Starting phenix.real_space_refine on Fri Mar 15 03:28:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ehg_28147/03_2024/8ehg_28147.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ehg_28147/03_2024/8ehg_28147.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ehg_28147/03_2024/8ehg_28147.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ehg_28147/03_2024/8ehg_28147.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ehg_28147/03_2024/8ehg_28147.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ehg_28147/03_2024/8ehg_28147.pdb" } resolution = 2.24 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= 0.001 sd= 0.112 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 "A GLU 10": "OE1" <-> "OE2" Residue "A GLU 14": "OE1" <-> "OE2" Residue "A ASP 67": "OD1" <-> "OD2" Residue "A ASP 140": "OD1" <-> "OD2" Residue "A ASP 143": "OD1" <-> "OD2" Residue "A PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 195": "OD1" <-> "OD2" Residue "A ASP 218": "OD1" <-> "OD2" Residue "A GLU 278": "OE1" <-> "OE2" Residue "A GLU 318": "OE1" <-> "OE2" Residue "B GLU 10": "OE1" <-> "OE2" Residue "B GLU 14": "OE1" <-> "OE2" Residue "B ASP 67": "OD1" <-> "OD2" Residue "B ASP 140": "OD1" <-> "OD2" Residue "B ASP 143": "OD1" <-> "OD2" Residue "B PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 195": "OD1" <-> "OD2" Residue "B ASP 218": "OD1" <-> "OD2" Residue "B GLU 278": "OE1" <-> "OE2" Residue "B GLU 318": "OE1" <-> "OE2" Residue "C GLU 10": "OE1" <-> "OE2" Residue "C GLU 14": "OE1" <-> "OE2" Residue "C ASP 67": "OD1" <-> "OD2" Residue "C ASP 140": "OD1" <-> "OD2" Residue "C ASP 143": "OD1" <-> "OD2" Residue "C PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 195": "OD1" <-> "OD2" Residue "C ASP 218": "OD1" <-> "OD2" Residue "C GLU 278": "OE1" <-> "OE2" Residue "C GLU 318": "OE1" <-> "OE2" Residue "D GLU 10": "OE1" <-> "OE2" Residue "D GLU 14": "OE1" <-> "OE2" Residue "D ASP 67": "OD1" <-> "OD2" Residue "D ASP 140": "OD1" <-> "OD2" Residue "D ASP 143": "OD1" <-> "OD2" Residue "D PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 195": "OD1" <-> "OD2" Residue "D ASP 218": "OD1" <-> "OD2" Residue "D GLU 278": "OE1" <-> "OE2" Residue "D GLU 318": "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: "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: "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: "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: 6.30, per 1000 atoms: 0.60 Number of scatterers: 10472 At special positions: 0 Unit cell: (103.627, 94.043, 79.667, 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: 4.22 Conformation dependent library (CDL) restraints added in 2.0 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 54.8% alpha, 13.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.15 Creating SS restraints... Processing helix chain 'A' and resid 8 through 23 Processing helix chain 'A' and resid 35 through 45 removed outlier: 4.326A pdb=" N LYS A 41 " --> pdb=" O GLY A 37 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ARG A 42 " --> pdb=" O SER A 38 " (cutoff:3.500A) 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: 3.864A pdb=" N TYR A 84 " --> pdb=" O HIS A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 100 Processing helix chain 'A' and resid 129 through 140 Processing helix chain 'A' and resid 159 through 180 Processing helix chain 'A' and resid 197 through 219 Processing helix chain 'A' and resid 222 through 226 Processing helix chain 'A' and resid 244 through 258 Processing helix chain 'A' and resid 275 through 288 Processing helix chain 'A' and resid 302 through 314 removed outlier: 6.625A pdb=" N SER A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N ALA A 309 " --> pdb=" O LEU A 305 " (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 338 removed outlier: 3.606A pdb=" N ARG A 330 " --> pdb=" O GLU A 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 23 Processing helix chain 'B' and resid 35 through 45 removed outlier: 4.326A pdb=" N LYS B 41 " --> pdb=" O GLY B 37 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ARG B 42 " --> pdb=" O SER B 38 " (cutoff:3.500A) 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: 3.864A pdb=" N TYR B 84 " --> pdb=" O HIS B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 100 Processing helix chain 'B' and resid 129 through 140 Processing helix chain 'B' and resid 159 through 180 Processing helix chain 'B' and resid 197 through 219 Processing helix chain 'B' and resid 222 through 226 Processing helix chain 'B' and resid 244 through 258 Processing helix chain 'B' and resid 275 through 288 Processing helix chain 'B' and resid 302 through 314 removed outlier: 6.625A pdb=" N SER B 308 " --> pdb=" O ALA B 304 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N ALA B 309 " --> pdb=" O LEU B 305 " (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 338 removed outlier: 3.606A pdb=" N ARG B 330 " --> pdb=" O GLU B 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 23 Processing helix chain 'C' and resid 35 through 45 removed outlier: 4.326A pdb=" N LYS C 41 " --> pdb=" O GLY C 37 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ARG C 42 " --> pdb=" O SER C 38 " (cutoff:3.500A) 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: 3.864A pdb=" N TYR C 84 " --> pdb=" O HIS C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 100 Processing helix chain 'C' and resid 129 through 140 Processing helix chain 'C' and resid 159 through 180 Processing helix chain 'C' and resid 197 through 219 Processing helix chain 'C' and resid 222 through 226 Processing helix chain 'C' and resid 244 through 258 Processing helix chain 'C' and resid 275 through 288 Processing helix chain 'C' and resid 302 through 314 removed outlier: 6.625A pdb=" N SER C 308 " --> pdb=" O ALA C 304 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N ALA C 309 " --> pdb=" O LEU C 305 " (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 338 removed outlier: 3.606A pdb=" N ARG C 330 " --> pdb=" O GLU C 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 23 Processing helix chain 'D' and resid 35 through 45 removed outlier: 4.326A pdb=" N LYS D 41 " --> pdb=" O GLY D 37 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ARG D 42 " --> pdb=" O SER D 38 " (cutoff:3.500A) 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: 3.864A pdb=" N TYR D 84 " --> pdb=" O HIS D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 100 Processing helix chain 'D' and resid 129 through 140 Processing helix chain 'D' and resid 159 through 180 Processing helix chain 'D' and resid 197 through 219 Processing helix chain 'D' and resid 222 through 226 Processing helix chain 'D' and resid 244 through 258 Processing helix chain 'D' and resid 275 through 288 Processing helix chain 'D' and resid 302 through 314 removed outlier: 6.625A pdb=" N SER D 308 " --> pdb=" O ALA D 304 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N ALA D 309 " --> pdb=" O LEU D 305 " (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 338 removed outlier: 3.606A pdb=" N ARG D 330 " --> pdb=" O GLU D 326 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 32 removed outlier: 6.756A pdb=" N GLY A 28 " --> pdb=" O GLY A 74 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N VAL A 76 " --> pdb=" O GLY A 28 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N LEU A 30 " --> pdb=" O VAL A 76 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N LEU A 78 " --> pdb=" O LEU A 30 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N ALA A 32 " --> pdb=" O LEU A 78 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N GLY A 74 " --> pdb=" O VAL A 103 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N GLY A 105 " --> pdb=" O GLY A 74 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N VAL A 76 " --> pdb=" O GLY A 105 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N LYS A 107 " --> pdb=" O VAL A 76 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N LEU A 78 " --> pdb=" O LYS A 107 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N VAL A 104 " --> pdb=" O PHE A 144 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N LYS A 146 " --> pdb=" O VAL A 104 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ILE A 106 " --> pdb=" O LYS A 146 " (cutoff:3.500A) removed outlier: 8.646A pdb=" N ARG A 148 " --> pdb=" O ILE A 106 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ALA A 145 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N GLU A 187 " --> pdb=" O ALA A 145 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N TRP A 147 " --> pdb=" O GLU A 187 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N GLU A 189 " --> pdb=" O TRP A 147 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N CYS A 149 " --> pdb=" O GLU A 189 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N LEU A 191 " --> pdb=" O CYS A 149 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N LEU A 151 " --> pdb=" O LEU A 191 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N LEU A 228 " --> pdb=" O THR A 268 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 112 through 114 Processing sheet with id=AA3, first strand: chain 'B' and resid 28 through 32 removed outlier: 6.756A pdb=" N GLY B 28 " --> pdb=" O GLY B 74 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N VAL B 76 " --> pdb=" O GLY B 28 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N LEU B 30 " --> pdb=" O VAL B 76 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N LEU B 78 " --> pdb=" O LEU B 30 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N ALA B 32 " --> pdb=" O LEU B 78 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N GLY B 74 " --> pdb=" O VAL B 103 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N GLY B 105 " --> pdb=" O GLY B 74 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N VAL B 76 " --> pdb=" O GLY B 105 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N LYS B 107 " --> pdb=" O VAL B 76 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N LEU B 78 " --> pdb=" O LYS B 107 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N VAL B 104 " --> pdb=" O PHE B 144 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N LYS B 146 " --> pdb=" O VAL B 104 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ILE B 106 " --> pdb=" O LYS B 146 " (cutoff:3.500A) removed outlier: 8.646A pdb=" N ARG B 148 " --> pdb=" O ILE B 106 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ALA B 145 " --> pdb=" O ILE B 185 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N GLU B 187 " --> pdb=" O ALA B 145 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N TRP B 147 " --> pdb=" O GLU B 187 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N GLU B 189 " --> pdb=" O TRP B 147 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N CYS B 149 " --> pdb=" O GLU B 189 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N LEU B 191 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N LEU B 151 " --> pdb=" O LEU B 191 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N LEU B 228 " --> pdb=" O THR B 268 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 112 through 114 Processing sheet with id=AA5, first strand: chain 'C' and resid 28 through 32 removed outlier: 6.756A pdb=" N GLY C 28 " --> pdb=" O GLY C 74 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N VAL C 76 " --> pdb=" O GLY C 28 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N LEU C 30 " --> pdb=" O VAL C 76 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N LEU C 78 " --> pdb=" O LEU C 30 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N ALA C 32 " --> pdb=" O LEU C 78 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N GLY C 74 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N GLY C 105 " --> pdb=" O GLY C 74 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N VAL C 76 " --> pdb=" O GLY C 105 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N LYS C 107 " --> pdb=" O VAL C 76 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N LEU C 78 " --> pdb=" O LYS C 107 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N VAL C 104 " --> pdb=" O PHE C 144 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N LYS C 146 " --> pdb=" O VAL C 104 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ILE C 106 " --> pdb=" O LYS C 146 " (cutoff:3.500A) removed outlier: 8.646A pdb=" N ARG C 148 " --> pdb=" O ILE C 106 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ALA C 145 " --> pdb=" O ILE C 185 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N GLU C 187 " --> pdb=" O ALA C 145 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N TRP C 147 " --> pdb=" O GLU C 187 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N GLU C 189 " --> pdb=" O TRP C 147 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N CYS C 149 " --> pdb=" O GLU C 189 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N LEU C 191 " --> pdb=" O CYS C 149 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N LEU C 151 " --> pdb=" O LEU C 191 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N LEU C 228 " --> pdb=" O THR C 268 " (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: 6.756A pdb=" N GLY D 28 " --> pdb=" O GLY D 74 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N VAL D 76 " --> pdb=" O GLY D 28 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N LEU D 30 " --> pdb=" O VAL D 76 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N LEU D 78 " --> pdb=" O LEU D 30 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N ALA D 32 " --> pdb=" O LEU D 78 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N GLY D 74 " --> pdb=" O VAL D 103 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N GLY D 105 " --> pdb=" O GLY D 74 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N VAL D 76 " --> pdb=" O GLY D 105 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N LYS D 107 " --> pdb=" O VAL D 76 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N LEU D 78 " --> pdb=" O LYS D 107 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N VAL D 104 " --> pdb=" O PHE D 144 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N LYS D 146 " --> pdb=" O VAL D 104 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ILE D 106 " --> pdb=" O LYS D 146 " (cutoff:3.500A) removed outlier: 8.646A pdb=" N ARG D 148 " --> pdb=" O ILE D 106 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ALA D 145 " --> pdb=" O ILE D 185 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N GLU D 187 " --> pdb=" O ALA D 145 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N TRP D 147 " --> pdb=" O GLU D 187 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N GLU D 189 " --> pdb=" O TRP D 147 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N CYS D 149 " --> pdb=" O GLU D 189 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N LEU D 191 " --> pdb=" O CYS D 149 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N LEU D 151 " --> pdb=" O LEU D 191 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N LEU D 228 " --> pdb=" O THR D 268 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 112 through 114 544 hydrogen bonds defined for protein. 1572 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: 3.16 Time building geometry restraints manager: 4.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3520 1.34 - 1.46: 1956 1.46 - 1.58: 5140 1.58 - 1.69: 0 1.69 - 1.81: 56 Bond restraints: 10672 Sorted by residual: bond pdb=" C GLY C 302 " pdb=" O GLY C 302 " ideal model delta sigma weight residual 1.245 1.234 0.011 1.19e-02 7.06e+03 8.33e-01 bond pdb=" C GLY B 302 " pdb=" O GLY B 302 " ideal model delta sigma weight residual 1.245 1.234 0.011 1.19e-02 7.06e+03 8.33e-01 bond pdb=" C GLY D 302 " pdb=" O GLY D 302 " ideal model delta sigma weight residual 1.245 1.234 0.011 1.19e-02 7.06e+03 8.33e-01 bond pdb=" C GLY A 302 " pdb=" O GLY A 302 " ideal model delta sigma weight residual 1.245 1.234 0.011 1.19e-02 7.06e+03 8.33e-01 bond pdb=" C VAL C 23 " pdb=" O VAL C 23 " ideal model delta sigma weight residual 1.236 1.226 0.010 1.19e-02 7.06e+03 7.46e-01 ... (remaining 10667 not shown) Histogram of bond angle deviations from ideal: 101.06 - 107.64: 440 107.64 - 114.23: 6180 114.23 - 120.81: 4392 120.81 - 127.40: 3336 127.40 - 133.98: 116 Bond angle restraints: 14464 Sorted by residual: angle pdb=" O GLY C 302 " pdb=" C GLY C 302 " pdb=" N ARG C 303 " ideal model delta sigma weight residual 121.85 123.29 -1.44 5.60e-01 3.19e+00 6.65e+00 angle pdb=" O GLY D 302 " pdb=" C GLY D 302 " pdb=" N ARG D 303 " ideal model delta sigma weight residual 121.85 123.29 -1.44 5.60e-01 3.19e+00 6.65e+00 angle pdb=" O GLY A 302 " pdb=" C GLY A 302 " pdb=" N ARG A 303 " ideal model delta sigma weight residual 121.85 123.29 -1.44 5.60e-01 3.19e+00 6.65e+00 angle pdb=" O GLY B 302 " pdb=" C GLY B 302 " pdb=" N ARG B 303 " ideal model delta sigma weight residual 121.85 123.29 -1.44 5.60e-01 3.19e+00 6.65e+00 angle pdb=" CA TYR B 213 " pdb=" CB TYR B 213 " pdb=" CG TYR B 213 " ideal model delta sigma weight residual 113.90 110.16 3.74 1.80e+00 3.09e-01 4.33e+00 ... (remaining 14459 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.24: 5852 17.24 - 34.48: 412 34.48 - 51.72: 160 51.72 - 68.96: 60 68.96 - 86.20: 20 Dihedral angle restraints: 6504 sinusoidal: 2572 harmonic: 3932 Sorted by residual: dihedral pdb=" CA THR D 122 " pdb=" C THR D 122 " pdb=" N THR D 123 " pdb=" CA THR D 123 " ideal model delta harmonic sigma weight residual 180.00 161.53 18.47 0 5.00e+00 4.00e-02 1.36e+01 dihedral pdb=" CA THR A 122 " pdb=" C THR A 122 " pdb=" N THR A 123 " pdb=" CA THR A 123 " ideal model delta harmonic sigma weight residual 180.00 161.53 18.47 0 5.00e+00 4.00e-02 1.36e+01 dihedral pdb=" CA THR C 122 " pdb=" C THR C 122 " pdb=" N THR C 123 " pdb=" CA THR C 123 " ideal model delta harmonic sigma weight residual 180.00 161.53 18.47 0 5.00e+00 4.00e-02 1.36e+01 ... (remaining 6501 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1014 0.027 - 0.054: 358 0.054 - 0.081: 160 0.081 - 0.108: 96 0.108 - 0.136: 16 Chirality restraints: 1644 Sorted by residual: chirality pdb=" CA VAL C 186 " pdb=" N VAL C 186 " pdb=" C VAL C 186 " pdb=" CB VAL C 186 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.59e-01 chirality pdb=" CA VAL A 186 " pdb=" N VAL A 186 " pdb=" C VAL A 186 " pdb=" CB VAL A 186 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.59e-01 chirality pdb=" CA VAL D 186 " pdb=" N VAL D 186 " pdb=" C VAL D 186 " pdb=" CB VAL D 186 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.59e-01 ... (remaining 1641 not shown) Planarity restraints: 1880 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 144 " -0.010 2.00e-02 2.50e+03 7.96e-03 1.11e+00 pdb=" CG PHE C 144 " 0.018 2.00e-02 2.50e+03 pdb=" CD1 PHE C 144 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE C 144 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE C 144 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE C 144 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE C 144 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 144 " -0.010 2.00e-02 2.50e+03 7.96e-03 1.11e+00 pdb=" CG PHE A 144 " 0.018 2.00e-02 2.50e+03 pdb=" CD1 PHE A 144 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE A 144 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE A 144 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 144 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE A 144 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 144 " 0.010 2.00e-02 2.50e+03 7.96e-03 1.11e+00 pdb=" CG PHE B 144 " -0.018 2.00e-02 2.50e+03 pdb=" CD1 PHE B 144 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE B 144 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE B 144 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 144 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE B 144 " 0.002 2.00e-02 2.50e+03 ... (remaining 1877 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 2868 2.81 - 3.33: 10508 3.33 - 3.86: 19924 3.86 - 4.38: 22936 4.38 - 4.90: 37662 Nonbonded interactions: 93898 Sorted by model distance: nonbonded pdb=" OH TYR A 84 " pdb=" OD2 ASP A 140 " model vdw 2.291 2.440 nonbonded pdb=" OH TYR B 84 " pdb=" OD2 ASP B 140 " model vdw 2.291 2.440 nonbonded pdb=" OH TYR D 84 " pdb=" OD2 ASP D 140 " model vdw 2.291 2.440 nonbonded pdb=" OH TYR C 84 " pdb=" OD2 ASP C 140 " model vdw 2.291 2.440 nonbonded pdb=" OE1 GLU B 277 " pdb=" OH TYR B 342 " model vdw 2.345 2.440 ... (remaining 93893 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 No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.550 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: 26.430 Check model and map are aligned: 0.200 Set scattering table: 0.080 Process input model: 31.680 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.060 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:12.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 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 : 0.003 0.022 10672 Z= 0.170 Angle : 0.531 7.067 14464 Z= 0.297 Chirality : 0.039 0.136 1644 Planarity : 0.004 0.025 1880 Dihedral : 16.087 86.201 3984 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.44 % Allowed : 10.07 % Favored : 88.49 % 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: 1.13 (0.23), residues: 1364 helix: 1.56 (0.19), residues: 708 sheet: -1.06 (0.35), residues: 176 loop : 0.44 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP C 147 HIS 0.003 0.001 HIS C 237 PHE 0.018 0.002 PHE C 144 TYR 0.016 0.002 TYR C 213 ARG 0.001 0.000 ARG B 258 *********************** 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. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 100 time to evaluate : 1.249 Fit side-chains outliers start: 16 outliers final: 8 residues processed: 112 average time/residue: 1.4835 time to fit residues: 177.4522 Evaluate side-chains 120 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 112 time to evaluate : 1.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 295 TRP Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 295 TRP Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 295 TRP Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 295 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 114 optimal weight: 0.4980 chunk 103 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 35 optimal weight: 0.5980 chunk 69 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 106 optimal weight: 5.9990 chunk 41 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 79 optimal weight: 0.8980 chunk 123 optimal weight: 0.9980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN B 95 GLN C 95 GLN D 95 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.0704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10672 Z= 0.244 Angle : 0.561 6.192 14464 Z= 0.295 Chirality : 0.043 0.132 1644 Planarity : 0.004 0.024 1880 Dihedral : 5.883 55.944 1484 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.52 % Allowed : 8.63 % Favored : 88.85 % 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: 1.50 (0.22), residues: 1364 helix: 1.95 (0.19), residues: 712 sheet: -1.33 (0.39), residues: 144 loop : 0.49 (0.27), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP C 147 HIS 0.003 0.001 HIS A 4 PHE 0.017 0.003 PHE A 144 TYR 0.025 0.002 TYR A 213 ARG 0.003 0.000 ARG D 258 *********************** REFINEMENT MACRO_CYCLE 2 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. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 108 time to evaluate : 1.291 Fit side-chains REVERT: A 34 GLU cc_start: 0.7352 (OUTLIER) cc_final: 0.6241 (pm20) REVERT: B 34 GLU cc_start: 0.7359 (OUTLIER) cc_final: 0.6250 (pm20) REVERT: C 34 GLU cc_start: 0.7354 (OUTLIER) cc_final: 0.6243 (pm20) REVERT: D 34 GLU cc_start: 0.7355 (OUTLIER) cc_final: 0.6245 (pm20) outliers start: 28 outliers final: 16 residues processed: 120 average time/residue: 1.6411 time to fit residues: 209.3307 Evaluate side-chains 120 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 100 time to evaluate : 1.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 GLU Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 295 TRP Chi-restraints excluded: chain B residue 34 GLU Chi-restraints excluded: chain B residue 49 GLU Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 295 TRP Chi-restraints excluded: chain C residue 34 GLU Chi-restraints excluded: chain C residue 49 GLU Chi-restraints excluded: chain C residue 66 ASP Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 295 TRP Chi-restraints excluded: chain D residue 34 GLU Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain D residue 66 ASP Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 295 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 68 optimal weight: 0.0170 chunk 38 optimal weight: 5.9990 chunk 102 optimal weight: 0.0030 chunk 84 optimal weight: 4.9990 chunk 34 optimal weight: 5.9990 chunk 123 optimal weight: 0.9990 chunk 133 optimal weight: 1.9990 chunk 110 optimal weight: 0.5980 chunk 122 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 overall best weight: 0.5228 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 HIS A 95 GLN B 20 HIS B 95 GLN C 20 HIS C 95 GLN D 20 HIS D 95 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.0769 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= 0.168 Angle : 0.482 5.990 14464 Z= 0.251 Chirality : 0.040 0.123 1644 Planarity : 0.004 0.024 1880 Dihedral : 5.620 55.691 1484 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 2.88 % Allowed : 8.99 % Favored : 88.13 % 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: 1.74 (0.23), residues: 1364 helix: 2.24 (0.19), residues: 720 sheet: -1.52 (0.38), residues: 164 loop : 0.61 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 147 HIS 0.002 0.001 HIS A 2 PHE 0.015 0.002 PHE B 144 TYR 0.018 0.002 TYR A 213 ARG 0.001 0.000 ARG A 258 *********************** REFINEMENT MACRO_CYCLE 3 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. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 96 time to evaluate : 1.274 Fit side-chains outliers start: 32 outliers final: 16 residues processed: 116 average time/residue: 1.6066 time to fit residues: 197.9731 Evaluate side-chains 120 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 104 time to evaluate : 1.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 295 TRP Chi-restraints excluded: chain B residue 49 GLU Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 295 TRP Chi-restraints excluded: chain C residue 49 GLU Chi-restraints excluded: chain C residue 66 ASP Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 295 TRP Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain D residue 66 ASP Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 295 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 0.9990 chunk 93 optimal weight: 0.0060 chunk 64 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 59 optimal weight: 0.8980 chunk 83 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 131 optimal weight: 1.9990 chunk 117 optimal weight: 0.0270 chunk 35 optimal weight: 0.5980 chunk 109 optimal weight: 2.9990 overall best weight: 0.4654 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN B 95 GLN C 95 GLN D 95 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.0868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 10672 Z= 0.159 Angle : 0.470 5.493 14464 Z= 0.245 Chirality : 0.039 0.121 1644 Planarity : 0.004 0.026 1880 Dihedral : 5.554 55.731 1484 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 4.32 % Allowed : 7.91 % Favored : 87.77 % 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: 1.85 (0.23), residues: 1364 helix: 2.37 (0.19), residues: 720 sheet: -1.51 (0.39), residues: 164 loop : 0.62 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 147 HIS 0.002 0.001 HIS C 2 PHE 0.015 0.002 PHE A 144 TYR 0.018 0.002 TYR C 213 ARG 0.002 0.000 ARG A 258 *********************** REFINEMENT MACRO_CYCLE 4 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. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 108 time to evaluate : 1.250 Fit side-chains REVERT: A 34 GLU cc_start: 0.7358 (OUTLIER) cc_final: 0.6136 (pm20) REVERT: B 34 GLU cc_start: 0.7364 (OUTLIER) cc_final: 0.6142 (pm20) REVERT: C 34 GLU cc_start: 0.7358 (OUTLIER) cc_final: 0.6133 (pm20) REVERT: D 34 GLU cc_start: 0.7359 (OUTLIER) cc_final: 0.6137 (pm20) outliers start: 48 outliers final: 20 residues processed: 140 average time/residue: 1.6182 time to fit residues: 239.9348 Evaluate side-chains 120 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 96 time to evaluate : 1.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain A residue 34 GLU Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 295 TRP Chi-restraints excluded: chain B residue 3 SER Chi-restraints excluded: chain B residue 34 GLU Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 295 TRP Chi-restraints excluded: chain C residue 3 SER Chi-restraints excluded: chain C residue 34 GLU Chi-restraints excluded: chain C residue 66 ASP Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 295 TRP Chi-restraints excluded: chain D residue 3 SER Chi-restraints excluded: chain D residue 34 GLU Chi-restraints excluded: chain D residue 66 ASP Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 295 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 74 optimal weight: 0.7980 chunk 1 optimal weight: 0.5980 chunk 97 optimal weight: 0.9990 chunk 54 optimal weight: 0.9990 chunk 112 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 chunk 0 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 44 optimal weight: 0.0570 overall best weight: 0.6900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN A 119 ASN B 95 GLN B 119 ASN C 95 GLN C 119 ASN D 95 GLN D 119 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.0977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10672 Z= 0.191 Angle : 0.499 5.093 14464 Z= 0.261 Chirality : 0.040 0.124 1644 Planarity : 0.004 0.025 1880 Dihedral : 5.668 55.519 1484 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 3.24 % Allowed : 9.71 % Favored : 87.05 % 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: 1.77 (0.23), residues: 1364 helix: 2.30 (0.19), residues: 720 sheet: -1.51 (0.39), residues: 164 loop : 0.57 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 147 HIS 0.002 0.001 HIS A 4 PHE 0.016 0.002 PHE C 144 TYR 0.021 0.002 TYR C 213 ARG 0.002 0.000 ARG C 258 *********************** REFINEMENT MACRO_CYCLE 5 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. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 104 time to evaluate : 1.349 Fit side-chains REVERT: A 34 GLU cc_start: 0.7357 (OUTLIER) cc_final: 0.6180 (pm20) REVERT: A 42 ARG cc_start: 0.6740 (OUTLIER) cc_final: 0.5781 (mpt-90) REVERT: B 34 GLU cc_start: 0.7364 (OUTLIER) cc_final: 0.6188 (pm20) REVERT: B 42 ARG cc_start: 0.6743 (OUTLIER) cc_final: 0.5785 (mpt-90) REVERT: C 34 GLU cc_start: 0.7360 (OUTLIER) cc_final: 0.6182 (pm20) REVERT: C 42 ARG cc_start: 0.6741 (OUTLIER) cc_final: 0.5784 (mpt-90) REVERT: D 34 GLU cc_start: 0.7361 (OUTLIER) cc_final: 0.6184 (pm20) REVERT: D 42 ARG cc_start: 0.6740 (OUTLIER) cc_final: 0.5783 (mpt-90) outliers start: 36 outliers final: 24 residues processed: 132 average time/residue: 1.7029 time to fit residues: 237.6209 Evaluate side-chains 136 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 104 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain A residue 34 GLU Chi-restraints excluded: chain A residue 42 ARG Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 295 TRP Chi-restraints excluded: chain B residue 3 SER Chi-restraints excluded: chain B residue 34 GLU Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 49 GLU Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 295 TRP Chi-restraints excluded: chain C residue 3 SER Chi-restraints excluded: chain C residue 34 GLU Chi-restraints excluded: chain C residue 42 ARG Chi-restraints excluded: chain C residue 49 GLU Chi-restraints excluded: chain C residue 66 ASP Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 295 TRP Chi-restraints excluded: chain D residue 3 SER Chi-restraints excluded: chain D residue 34 GLU Chi-restraints excluded: chain D residue 42 ARG Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain D residue 66 ASP Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 295 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 118 optimal weight: 0.5980 chunk 25 optimal weight: 0.4980 chunk 77 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 131 optimal weight: 0.6980 chunk 109 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 69 optimal weight: 0.0670 chunk 126 optimal weight: 1.9990 overall best weight: 0.7720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN A 119 ASN B 95 GLN B 119 ASN C 95 GLN C 119 ASN D 95 GLN D 119 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.0997 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= 0.204 Angle : 0.516 5.570 14464 Z= 0.269 Chirality : 0.041 0.126 1644 Planarity : 0.004 0.025 1880 Dihedral : 5.750 55.207 1484 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 3.60 % Allowed : 9.71 % Favored : 86.69 % 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: 1.69 (0.23), residues: 1364 helix: 2.22 (0.18), residues: 720 sheet: -1.53 (0.39), residues: 164 loop : 0.55 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 147 HIS 0.002 0.001 HIS D 2 PHE 0.016 0.002 PHE C 144 TYR 0.022 0.002 TYR C 213 ARG 0.002 0.000 ARG A 258 *********************** REFINEMENT MACRO_CYCLE 6 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. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 104 time to evaluate : 1.173 Fit side-chains REVERT: A 42 ARG cc_start: 0.6798 (OUTLIER) cc_final: 0.6083 (mpt-90) REVERT: B 42 ARG cc_start: 0.6799 (OUTLIER) cc_final: 0.6088 (mpt-90) REVERT: C 42 ARG cc_start: 0.6797 (OUTLIER) cc_final: 0.6087 (mpt-90) REVERT: D 42 ARG cc_start: 0.6796 (OUTLIER) cc_final: 0.6085 (mpt-90) outliers start: 40 outliers final: 20 residues processed: 132 average time/residue: 1.6302 time to fit residues: 228.2194 Evaluate side-chains 128 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 104 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain A residue 42 ARG Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 295 TRP Chi-restraints excluded: chain B residue 3 SER Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 295 TRP Chi-restraints excluded: chain C residue 3 SER Chi-restraints excluded: chain C residue 42 ARG Chi-restraints excluded: chain C residue 66 ASP Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 295 TRP Chi-restraints excluded: chain D residue 3 SER Chi-restraints excluded: chain D residue 42 ARG Chi-restraints excluded: chain D residue 66 ASP Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 295 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 14 optimal weight: 0.9990 chunk 74 optimal weight: 0.8980 chunk 96 optimal weight: 0.4980 chunk 110 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 chunk 79 optimal weight: 0.0970 chunk 60 optimal weight: 0.0010 chunk 81 optimal weight: 0.5980 chunk 52 optimal weight: 0.9980 overall best weight: 0.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN B 95 GLN C 95 GLN D 95 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.1001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 10672 Z= 0.155 Angle : 0.468 5.889 14464 Z= 0.243 Chirality : 0.039 0.119 1644 Planarity : 0.003 0.027 1880 Dihedral : 5.502 55.183 1484 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 2.88 % Allowed : 10.43 % Favored : 86.69 % 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: 1.90 (0.23), residues: 1364 helix: 2.42 (0.19), residues: 720 sheet: -1.45 (0.40), residues: 164 loop : 0.60 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 147 HIS 0.002 0.001 HIS A 4 PHE 0.015 0.002 PHE D 144 TYR 0.016 0.002 TYR B 213 ARG 0.002 0.000 ARG C 258 *********************** REFINEMENT MACRO_CYCLE 7 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. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 104 time to evaluate : 1.193 Fit side-chains REVERT: A 42 ARG cc_start: 0.6695 (OUTLIER) cc_final: 0.6053 (mpt-90) REVERT: B 42 ARG cc_start: 0.6696 (OUTLIER) cc_final: 0.6058 (mpt-90) REVERT: C 42 ARG cc_start: 0.6695 (OUTLIER) cc_final: 0.6056 (mpt-90) REVERT: D 42 ARG cc_start: 0.6693 (OUTLIER) cc_final: 0.6053 (mpt-90) outliers start: 32 outliers final: 20 residues processed: 132 average time/residue: 1.5735 time to fit residues: 220.2908 Evaluate side-chains 128 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 104 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain A residue 42 ARG Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 295 TRP Chi-restraints excluded: chain B residue 3 SER Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 295 TRP Chi-restraints excluded: chain C residue 3 SER Chi-restraints excluded: chain C residue 42 ARG Chi-restraints excluded: chain C residue 66 ASP Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 295 TRP Chi-restraints excluded: chain D residue 3 SER Chi-restraints excluded: chain D residue 42 ARG Chi-restraints excluded: chain D residue 66 ASP Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 295 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 64 optimal weight: 3.9990 chunk 12 optimal weight: 0.5980 chunk 103 optimal weight: 3.9990 chunk 119 optimal weight: 0.9980 chunk 125 optimal weight: 0.0040 chunk 114 optimal weight: 1.9990 overall best weight: 0.9196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN B 95 GLN C 95 GLN D 95 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.1060 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= 0.226 Angle : 0.536 6.176 14464 Z= 0.280 Chirality : 0.041 0.129 1644 Planarity : 0.004 0.026 1880 Dihedral : 5.807 55.002 1484 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 2.52 % Allowed : 10.79 % Favored : 86.69 % 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: 1.71 (0.22), residues: 1364 helix: 2.25 (0.18), residues: 712 sheet: -1.53 (0.39), residues: 164 loop : 0.58 (0.28), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP D 147 HIS 0.003 0.001 HIS A 2 PHE 0.017 0.002 PHE A 144 TYR 0.024 0.002 TYR A 213 ARG 0.002 0.000 ARG A 258 *********************** REFINEMENT MACRO_CYCLE 8 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. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 104 time to evaluate : 1.223 Fit side-chains REVERT: A 42 ARG cc_start: 0.6775 (OUTLIER) cc_final: 0.5863 (mpt-90) REVERT: B 42 ARG cc_start: 0.6776 (OUTLIER) cc_final: 0.5864 (mpt-90) REVERT: C 42 ARG cc_start: 0.6772 (OUTLIER) cc_final: 0.5865 (mpt-90) REVERT: D 42 ARG cc_start: 0.6776 (OUTLIER) cc_final: 0.5863 (mpt-90) outliers start: 28 outliers final: 24 residues processed: 132 average time/residue: 1.6349 time to fit residues: 228.5557 Evaluate side-chains 120 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 92 time to evaluate : 1.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain A residue 42 ARG Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 295 TRP Chi-restraints excluded: chain B residue 3 SER Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 295 TRP Chi-restraints excluded: chain C residue 3 SER Chi-restraints excluded: chain C residue 42 ARG Chi-restraints excluded: chain C residue 66 ASP Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 295 TRP Chi-restraints excluded: chain D residue 3 SER Chi-restraints excluded: chain D residue 42 ARG Chi-restraints excluded: chain D residue 66 ASP Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 295 TRP 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: 1.9990 chunk 73 optimal weight: 0.6980 chunk 53 optimal weight: 0.5980 chunk 95 optimal weight: 1.9990 chunk 37 optimal weight: 7.9990 chunk 110 optimal weight: 0.3980 chunk 115 optimal weight: 0.9980 chunk 121 optimal weight: 0.0050 chunk 80 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN B 95 GLN C 95 GLN D 95 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.1029 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= 0.172 Angle : 0.496 7.719 14464 Z= 0.256 Chirality : 0.040 0.122 1644 Planarity : 0.004 0.026 1880 Dihedral : 5.613 54.966 1484 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 3.24 % Allowed : 9.71 % Favored : 87.05 % 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: 1.76 (0.23), residues: 1364 helix: 2.31 (0.19), residues: 720 sheet: -1.50 (0.40), residues: 164 loop : 0.54 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 147 HIS 0.002 0.001 HIS D 4 PHE 0.015 0.002 PHE A 144 TYR 0.018 0.002 TYR B 213 ARG 0.003 0.000 ARG C 42 *********************** REFINEMENT MACRO_CYCLE 9 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. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 92 time to evaluate : 1.124 Fit side-chains REVERT: A 42 ARG cc_start: 0.6654 (OUTLIER) cc_final: 0.6138 (mpt-90) REVERT: B 42 ARG cc_start: 0.6656 (OUTLIER) cc_final: 0.6140 (mpt-90) REVERT: C 42 ARG cc_start: 0.6654 (OUTLIER) cc_final: 0.6138 (mpt-90) REVERT: D 42 ARG cc_start: 0.6657 (OUTLIER) cc_final: 0.6141 (mpt-90) outliers start: 36 outliers final: 24 residues processed: 124 average time/residue: 1.5521 time to fit residues: 204.4642 Evaluate side-chains 128 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 100 time to evaluate : 1.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain A residue 42 ARG Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 295 TRP Chi-restraints excluded: chain B residue 3 SER Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 295 TRP Chi-restraints excluded: chain C residue 3 SER Chi-restraints excluded: chain C residue 42 ARG Chi-restraints excluded: chain C residue 66 ASP Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 295 TRP Chi-restraints excluded: chain D residue 3 SER Chi-restraints excluded: chain D residue 42 ARG Chi-restraints excluded: chain D residue 66 ASP Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 295 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 0.8980 chunk 61 optimal weight: 0.0470 chunk 89 optimal weight: 0.6980 chunk 135 optimal weight: 3.9990 chunk 124 optimal weight: 0.5980 chunk 107 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 chunk 83 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 85 optimal weight: 0.6980 chunk 114 optimal weight: 0.9980 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN B 95 GLN C 95 GLN D 95 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.1041 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= 0.172 Angle : 0.496 7.965 14464 Z= 0.255 Chirality : 0.040 0.121 1644 Planarity : 0.004 0.027 1880 Dihedral : 5.572 54.873 1484 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 2.88 % Allowed : 9.71 % Favored : 87.41 % 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: 1.78 (0.23), residues: 1364 helix: 2.34 (0.19), residues: 720 sheet: -1.48 (0.40), residues: 164 loop : 0.50 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 147 HIS 0.002 0.001 HIS C 4 PHE 0.015 0.002 PHE D 144 TYR 0.019 0.002 TYR B 213 ARG 0.003 0.000 ARG C 42 ********************** REFINEMENT MACRO_CYCLE 10 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. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 100 time to evaluate : 1.287 Fit side-chains REVERT: A 42 ARG cc_start: 0.6672 (OUTLIER) cc_final: 0.6174 (mpt-90) REVERT: B 42 ARG cc_start: 0.6672 (OUTLIER) cc_final: 0.6174 (mpt-90) REVERT: C 42 ARG cc_start: 0.6672 (OUTLIER) cc_final: 0.6172 (mpt-90) REVERT: D 42 ARG cc_start: 0.6672 (OUTLIER) cc_final: 0.6176 (mpt-90) outliers start: 32 outliers final: 24 residues processed: 128 average time/residue: 1.5550 time to fit residues: 212.1716 Evaluate side-chains 128 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 100 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain A residue 42 ARG Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 295 TRP Chi-restraints excluded: chain B residue 3 SER Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 295 TRP Chi-restraints excluded: chain C residue 3 SER Chi-restraints excluded: chain C residue 42 ARG Chi-restraints excluded: chain C residue 66 ASP Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 295 TRP Chi-restraints excluded: chain D residue 3 SER Chi-restraints excluded: chain D residue 42 ARG Chi-restraints excluded: chain D residue 66 ASP Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 295 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 33 optimal weight: 2.9990 chunk 99 optimal weight: 0.9980 chunk 15 optimal weight: 0.5980 chunk 29 optimal weight: 0.9990 chunk 108 optimal weight: 0.9980 chunk 45 optimal weight: 0.5980 chunk 110 optimal weight: 4.9990 chunk 13 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 94 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN B 95 GLN C 95 GLN D 95 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.177268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.159432 restraints weight = 8519.110| |-----------------------------------------------------------------------------| r_work (start): 0.3821 rms_B_bonded: 0.71 r_work: 0.3725 rms_B_bonded: 1.22 restraints_weight: 0.5000 r_work: 0.3642 rms_B_bonded: 2.15 restraints_weight: 0.2500 r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.1085 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= 0.217 Angle : 0.542 9.091 14464 Z= 0.280 Chirality : 0.041 0.127 1644 Planarity : 0.004 0.026 1880 Dihedral : 5.774 54.784 1484 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 2.16 % Allowed : 10.43 % Favored : 87.41 % 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: 1.67 (0.22), residues: 1364 helix: 2.24 (0.18), residues: 712 sheet: -1.52 (0.39), residues: 164 loop : 0.49 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 147 HIS 0.003 0.001 HIS B 4 PHE 0.017 0.002 PHE B 144 TYR 0.024 0.002 TYR D 213 ARG 0.004 0.000 ARG B 42 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4577.33 seconds wall clock time: 81 minutes 46.46 seconds (4906.46 seconds total)