 Z= 0.233 Angle : 0.694 8.661 14464 Z= 0.355 Chirality : 0.044 0.193 1644 Planarity : 0.004 0.028 1880 Dihedral : 4.496 17.555 1472 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 19.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.33 (0.23), residues: 1364 helix: 1.12 (0.19), residues: 688 sheet: -0.82 (0.31), residues: 228 loop : -0.47 (0.31), residues: 448 =============================================================================== Job complete usr+sys time: 1711.80 seconds wall clock time: 32 minutes 17.92 seconds (1937.92 seconds total)