Starting phenix.real_space_refine on Fri Mar 15 03:33:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k9l_22754/03_2024/7k9l_22754.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k9l_22754/03_2024/7k9l_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_22754/03_2024/7k9l_22754.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k9l_22754/03_2024/7k9l_22754.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k9l_22754/03_2024/7k9l_22754.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k9l_22754/03_2024/7k9l_22754.pdb" } resolution = 4.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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-dev-5265/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: 5.76, per 1000 atoms: 0.55 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: 3.98 Conformation dependent library (CDL) restraints added in 1.8 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: 0.87 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: 2.74 Time building geometry restraints manager: 4.36 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: 2.010 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: 0.000 Extract box with map and model: 6.120 Check model and map are aligned: 0.170 Set scattering table: 0.100 Process input model: 28.810 Find NCS groups from input model: 0.570 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:2.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.260 ------------------------------------------------------------------------------- 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 % Allowed : 10.79 % Favored : 85.25 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP A 295 HIS 0.007 0.002 HIS B 219 PHE 0.013 0.003 PHE C 93 TYR 0.021 0.004 TYR B 58 ARG 0.009 0.001 ARG D 42 *********************** 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 : 0.301 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 LYS cc_start: 0.8999 (mttt) cc_final: 0.8664 (mmtp) REVERT: A 21 ARG cc_start: 0.8944 (mtm-85) cc_final: 0.8633 (mtp85) REVERT: A 61 LEU cc_start: 0.8986 (mt) cc_final: 0.8585 (mt) REVERT: A 81 GLU cc_start: 0.9243 (OUTLIER) cc_final: 0.8786 (pp20) REVERT: A 89 ASP cc_start: 0.6687 (OUTLIER) cc_final: 0.6445 (p0) REVERT: A 104 VAL cc_start: 0.8846 (t) cc_final: 0.8534 (t) REVERT: A 113 VAL cc_start: 0.9303 (t) cc_final: 0.8977 (t) REVERT: A 115 LEU cc_start: 0.9133 (mt) cc_final: 0.8883 (mm) REVERT: A 122 THR cc_start: 0.8325 (t) cc_final: 0.7883 (t) REVERT: A 144 PHE cc_start: 0.8375 (p90) cc_final: 0.8166 (p90) REVERT: A 149 CYS cc_start: 0.8233 (p) cc_final: 0.7731 (t) REVERT: A 152 LYS cc_start: 0.8278 (pttp) cc_final: 0.7948 (pttp) REVERT: A 178 GLN cc_start: 0.9144 (mt0) cc_final: 0.8876 (mt0) REVERT: A 191 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8884 (tp) REVERT: A 199 LYS cc_start: 0.9384 (mtmm) cc_final: 0.8929 (mmmt) REVERT: A 203 TYR cc_start: 0.8758 (t80) cc_final: 0.8533 (t80) REVERT: A 242 LYS cc_start: 0.8842 (mmtt) cc_final: 0.8628 (tttm) REVERT: A 247 GLU cc_start: 0.9286 (mt-10) cc_final: 0.8740 (mt-10) REVERT: A 254 THR cc_start: 0.8950 (p) cc_final: 0.8730 (t) REVERT: A 282 ASN cc_start: 0.9117 (m-40) cc_final: 0.8915 (m-40) REVERT: A 284 ASN cc_start: 0.8287 (t0) cc_final: 0.7532 (t0) REVERT: A 291 LEU cc_start: 0.8450 (mt) cc_final: 0.8099 (tp) REVERT: A 292 LEU cc_start: 0.8655 (mm) cc_final: 0.8436 (mm) REVERT: A 305 LEU cc_start: 0.9363 (tp) cc_final: 0.9052 (tp) REVERT: A 310 LEU cc_start: 0.9112 (tp) cc_final: 0.8849 (mt) REVERT: A 313 TRP cc_start: 0.7413 (t60) cc_final: 0.6422 (t60) outliers start: 11 outliers final: 3 residues processed: 158 average time/residue: 0.1718 time to fit residues: 30.9506 Evaluate side-chains 116 residues out of total 278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 110 time to evaluate : 0.296 ------------------------------------------------------------------------------- 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: 0.0770 chunk 103 optimal weight: 5.9990 chunk 57 optimal weight: 9.9990 chunk 35 optimal weight: 6.9990 chunk 69 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 chunk 106 optimal weight: 9.9990 chunk 41 optimal weight: 10.0000 chunk 64 optimal weight: 6.9990 chunk 79 optimal weight: 0.0170 chunk 123 optimal weight: 3.9990 overall best weight: 2.8182 ------------------------------------------------------------------------------- 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 237 HIS D 245 HIS D 284 ASN ** D 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 324 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.3458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 10672 Z= 0.289 Angle : 0.691 7.159 14464 Z= 0.364 Chirality : 0.044 0.159 1644 Planarity : 0.010 0.164 1880 Dihedral : 5.619 26.133 1472 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 20.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % 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: -0.06 (0.21), residues: 1364 helix: 0.82 (0.18), residues: 688 sheet: -1.50 (0.35), residues: 200 loop : -0.47 (0.27), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 295 HIS 0.008 0.002 HIS D 219 PHE 0.021 0.002 PHE D 93 TYR 0.011 0.001 TYR A 327 ARG 0.006 0.001 ARG C 42 *********************** 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 136 residues out of total 278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 0.306 Fit side-chains revert: symmetry clash REVERT: D 10 GLU cc_start: 0.9273 (pm20) cc_final: 0.8534 (mp0) REVERT: D 14 GLU cc_start: 0.8923 (mp0) cc_final: 0.8647 (mm-30) REVERT: D 79 PHE cc_start: 0.7871 (t80) cc_final: 0.7528 (t80) REVERT: D 104 VAL cc_start: 0.8756 (t) cc_final: 0.8397 (t) REVERT: D 138 LYS cc_start: 0.8380 (tptt) cc_final: 0.7894 (ttmt) REVERT: D 178 GLN cc_start: 0.9147 (mt0) cc_final: 0.8920 (mt0) REVERT: D 248 ILE cc_start: 0.9388 (mt) cc_final: 0.9160 (tt) REVERT: D 284 ASN cc_start: 0.8354 (t0) cc_final: 0.7673 (t0) REVERT: D 305 LEU cc_start: 0.9458 (tp) cc_final: 0.9107 (tp) REVERT: D 313 TRP cc_start: 0.7470 (t60) cc_final: 0.6266 (t60) REVERT: D 325 GLU cc_start: 0.9028 (tp30) cc_final: 0.8824 (tp30) REVERT: D 326 GLU cc_start: 0.9130 (mm-30) cc_final: 0.8782 (mm-30) REVERT: D 329 LYS cc_start: 0.8798 (mttp) cc_final: 0.8381 (mttm) REVERT: D 332 LEU cc_start: 0.8402 (tp) cc_final: 0.8195 (pp) outliers start: 0 outliers final: 0 residues processed: 136 average time/residue: 0.1511 time to fit residues: 23.9388 Evaluate side-chains 85 residues out of total 278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 0.317 ------------------------------------------------------------------------------- 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: 9.9990 chunk 38 optimal weight: 10.0000 chunk 102 optimal weight: 8.9990 chunk 84 optimal weight: 4.9990 chunk 34 optimal weight: 8.9990 chunk 123 optimal weight: 4.9990 chunk 133 optimal weight: 7.9990 chunk 110 optimal weight: 0.5980 chunk 122 optimal weight: 0.9990 chunk 42 optimal weight: 0.0050 chunk 99 optimal weight: 0.1980 overall best weight: 1.3598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN B 60 GLN B 245 HIS B 282 ASN ** B 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 334 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.4289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10672 Z= 0.207 Angle : 0.623 8.041 14464 Z= 0.314 Chirality : 0.042 0.128 1644 Planarity : 0.005 0.049 1880 Dihedral : 4.863 18.283 1472 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 18.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.36 % Allowed : 3.24 % Favored : 96.40 % 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: 0.53 (0.22), residues: 1364 helix: 1.21 (0.19), residues: 692 sheet: -1.02 (0.36), residues: 200 loop : -0.13 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 295 HIS 0.006 0.001 HIS B 219 PHE 0.009 0.001 PHE C 144 TYR 0.014 0.001 TYR D 213 ARG 0.006 0.001 ARG D 42 *********************** 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 128 residues out of total 278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 127 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 12 LYS cc_start: 0.8927 (mttt) cc_final: 0.8571 (mmmm) REVERT: B 30 LEU cc_start: 0.8056 (tt) cc_final: 0.7849 (tp) REVERT: B 138 LYS cc_start: 0.8345 (tptt) cc_final: 0.7778 (ttmt) REVERT: B 178 GLN cc_start: 0.9014 (mt0) cc_final: 0.8724 (mt0) REVERT: B 191 LEU cc_start: 0.9455 (tp) cc_final: 0.9175 (tp) REVERT: B 247 GLU cc_start: 0.9213 (mt-10) cc_final: 0.8706 (mt-10) REVERT: B 254 THR cc_start: 0.9024 (p) cc_final: 0.8810 (t) REVERT: B 276 GLU cc_start: 0.8013 (pm20) cc_final: 0.7546 (pm20) REVERT: B 282 ASN cc_start: 0.9146 (m110) cc_final: 0.8931 (m110) REVERT: B 284 ASN cc_start: 0.8178 (t0) cc_final: 0.7436 (m-40) REVERT: B 305 LEU cc_start: 0.9475 (tp) cc_final: 0.8910 (tp) REVERT: B 311 LYS cc_start: 0.8892 (ttpt) cc_final: 0.8645 (pttm) REVERT: B 332 LEU cc_start: 0.8392 (tp) cc_final: 0.8142 (pp) outliers start: 1 outliers final: 1 residues processed: 128 average time/residue: 0.1553 time to fit residues: 23.0783 Evaluate side-chains 95 residues out of total 278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 94 time to evaluate : 0.311 ------------------------------------------------------------------------------- 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: 3.9990 chunk 93 optimal weight: 4.9990 chunk 64 optimal weight: 5.9990 chunk 13 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 83 optimal weight: 20.0000 chunk 124 optimal weight: 0.8980 chunk 131 optimal weight: 0.8980 chunk 117 optimal weight: 20.0000 chunk 35 optimal weight: 6.9990 chunk 109 optimal weight: 7.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.4882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 10672 Z= 0.277 Angle : 0.656 7.833 14464 Z= 0.337 Chirality : 0.042 0.170 1644 Planarity : 0.005 0.054 1880 Dihedral : 4.924 17.556 1472 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 22.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % 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: 0.40 (0.22), residues: 1364 helix: 1.18 (0.19), residues: 688 sheet: -1.03 (0.35), residues: 224 loop : -0.29 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP D 295 HIS 0.005 0.001 HIS A 196 PHE 0.010 0.002 PHE B 93 TYR 0.022 0.002 TYR A 137 ARG 0.005 0.001 ARG D 42 *********************** 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 119 residues out of total 278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 12 LYS cc_start: 0.9050 (mttt) cc_final: 0.8693 (mmmm) REVERT: B 14 GLU cc_start: 0.8857 (mp0) cc_final: 0.8593 (mm-30) REVERT: B 138 LYS cc_start: 0.8382 (tptt) cc_final: 0.7989 (tttt) REVERT: B 144 PHE cc_start: 0.8454 (p90) cc_final: 0.8193 (p90) REVERT: B 178 GLN cc_start: 0.8998 (mt0) cc_final: 0.8782 (mt0) REVERT: B 247 GLU cc_start: 0.9196 (mt-10) cc_final: 0.8670 (mt-10) REVERT: B 276 GLU cc_start: 0.8123 (pm20) cc_final: 0.7626 (pm20) REVERT: B 282 ASN cc_start: 0.9127 (m110) cc_final: 0.8786 (m110) REVERT: B 283 LEU cc_start: 0.9224 (tp) cc_final: 0.8918 (tp) REVERT: B 284 ASN cc_start: 0.8076 (t0) cc_final: 0.7813 (m110) REVERT: B 332 LEU cc_start: 0.8320 (tp) cc_final: 0.8116 (tp) outliers start: 0 outliers final: 0 residues processed: 119 average time/residue: 0.1485 time to fit residues: 20.6890 Evaluate side-chains 87 residues out of total 278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 0.293 ------------------------------------------------------------------------------- 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: 4.9990 chunk 97 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 112 optimal weight: 0.0030 chunk 90 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 67 optimal weight: 5.9990 chunk 117 optimal weight: 20.0000 chunk 33 optimal weight: 6.9990 chunk 44 optimal weight: 0.0040 overall best weight: 0.9806 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN B 156 HIS ** B 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 306 GLN B 334 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.5209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 10672 Z= 0.179 Angle : 0.605 7.323 14464 Z= 0.301 Chirality : 0.041 0.126 1644 Planarity : 0.005 0.054 1880 Dihedral : 4.642 16.770 1472 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 15.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 0.36 % Allowed : 2.88 % Favored : 96.76 % 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: 0.77 (0.23), residues: 1364 helix: 1.42 (0.19), residues: 696 sheet: -0.92 (0.34), residues: 216 loop : -0.00 (0.32), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP B 295 HIS 0.007 0.001 HIS B 156 PHE 0.009 0.001 PHE C 144 TYR 0.041 0.002 TYR D 137 ARG 0.007 0.001 ARG C 42 *********************** 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 120 residues out of total 278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 119 time to evaluate : 0.278 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 12 LYS cc_start: 0.9000 (mttt) cc_final: 0.8601 (mmtp) REVERT: B 14 GLU cc_start: 0.9007 (mm-30) cc_final: 0.8668 (mm-30) REVERT: B 61 LEU cc_start: 0.8890 (mt) cc_final: 0.8506 (mt) REVERT: B 72 CYS cc_start: 0.9009 (m) cc_final: 0.8766 (m) REVERT: B 73 ILE cc_start: 0.9217 (mm) cc_final: 0.8882 (tp) REVERT: B 115 LEU cc_start: 0.8036 (mm) cc_final: 0.7707 (mm) REVERT: B 138 LYS cc_start: 0.8258 (tptt) cc_final: 0.7755 (ttmt) REVERT: B 140 ASP cc_start: 0.8488 (m-30) cc_final: 0.8211 (m-30) REVERT: B 195 ASP cc_start: 0.8753 (p0) cc_final: 0.8062 (t0) REVERT: B 276 GLU cc_start: 0.8079 (pm20) cc_final: 0.7548 (pm20) REVERT: B 282 ASN cc_start: 0.9162 (m110) cc_final: 0.8821 (m110) REVERT: B 283 LEU cc_start: 0.9234 (tp) cc_final: 0.8954 (tp) REVERT: B 284 ASN cc_start: 0.8216 (t0) cc_final: 0.7922 (m110) REVERT: B 313 TRP cc_start: 0.7908 (t60) cc_final: 0.6851 (t60) REVERT: B 332 LEU cc_start: 0.8322 (tp) cc_final: 0.8048 (pp) outliers start: 1 outliers final: 0 residues processed: 120 average time/residue: 0.1525 time to fit residues: 21.3982 Evaluate side-chains 97 residues out of total 278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 97 time to evaluate : 0.269 ------------------------------------------------------------------------------- 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: 6.9990 chunk 25 optimal weight: 0.8980 chunk 77 optimal weight: 7.9990 chunk 32 optimal weight: 6.9990 chunk 131 optimal weight: 6.9990 chunk 109 optimal weight: 0.7980 chunk 60 optimal weight: 0.2980 chunk 10 optimal weight: 0.4980 chunk 43 optimal weight: 6.9990 chunk 69 optimal weight: 7.9990 chunk 126 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 60 GLN ** B 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.5398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 10672 Z= 0.160 Angle : 0.600 8.100 14464 Z= 0.295 Chirality : 0.042 0.167 1644 Planarity : 0.005 0.056 1880 Dihedral : 4.405 16.481 1472 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 15.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.36 % Allowed : 1.80 % Favored : 97.84 % 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: 0.76 (0.23), residues: 1364 helix: 1.58 (0.19), residues: 700 sheet: -0.94 (0.30), residues: 272 loop : -0.18 (0.34), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP C 295 HIS 0.003 0.001 HIS B 219 PHE 0.010 0.002 PHE B 144 TYR 0.020 0.002 TYR C 137 ARG 0.007 0.001 ARG C 42 *********************** 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 121 residues out of total 278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 120 time to evaluate : 0.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 12 LYS cc_start: 0.8964 (mttt) cc_final: 0.8585 (mmtp) REVERT: B 14 GLU cc_start: 0.9067 (mm-30) cc_final: 0.8725 (mm-30) REVERT: B 61 LEU cc_start: 0.8909 (mt) cc_final: 0.8479 (mt) REVERT: B 72 CYS cc_start: 0.9064 (m) cc_final: 0.8823 (m) REVERT: B 73 ILE cc_start: 0.9182 (mm) cc_final: 0.8920 (tp) REVERT: B 115 LEU cc_start: 0.8105 (mm) cc_final: 0.7809 (mm) REVERT: B 138 LYS cc_start: 0.8341 (tptt) cc_final: 0.7788 (ttmt) REVERT: B 140 ASP cc_start: 0.8415 (m-30) cc_final: 0.8165 (m-30) REVERT: B 250 MET cc_start: 0.8774 (tmm) cc_final: 0.8447 (tpp) REVERT: B 276 GLU cc_start: 0.8073 (pm20) cc_final: 0.7590 (pm20) REVERT: B 282 ASN cc_start: 0.9128 (m110) cc_final: 0.8808 (m110) REVERT: B 283 LEU cc_start: 0.9192 (tp) cc_final: 0.8912 (tp) REVERT: B 284 ASN cc_start: 0.8303 (t0) cc_final: 0.7965 (m110) REVERT: B 305 LEU cc_start: 0.9425 (tp) cc_final: 0.9050 (tp) REVERT: B 313 TRP cc_start: 0.7800 (t60) cc_final: 0.6767 (t60) REVERT: B 332 LEU cc_start: 0.8313 (tp) cc_final: 0.8055 (pp) outliers start: 1 outliers final: 0 residues processed: 121 average time/residue: 0.1447 time to fit residues: 20.6497 Evaluate side-chains 96 residues out of total 278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 0.315 ------------------------------------------------------------------------------- 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: 5.9990 chunk 74 optimal weight: 0.0470 chunk 96 optimal weight: 2.9990 chunk 110 optimal weight: 4.9990 chunk 73 optimal weight: 3.9990 chunk 131 optimal weight: 0.0060 chunk 82 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 81 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 overall best weight: 1.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN B 54 ASN B 60 GLN ** B 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 334 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.5526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10672 Z= 0.195 Angle : 0.588 7.928 14464 Z= 0.296 Chirality : 0.041 0.130 1644 Planarity : 0.005 0.060 1880 Dihedral : 4.436 15.943 1472 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 16.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 0.36 % Allowed : 1.44 % Favored : 98.20 % 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: 0.83 (0.23), residues: 1364 helix: 1.61 (0.20), residues: 696 sheet: -1.07 (0.29), residues: 268 loop : 0.03 (0.35), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP D 295 HIS 0.006 0.001 HIS B 219 PHE 0.009 0.002 PHE B 144 TYR 0.019 0.002 TYR C 137 ARG 0.008 0.001 ARG C 42 *********************** 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 118 residues out of total 278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 117 time to evaluate : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 12 LYS cc_start: 0.9016 (mttt) cc_final: 0.8632 (mmmm) REVERT: B 14 GLU cc_start: 0.9088 (mm-30) cc_final: 0.8734 (mm-30) REVERT: B 61 LEU cc_start: 0.8816 (mt) cc_final: 0.8523 (mt) REVERT: B 115 LEU cc_start: 0.8215 (mm) cc_final: 0.7886 (mm) REVERT: B 138 LYS cc_start: 0.8366 (tptt) cc_final: 0.7889 (ttmt) REVERT: B 140 ASP cc_start: 0.8429 (m-30) cc_final: 0.8163 (m-30) REVERT: B 144 PHE cc_start: 0.8558 (p90) cc_final: 0.8355 (p90) REVERT: B 165 GLU cc_start: 0.8509 (tm-30) cc_final: 0.8254 (tm-30) REVERT: B 178 GLN cc_start: 0.8949 (mt0) cc_final: 0.8702 (mt0) REVERT: B 250 MET cc_start: 0.8736 (tmm) cc_final: 0.8425 (tpp) REVERT: B 276 GLU cc_start: 0.8095 (pm20) cc_final: 0.7556 (pm20) REVERT: B 282 ASN cc_start: 0.9072 (m110) cc_final: 0.8759 (m110) REVERT: B 283 LEU cc_start: 0.9112 (tp) cc_final: 0.8870 (tp) REVERT: B 284 ASN cc_start: 0.8350 (t0) cc_final: 0.8008 (m110) REVERT: B 305 LEU cc_start: 0.9491 (tp) cc_final: 0.9112 (tp) REVERT: B 313 TRP cc_start: 0.7680 (t60) cc_final: 0.7174 (t60) REVERT: B 332 LEU cc_start: 0.8304 (tp) cc_final: 0.8076 (pp) REVERT: B 336 LEU cc_start: 0.8874 (mt) cc_final: 0.8664 (mt) outliers start: 1 outliers final: 0 residues processed: 117 average time/residue: 0.1548 time to fit residues: 21.2233 Evaluate side-chains 87 residues out of total 278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 0.305 ------------------------------------------------------------------------------- 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: 0.0770 chunk 39 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 83 optimal weight: 10.0000 chunk 89 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 103 optimal weight: 6.9990 chunk 119 optimal weight: 3.9990 chunk 125 optimal weight: 8.9990 chunk 114 optimal weight: 3.9990 overall best weight: 2.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 60 GLN ** B 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.5674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10672 Z= 0.251 Angle : 0.637 8.062 14464 Z= 0.326 Chirality : 0.043 0.195 1644 Planarity : 0.005 0.065 1880 Dihedral : 4.730 16.930 1472 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 20.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 0.36 % Allowed : 0.36 % Favored : 99.28 % 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: 0.55 (0.23), residues: 1364 helix: 1.50 (0.19), residues: 700 sheet: -0.98 (0.31), residues: 248 loop : -0.60 (0.33), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP D 295 HIS 0.007 0.001 HIS A 156 PHE 0.011 0.002 PHE B 93 TYR 0.020 0.002 TYR C 137 ARG 0.009 0.001 ARG C 42 *********************** 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: 1 poor density : 118 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 12 LYS cc_start: 0.8993 (mttt) cc_final: 0.8604 (mmmm) REVERT: B 14 GLU cc_start: 0.9109 (mm-30) cc_final: 0.8702 (mm-30) REVERT: B 72 CYS cc_start: 0.9226 (m) cc_final: 0.9021 (m) REVERT: B 115 LEU cc_start: 0.8189 (mm) cc_final: 0.7899 (mm) REVERT: B 138 LYS cc_start: 0.8433 (tptt) cc_final: 0.7863 (ttmt) REVERT: B 144 PHE cc_start: 0.8583 (p90) cc_final: 0.8342 (p90) REVERT: B 165 GLU cc_start: 0.8518 (tm-30) cc_final: 0.8266 (tm-30) REVERT: B 178 GLN cc_start: 0.8955 (mt0) cc_final: 0.8745 (mt0) REVERT: B 214 LYS cc_start: 0.9263 (tmtt) cc_final: 0.8734 (tppt) REVERT: B 276 GLU cc_start: 0.8072 (pm20) cc_final: 0.7557 (pm20) REVERT: B 282 ASN cc_start: 0.9029 (m110) cc_final: 0.8668 (m110) REVERT: B 283 LEU cc_start: 0.9112 (tp) cc_final: 0.8803 (tp) REVERT: B 284 ASN cc_start: 0.8353 (t0) cc_final: 0.7977 (m110) REVERT: B 305 LEU cc_start: 0.9487 (tp) cc_final: 0.9063 (tp) REVERT: B 332 LEU cc_start: 0.8273 (tp) cc_final: 0.8043 (tp) outliers start: 1 outliers final: 1 residues processed: 118 average time/residue: 0.1468 time to fit residues: 20.3426 Evaluate side-chains 88 residues out of total 278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 87 time to evaluate : 0.345 ------------------------------------------------------------------------------- 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: 0.9980 chunk 125 optimal weight: 5.9990 chunk 73 optimal weight: 4.9990 chunk 53 optimal weight: 5.9990 chunk 95 optimal weight: 3.9990 chunk 37 optimal weight: 8.9990 chunk 110 optimal weight: 0.7980 chunk 115 optimal weight: 0.8980 chunk 121 optimal weight: 4.9990 chunk 80 optimal weight: 0.0070 chunk 129 optimal weight: 3.9990 overall best weight: 1.3400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN ** B 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 334 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.5909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10672 Z= 0.201 Angle : 0.627 8.279 14464 Z= 0.310 Chirality : 0.041 0.130 1644 Planarity : 0.005 0.065 1880 Dihedral : 4.464 16.023 1472 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 18.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % 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: 1.51 (0.20), residues: 700 sheet: -1.20 (0.33), residues: 196 loop : -0.51 (0.30), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP C 295 HIS 0.003 0.001 HIS C 219 PHE 0.022 0.002 PHE B 299 TYR 0.017 0.001 TYR A 137 ARG 0.009 0.001 ARG D 42 *********************** 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 117 residues out of total 278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 12 LYS cc_start: 0.8979 (mttt) cc_final: 0.8592 (mmmm) REVERT: B 14 GLU cc_start: 0.9075 (mm-30) cc_final: 0.8672 (mm-30) REVERT: B 61 LEU cc_start: 0.8791 (mt) cc_final: 0.8488 (mt) REVERT: B 115 LEU cc_start: 0.7944 (mm) cc_final: 0.7640 (mp) REVERT: B 144 PHE cc_start: 0.8541 (p90) cc_final: 0.8254 (p90) REVERT: B 165 GLU cc_start: 0.8481 (tm-30) cc_final: 0.8262 (tm-30) REVERT: B 178 GLN cc_start: 0.8922 (mt0) cc_final: 0.8713 (mt0) REVERT: B 229 LYS cc_start: 0.7967 (tttp) cc_final: 0.7231 (tptm) REVERT: B 276 GLU cc_start: 0.7973 (pm20) cc_final: 0.7480 (pm20) REVERT: B 282 ASN cc_start: 0.9057 (m110) cc_final: 0.8697 (m110) REVERT: B 283 LEU cc_start: 0.9132 (tp) cc_final: 0.8902 (tp) REVERT: B 284 ASN cc_start: 0.8495 (t0) cc_final: 0.8115 (m110) REVERT: B 305 LEU cc_start: 0.9427 (tp) cc_final: 0.9048 (tp) REVERT: B 313 TRP cc_start: 0.7794 (t60) cc_final: 0.6955 (t60) REVERT: B 332 LEU cc_start: 0.8293 (tp) cc_final: 0.8044 (pp) REVERT: B 336 LEU cc_start: 0.8921 (mt) cc_final: 0.8712 (mt) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.1392 time to fit residues: 19.2609 Evaluate side-chains 95 residues out of total 278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 0.230 ------------------------------------------------------------------------------- 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: 0.0770 chunk 61 optimal weight: 0.6980 chunk 89 optimal weight: 4.9990 chunk 135 optimal weight: 6.9990 chunk 124 optimal weight: 0.5980 chunk 107 optimal weight: 4.9990 chunk 11 optimal weight: 0.8980 chunk 83 optimal weight: 20.0000 chunk 66 optimal weight: 3.9990 chunk 85 optimal weight: 0.6980 chunk 114 optimal weight: 3.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.6021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 10672 Z= 0.170 Angle : 0.593 8.004 14464 Z= 0.293 Chirality : 0.042 0.197 1644 Planarity : 0.005 0.065 1880 Dihedral : 4.315 14.930 1472 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 14.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 0.86 (0.24), residues: 1364 helix: 1.78 (0.20), residues: 696 sheet: -0.96 (0.31), residues: 220 loop : -0.44 (0.32), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP C 295 HIS 0.004 0.001 HIS D 219 PHE 0.023 0.003 PHE A 299 TYR 0.017 0.001 TYR C 137 ARG 0.009 0.001 ARG A 42 ********************** 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 117 residues out of total 278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 0.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 12 LYS cc_start: 0.8948 (mttt) cc_final: 0.8553 (mmmm) REVERT: B 14 GLU cc_start: 0.9085 (mm-30) cc_final: 0.8687 (mm-30) REVERT: B 61 LEU cc_start: 0.8771 (mt) cc_final: 0.8404 (mt) REVERT: B 115 LEU cc_start: 0.7917 (mm) cc_final: 0.7642 (mp) REVERT: B 144 PHE cc_start: 0.8473 (p90) cc_final: 0.8132 (p90) REVERT: B 165 GLU cc_start: 0.8509 (tm-30) cc_final: 0.8252 (tm-30) REVERT: B 178 GLN cc_start: 0.8890 (mt0) cc_final: 0.8653 (mt0) REVERT: B 229 LYS cc_start: 0.7907 (tttp) cc_final: 0.7173 (tptm) REVERT: B 276 GLU cc_start: 0.7932 (pm20) cc_final: 0.7299 (pm20) REVERT: B 277 GLU cc_start: 0.9146 (mm-30) cc_final: 0.8726 (mm-30) REVERT: B 282 ASN cc_start: 0.9035 (m110) cc_final: 0.8638 (m110) REVERT: B 283 LEU cc_start: 0.9147 (tp) cc_final: 0.8903 (tp) REVERT: B 284 ASN cc_start: 0.8670 (t0) cc_final: 0.8270 (m110) REVERT: B 305 LEU cc_start: 0.9314 (tp) cc_final: 0.8882 (tp) REVERT: B 313 TRP cc_start: 0.7798 (t60) cc_final: 0.6904 (t60) REVERT: B 332 LEU cc_start: 0.8301 (tp) cc_final: 0.8035 (pp) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.1539 time to fit residues: 21.2429 Evaluate side-chains 85 residues out of total 278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 0.303 ------------------------------------------------------------------------------- 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: 0.0010 chunk 15 optimal weight: 20.0000 chunk 29 optimal weight: 0.8980 chunk 108 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 chunk 110 optimal weight: 0.0040 chunk 13 optimal weight: 0.8980 chunk 19 optimal weight: 0.0770 chunk 94 optimal weight: 5.9990 chunk 6 optimal weight: 3.9990 overall best weight: 0.3756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 54 ASN ** B 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.106160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.083924 restraints weight = 5615.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.087477 restraints weight = 3650.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.090250 restraints weight = 2578.539| |-----------------------------------------------------------------------------| r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.6158 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= 0.176 Angle : 0.623 8.206 14464 Z= 0.300 Chirality : 0.041 0.137 1644 Planarity : 0.005 0.065 1880 Dihedral : 4.226 14.727 1472 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 0.88 (0.24), residues: 1364 helix: 1.83 (0.20), residues: 700 sheet: -0.90 (0.31), residues: 220 loop : -0.55 (0.32), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP D 295 HIS 0.009 0.001 HIS A 219 PHE 0.026 0.004 PHE D 299 TYR 0.016 0.001 TYR A 137 ARG 0.002 0.000 ARG D 257 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1744.12 seconds wall clock time: 32 minutes 40.03 seconds (1960.03 seconds total)