Starting phenix.real_space_refine on Fri Mar 15 03:33:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ka3_22757/03_2024/7ka3_22757.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ka3_22757/03_2024/7ka3_22757.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ka3_22757/03_2024/7ka3_22757.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ka3_22757/03_2024/7ka3_22757.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ka3_22757/03_2024/7ka3_22757.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ka3_22757/03_2024/7ka3_22757.pdb" } resolution = 3.3 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 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 ASP 33": "OD1" <-> "OD2" Residue "B PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 187": "OE1" <-> "OE2" Residue "B ASP 195": "OD1" <-> "OD2" Residue "B GLU 246": "OE1" <-> "OE2" Residue "B GLU 276": "OE1" <-> "OE2" Residue "B PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 318": "OE1" <-> "OE2" Residue "A ASP 17": "OD1" <-> "OD2" Residue "A ASP 33": "OD1" <-> "OD2" Residue "A PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 187": "OE1" <-> "OE2" Residue "A ASP 195": "OD1" <-> "OD2" Residue "A GLU 246": "OE1" <-> "OE2" Residue "A GLU 276": "OE1" <-> "OE2" Residue "A PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 318": "OE1" <-> "OE2" Residue "C ASP 17": "OD1" <-> "OD2" Residue "C ASP 33": "OD1" <-> "OD2" Residue "C PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 187": "OE1" <-> "OE2" Residue "C ASP 195": "OD1" <-> "OD2" Residue "C GLU 246": "OE1" <-> "OE2" Residue "C GLU 276": "OE1" <-> "OE2" Residue "C PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 318": "OE1" <-> "OE2" Residue "D ASP 17": "OD1" <-> "OD2" Residue "D ASP 33": "OD1" <-> "OD2" Residue "D PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 187": "OE1" <-> "OE2" Residue "D ASP 195": "OD1" <-> "OD2" Residue "D GLU 246": "OE1" <-> "OE2" Residue "D GLU 276": "OE1" <-> "OE2" Residue "D PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 318": "OE1" <-> "OE2" Time to flip residues: 0.04s 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: 6.03, per 1000 atoms: 0.58 Number of scatterers: 10472 At special positions: 0 Unit cell: (97.37, 80.99, 105.56, 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: 3.93 Conformation dependent library (CDL) restraints added in 2.1 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 55.2% alpha, 12.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.54 Creating SS restraints... Processing helix chain 'B' and resid 8 through 23 removed outlier: 3.599A pdb=" N VAL B 23 " --> pdb=" O ALA B 19 " (cutoff:3.500A) 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 removed outlier: 3.522A pdb=" N VAL B 69 " --> pdb=" O ASP B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 85 removed outlier: 3.511A pdb=" N GLN B 85 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 100 removed outlier: 3.993A 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 180 removed outlier: 3.703A pdb=" N ASN B 180 " --> pdb=" O ILE B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 219 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 287 removed outlier: 3.503A pdb=" N ALA B 279 " --> pdb=" O SER B 275 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N SER B 280 " --> pdb=" O GLU B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 314 removed outlier: 3.946A pdb=" N GLN B 306 " --> pdb=" O GLY B 302 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N SER B 308 " --> pdb=" O ALA B 304 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N ALA B 309 " --> pdb=" O LEU B 305 " (cutoff:3.500A) removed outlier: 3.578A 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 removed outlier: 3.600A pdb=" N VAL A 23 " --> pdb=" O ALA A 19 " (cutoff:3.500A) 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 removed outlier: 3.522A pdb=" N VAL A 69 " --> pdb=" O ASP A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 85 removed outlier: 3.512A pdb=" N GLN A 85 " --> pdb=" O THR A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 100 removed outlier: 3.993A 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 180 removed outlier: 3.703A pdb=" N ASN A 180 " --> pdb=" O ILE A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 219 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 287 removed outlier: 3.502A pdb=" N ALA A 279 " --> pdb=" O SER A 275 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N SER A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 314 removed outlier: 3.946A pdb=" N GLN A 306 " --> pdb=" O GLY A 302 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N SER A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N ALA A 309 " --> pdb=" O LEU A 305 " (cutoff:3.500A) removed outlier: 3.577A 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 removed outlier: 3.601A pdb=" N VAL C 23 " --> pdb=" O ALA C 19 " (cutoff:3.500A) 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 removed outlier: 3.521A pdb=" N VAL C 69 " --> pdb=" O ASP C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 85 removed outlier: 3.512A pdb=" N GLN C 85 " --> pdb=" O THR C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 100 removed outlier: 3.993A 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 180 removed outlier: 3.703A pdb=" N ASN C 180 " --> pdb=" O ILE C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 219 Processing helix chain 'C' and resid 222 through 226 removed outlier: 3.594A pdb=" N THR C 226 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 258 Processing helix chain 'C' and resid 275 through 287 removed outlier: 3.502A pdb=" N ALA C 279 " --> pdb=" O SER C 275 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N SER C 280 " --> pdb=" O GLU C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 314 removed outlier: 3.947A pdb=" N GLN C 306 " --> pdb=" O GLY C 302 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N SER C 308 " --> pdb=" O ALA C 304 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N ALA C 309 " --> pdb=" O LEU C 305 " (cutoff:3.500A) removed outlier: 3.578A 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 removed outlier: 3.600A pdb=" N VAL D 23 " --> pdb=" O ALA D 19 " (cutoff:3.500A) 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 removed outlier: 3.521A pdb=" N VAL D 69 " --> pdb=" O ASP D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 85 removed outlier: 3.511A pdb=" N GLN D 85 " --> pdb=" O THR D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 100 removed outlier: 3.993A 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 180 removed outlier: 3.704A pdb=" N ASN D 180 " --> pdb=" O ILE D 176 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 219 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 287 removed outlier: 3.503A pdb=" N ALA D 279 " --> pdb=" O SER D 275 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N SER D 280 " --> pdb=" O GLU D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 314 removed outlier: 3.946A pdb=" N GLN D 306 " --> pdb=" O GLY D 302 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N SER D 308 " --> pdb=" O ALA D 304 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N ALA D 309 " --> pdb=" O LEU D 305 " (cutoff:3.500A) removed outlier: 3.578A 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 31 removed outlier: 6.460A pdb=" N GLY B 28 " --> pdb=" O GLY B 75 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N ILE B 77 " --> pdb=" O GLY B 28 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N LEU B 30 " --> pdb=" O ILE B 77 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N GLY B 74 " --> pdb=" O VAL B 103 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N GLY B 105 " --> pdb=" O GLY B 74 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N VAL B 76 " --> pdb=" O GLY B 105 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N LYS B 107 " --> pdb=" O VAL B 76 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N LEU B 78 " --> pdb=" O LYS B 107 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N VAL B 104 " --> pdb=" O ASP B 143 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N ALA B 145 " --> pdb=" O VAL B 104 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N ILE B 106 " --> pdb=" O ALA B 145 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N TRP B 147 " --> pdb=" O ILE B 106 " (cutoff:3.500A) removed outlier: 8.257A pdb=" N ILE B 185 " --> pdb=" O ASP B 143 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ALA B 145 " --> pdb=" O ILE B 185 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N GLU B 187 " --> pdb=" O ALA B 145 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N TRP B 147 " --> pdb=" O GLU B 187 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N GLU B 189 " --> pdb=" O TRP B 147 " (cutoff:3.500A) removed outlier: 6.064A 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: 7.331A pdb=" N LEU B 151 " --> pdb=" O LEU B 191 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N LEU B 228 " --> pdb=" O THR B 268 " (cutoff:3.500A) removed outlier: 3.548A 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 31 removed outlier: 6.460A pdb=" N GLY A 28 " --> pdb=" O GLY A 75 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N ILE A 77 " --> pdb=" O GLY A 28 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N LEU A 30 " --> pdb=" O ILE A 77 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N GLY A 74 " --> pdb=" O VAL A 103 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N GLY A 105 " --> pdb=" O GLY A 74 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N VAL A 76 " --> pdb=" O GLY A 105 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N LYS A 107 " --> pdb=" O VAL A 76 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N LEU A 78 " --> pdb=" O LYS A 107 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N VAL A 104 " --> pdb=" O ASP A 143 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N ALA A 145 " --> pdb=" O VAL A 104 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N ILE A 106 " --> pdb=" O ALA A 145 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N TRP A 147 " --> pdb=" O ILE A 106 " (cutoff:3.500A) removed outlier: 8.258A pdb=" N ILE A 185 " --> pdb=" O ASP A 143 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ALA A 145 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N GLU A 187 " --> pdb=" O ALA A 145 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N TRP A 147 " --> pdb=" O GLU A 187 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N GLU A 189 " --> pdb=" O TRP A 147 " (cutoff:3.500A) removed outlier: 6.063A 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: 7.330A pdb=" N LEU A 151 " --> pdb=" O LEU A 191 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N LEU A 228 " --> pdb=" O THR A 268 " (cutoff:3.500A) removed outlier: 3.548A 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 31 removed outlier: 6.461A pdb=" N GLY C 28 " --> pdb=" O GLY C 75 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N ILE C 77 " --> pdb=" O GLY C 28 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N LEU C 30 " --> pdb=" O ILE C 77 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N GLY C 74 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N GLY C 105 " --> pdb=" O GLY C 74 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N VAL C 76 " --> pdb=" O GLY C 105 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N LYS C 107 " --> pdb=" O VAL C 76 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N LEU C 78 " --> pdb=" O LYS C 107 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N VAL C 104 " --> pdb=" O ASP C 143 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N ALA C 145 " --> pdb=" O VAL C 104 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N ILE C 106 " --> pdb=" O ALA C 145 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N TRP C 147 " --> pdb=" O ILE C 106 " (cutoff:3.500A) removed outlier: 8.258A pdb=" N ILE C 185 " --> pdb=" O ASP C 143 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ALA C 145 " --> pdb=" O ILE C 185 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N GLU C 187 " --> pdb=" O ALA C 145 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N TRP C 147 " --> pdb=" O GLU C 187 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N GLU C 189 " --> pdb=" O TRP C 147 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N CYS C 149 " --> pdb=" O GLU C 189 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N LEU C 191 " --> pdb=" O CYS C 149 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N LEU C 151 " --> pdb=" O LEU C 191 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N LEU C 228 " --> pdb=" O THR C 268 " (cutoff:3.500A) removed outlier: 3.548A 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 31 removed outlier: 6.460A pdb=" N GLY D 28 " --> pdb=" O GLY D 75 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N ILE D 77 " --> pdb=" O GLY D 28 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N LEU D 30 " --> pdb=" O ILE D 77 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N GLY D 74 " --> pdb=" O VAL D 103 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N GLY D 105 " --> pdb=" O GLY D 74 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N VAL D 76 " --> pdb=" O GLY D 105 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N LYS D 107 " --> pdb=" O VAL D 76 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N LEU D 78 " --> pdb=" O LYS D 107 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N VAL D 104 " --> pdb=" O ASP D 143 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N ALA D 145 " --> pdb=" O VAL D 104 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N ILE D 106 " --> pdb=" O ALA D 145 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N TRP D 147 " --> pdb=" O ILE D 106 " (cutoff:3.500A) removed outlier: 8.257A pdb=" N ILE D 185 " --> pdb=" O ASP D 143 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ALA D 145 " --> pdb=" O ILE D 185 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N GLU D 187 " --> pdb=" O ALA D 145 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N TRP D 147 " --> pdb=" O GLU D 187 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N GLU D 189 " --> pdb=" O TRP D 147 " (cutoff:3.500A) removed outlier: 6.064A 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: 7.330A pdb=" N LEU D 151 " --> pdb=" O LEU D 191 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N LEU D 228 " --> pdb=" O THR D 268 " (cutoff:3.500A) removed outlier: 3.548A 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 114 524 hydrogen bonds defined for protein. 1536 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: 3.12 Time building geometry restraints manager: 4.25 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: 3479 1.34 - 1.46: 1920 1.46 - 1.58: 5217 1.58 - 1.69: 0 1.69 - 1.81: 56 Bond restraints: 10672 Sorted by residual: bond pdb=" C ASN A 70 " pdb=" N PRO A 71 " ideal model delta sigma weight residual 1.334 1.398 -0.064 2.34e-02 1.83e+03 7.52e+00 bond pdb=" C ASN B 70 " pdb=" N PRO B 71 " ideal model delta sigma weight residual 1.334 1.397 -0.064 2.34e-02 1.83e+03 7.37e+00 bond pdb=" C ASN D 70 " pdb=" N PRO D 71 " ideal model delta sigma weight residual 1.334 1.397 -0.063 2.34e-02 1.83e+03 7.28e+00 bond pdb=" C ASN C 70 " pdb=" N PRO C 71 " ideal model delta sigma weight residual 1.334 1.397 -0.063 2.34e-02 1.83e+03 7.28e+00 bond pdb=" C PHE C 93 " pdb=" N PRO C 94 " ideal model delta sigma weight residual 1.335 1.354 -0.019 1.36e-02 5.41e+03 1.94e+00 ... (remaining 10667 not shown) Histogram of bond angle deviations from ideal: 100.66 - 107.33: 427 107.33 - 114.00: 6065 114.00 - 120.67: 4260 120.67 - 127.34: 3604 127.34 - 134.01: 108 Bond angle restraints: 14464 Sorted by residual: angle pdb=" C ASN D 319 " pdb=" N LEU D 320 " pdb=" CA LEU D 320 " ideal model delta sigma weight residual 121.19 127.32 -6.13 1.59e+00 3.96e-01 1.49e+01 angle pdb=" C ASN A 319 " pdb=" N LEU A 320 " pdb=" CA LEU A 320 " ideal model delta sigma weight residual 121.19 127.29 -6.10 1.59e+00 3.96e-01 1.47e+01 angle pdb=" C ASN B 319 " pdb=" N LEU B 320 " pdb=" CA LEU B 320 " ideal model delta sigma weight residual 121.19 127.29 -6.10 1.59e+00 3.96e-01 1.47e+01 angle pdb=" C ASN C 319 " pdb=" N LEU C 320 " pdb=" CA LEU C 320 " ideal model delta sigma weight residual 121.19 127.28 -6.09 1.59e+00 3.96e-01 1.46e+01 angle pdb=" CA LEU B 61 " pdb=" CB LEU B 61 " pdb=" CG LEU B 61 " ideal model delta sigma weight residual 116.30 125.75 -9.45 3.50e+00 8.16e-02 7.30e+00 ... (remaining 14459 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.48: 5912 17.48 - 34.95: 485 34.95 - 52.43: 83 52.43 - 69.91: 12 69.91 - 87.38: 12 Dihedral angle restraints: 6504 sinusoidal: 2572 harmonic: 3932 Sorted by residual: dihedral pdb=" CA LEU A 270 " pdb=" C LEU A 270 " pdb=" N SER A 271 " pdb=" CA SER A 271 " ideal model delta harmonic sigma weight residual 180.00 162.16 17.84 0 5.00e+00 4.00e-02 1.27e+01 dihedral pdb=" CA LEU D 270 " pdb=" C LEU D 270 " pdb=" N SER D 271 " pdb=" CA SER D 271 " ideal model delta harmonic sigma weight residual 180.00 162.20 17.80 0 5.00e+00 4.00e-02 1.27e+01 dihedral pdb=" CA LEU B 270 " pdb=" C LEU B 270 " pdb=" N SER B 271 " pdb=" CA SER B 271 " ideal model delta harmonic sigma weight residual 180.00 162.21 17.79 0 5.00e+00 4.00e-02 1.27e+01 ... (remaining 6501 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 960 0.029 - 0.059: 395 0.059 - 0.088: 177 0.088 - 0.117: 96 0.117 - 0.146: 16 Chirality restraints: 1644 Sorted by residual: chirality pdb=" CA VAL D 113 " pdb=" N VAL D 113 " pdb=" C VAL D 113 " pdb=" CB VAL D 113 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.36e-01 chirality pdb=" CA VAL C 113 " pdb=" N VAL C 113 " pdb=" C VAL C 113 " pdb=" CB VAL C 113 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.28e-01 chirality pdb=" CA VAL B 113 " pdb=" N VAL B 113 " pdb=" C VAL B 113 " pdb=" CB VAL B 113 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.15e-01 ... (remaining 1641 not shown) Planarity restraints: 1880 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS C 329 " 0.013 2.00e-02 2.50e+03 2.62e-02 6.87e+00 pdb=" C LYS C 329 " -0.045 2.00e-02 2.50e+03 pdb=" O LYS C 329 " 0.017 2.00e-02 2.50e+03 pdb=" N ARG C 330 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 329 " 0.013 2.00e-02 2.50e+03 2.62e-02 6.86e+00 pdb=" C LYS B 329 " -0.045 2.00e-02 2.50e+03 pdb=" O LYS B 329 " 0.017 2.00e-02 2.50e+03 pdb=" N ARG B 330 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 329 " -0.013 2.00e-02 2.50e+03 2.62e-02 6.84e+00 pdb=" C LYS A 329 " 0.045 2.00e-02 2.50e+03 pdb=" O LYS A 329 " -0.017 2.00e-02 2.50e+03 pdb=" N ARG A 330 " -0.015 2.00e-02 2.50e+03 ... (remaining 1877 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.82: 3100 2.82 - 3.34: 9356 3.34 - 3.86: 18013 3.86 - 4.38: 20884 4.38 - 4.90: 36001 Nonbonded interactions: 87354 Sorted by model distance: nonbonded pdb=" O ILE B 248 " pdb=" OG1 THR B 252 " model vdw 2.294 2.440 nonbonded pdb=" O ILE A 248 " pdb=" OG1 THR A 252 " model vdw 2.294 2.440 nonbonded pdb=" O ILE C 248 " pdb=" OG1 THR C 252 " model vdw 2.294 2.440 nonbonded pdb=" O ILE D 248 " pdb=" OG1 THR D 252 " model vdw 2.295 2.440 nonbonded pdb=" OE2 GLU D 277 " pdb=" OH TYR D 342 " model vdw 2.347 2.440 ... (remaining 87349 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: 1.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 6.240 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 30.940 Find NCS groups from input model: 0.680 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:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 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 : 0.004 0.064 10672 Z= 0.279 Angle : 0.761 9.454 14464 Z= 0.441 Chirality : 0.043 0.146 1644 Planarity : 0.008 0.059 1880 Dihedral : 13.663 87.383 3984 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 0.36 % Allowed : 7.82 % Favored : 91.82 % 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: -2.21 (0.19), residues: 1364 helix: -1.29 (0.15), residues: 672 sheet: -2.19 (0.33), residues: 204 loop : -1.04 (0.26), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP A 295 HIS 0.003 0.001 HIS B 245 PHE 0.016 0.002 PHE C 144 TYR 0.014 0.002 TYR A 213 ARG 0.003 0.000 ARG B 55 *********************** 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 217 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 213 time to evaluate : 1.297 Fit side-chains REVERT: B 250 MET cc_start: 0.7093 (tpp) cc_final: 0.6732 (tpt) REVERT: A 193 ASP cc_start: 0.8246 (m-30) cc_final: 0.7996 (p0) REVERT: A 250 MET cc_start: 0.7243 (tpp) cc_final: 0.7020 (tpt) REVERT: A 278 GLU cc_start: 0.6947 (pt0) cc_final: 0.6740 (pt0) REVERT: C 193 ASP cc_start: 0.8251 (m-30) cc_final: 0.7861 (p0) REVERT: C 250 MET cc_start: 0.7250 (tpp) cc_final: 0.7017 (tpt) REVERT: C 278 GLU cc_start: 0.6970 (pt0) cc_final: 0.6759 (pt0) REVERT: D 250 MET cc_start: 0.7124 (tpp) cc_final: 0.6757 (tpt) outliers start: 4 outliers final: 4 residues processed: 213 average time/residue: 0.2654 time to fit residues: 76.8676 Evaluate side-chains 154 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 150 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain D residue 252 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 114 optimal weight: 0.5980 chunk 103 optimal weight: 0.8980 chunk 57 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 chunk 69 optimal weight: 0.7980 chunk 55 optimal weight: 0.7980 chunk 106 optimal weight: 2.9990 chunk 41 optimal weight: 6.9990 chunk 64 optimal weight: 2.9990 chunk 79 optimal weight: 5.9990 chunk 123 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 60 GLN B 125 GLN B 324 GLN A 60 GLN A 125 GLN A 324 GLN C 60 GLN C 125 GLN ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 324 GLN D 60 GLN D 125 GLN D 324 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.1446 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= 0.183 Angle : 0.506 6.887 14464 Z= 0.261 Chirality : 0.040 0.135 1644 Planarity : 0.004 0.040 1880 Dihedral : 4.460 23.755 1476 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.44 % Allowed : 10.88 % Favored : 87.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.22), residues: 1364 helix: 0.75 (0.18), residues: 692 sheet: -2.16 (0.32), residues: 224 loop : -0.47 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 147 HIS 0.002 0.000 HIS B 156 PHE 0.007 0.001 PHE B 144 TYR 0.012 0.001 TYR A 213 ARG 0.005 0.000 ARG B 56 *********************** 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 196 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 180 time to evaluate : 1.167 Fit side-chains REVERT: B 56 ARG cc_start: 0.7690 (ttp80) cc_final: 0.7409 (ttt-90) REVERT: B 250 MET cc_start: 0.7312 (tpp) cc_final: 0.6908 (tpt) REVERT: A 193 ASP cc_start: 0.8303 (m-30) cc_final: 0.7966 (p0) REVERT: A 250 MET cc_start: 0.7415 (tpp) cc_final: 0.7214 (tpt) REVERT: C 193 ASP cc_start: 0.8306 (m-30) cc_final: 0.7898 (p0) REVERT: D 56 ARG cc_start: 0.7751 (ttp80) cc_final: 0.7485 (ttt-90) REVERT: D 250 MET cc_start: 0.7305 (tpp) cc_final: 0.6929 (tpt) outliers start: 16 outliers final: 8 residues processed: 186 average time/residue: 0.2583 time to fit residues: 66.0139 Evaluate side-chains 166 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 158 time to evaluate : 1.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 193 ASP Chi-restraints excluded: chain B residue 308 SER Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain C residue 164 MET Chi-restraints excluded: chain C residue 308 SER Chi-restraints excluded: chain D residue 193 ASP Chi-restraints excluded: chain D residue 308 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 68 optimal weight: 4.9990 chunk 38 optimal weight: 9.9990 chunk 102 optimal weight: 6.9990 chunk 84 optimal weight: 1.9990 chunk 34 optimal weight: 0.0970 chunk 123 optimal weight: 2.9990 chunk 133 optimal weight: 10.0000 chunk 110 optimal weight: 4.9990 chunk 122 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 99 optimal weight: 0.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 50 ASN B 274 GLN B 324 GLN A 274 GLN A 324 GLN C 231 ASN C 274 GLN C 324 GLN D 50 ASN D 274 GLN D 324 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10672 Z= 0.243 Angle : 0.494 5.787 14464 Z= 0.256 Chirality : 0.040 0.124 1644 Planarity : 0.004 0.035 1880 Dihedral : 4.177 15.483 1472 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.71 % Allowed : 12.14 % Favored : 86.15 % 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: 0.60 (0.23), residues: 1364 helix: 1.74 (0.19), residues: 692 sheet: -2.24 (0.31), residues: 224 loop : -0.12 (0.31), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 147 HIS 0.002 0.001 HIS C 20 PHE 0.008 0.001 PHE B 144 TYR 0.016 0.001 TYR B 213 ARG 0.004 0.001 ARG C 56 *********************** 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 185 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 166 time to evaluate : 1.077 Fit side-chains REVERT: B 56 ARG cc_start: 0.7636 (ttp80) cc_final: 0.7319 (ttt-90) REVERT: B 250 MET cc_start: 0.7330 (tpp) cc_final: 0.6983 (tpt) REVERT: A 193 ASP cc_start: 0.8359 (m-30) cc_final: 0.7931 (p0) REVERT: A 250 MET cc_start: 0.7372 (tpp) cc_final: 0.6991 (tpt) REVERT: C 193 ASP cc_start: 0.8327 (m-30) cc_final: 0.7828 (p0) REVERT: D 56 ARG cc_start: 0.7647 (ttp80) cc_final: 0.7378 (ttt-90) REVERT: D 250 MET cc_start: 0.7338 (tpp) cc_final: 0.7003 (tpt) outliers start: 19 outliers final: 17 residues processed: 176 average time/residue: 0.2548 time to fit residues: 60.9641 Evaluate side-chains 173 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 156 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 193 ASP Chi-restraints excluded: chain B residue 308 SER Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain C residue 164 MET Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 189 GLU Chi-restraints excluded: chain C residue 308 SER Chi-restraints excluded: chain D residue 45 SER Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 189 GLU Chi-restraints excluded: chain D residue 193 ASP Chi-restraints excluded: chain D residue 308 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 83 optimal weight: 0.7980 chunk 124 optimal weight: 0.8980 chunk 131 optimal weight: 2.9990 chunk 117 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 109 optimal weight: 4.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 50 ASN C 50 ASN ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10672 Z= 0.181 Angle : 0.452 5.751 14464 Z= 0.232 Chirality : 0.039 0.117 1644 Planarity : 0.003 0.033 1880 Dihedral : 3.950 15.954 1472 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.07 % Allowed : 13.13 % Favored : 84.80 % 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: 1.10 (0.23), residues: 1364 helix: 2.19 (0.19), residues: 688 sheet: -1.80 (0.33), residues: 204 loop : -0.18 (0.30), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 147 HIS 0.002 0.001 HIS D 156 PHE 0.015 0.001 PHE C 79 TYR 0.012 0.001 TYR B 213 ARG 0.006 0.000 ARG A 56 *********************** 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 195 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 172 time to evaluate : 1.121 Fit side-chains REVERT: B 56 ARG cc_start: 0.7607 (ttp80) cc_final: 0.7346 (ttt-90) REVERT: B 250 MET cc_start: 0.7317 (tpp) cc_final: 0.6954 (tpt) REVERT: A 193 ASP cc_start: 0.8367 (m-30) cc_final: 0.7897 (p0) REVERT: A 250 MET cc_start: 0.7361 (tpp) cc_final: 0.6968 (tpt) REVERT: C 193 ASP cc_start: 0.8332 (m-30) cc_final: 0.7798 (p0) REVERT: D 56 ARG cc_start: 0.7641 (ttp80) cc_final: 0.7364 (ttt-90) REVERT: D 250 MET cc_start: 0.7360 (tpp) cc_final: 0.6993 (tpt) outliers start: 23 outliers final: 16 residues processed: 184 average time/residue: 0.2814 time to fit residues: 69.8181 Evaluate side-chains 180 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 164 time to evaluate : 1.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 193 ASP Chi-restraints excluded: chain B residue 308 SER Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain C residue 156 HIS Chi-restraints excluded: chain C residue 164 MET Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 189 GLU Chi-restraints excluded: chain C residue 308 SER Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 189 GLU Chi-restraints excluded: chain D residue 193 ASP Chi-restraints excluded: chain D residue 308 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 74 optimal weight: 6.9990 chunk 1 optimal weight: 0.9980 chunk 97 optimal weight: 0.4980 chunk 54 optimal weight: 1.9990 chunk 112 optimal weight: 0.7980 chunk 90 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 117 optimal weight: 0.0980 chunk 33 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 10672 Z= 0.177 Angle : 0.448 6.514 14464 Z= 0.229 Chirality : 0.039 0.120 1644 Planarity : 0.003 0.032 1880 Dihedral : 3.865 15.389 1472 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.89 % Allowed : 12.95 % Favored : 85.16 % 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: 1.32 (0.23), residues: 1364 helix: 2.40 (0.19), residues: 688 sheet: -1.74 (0.33), residues: 204 loop : -0.11 (0.30), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 147 HIS 0.002 0.001 HIS A 156 PHE 0.010 0.001 PHE C 79 TYR 0.011 0.001 TYR C 213 ARG 0.003 0.000 ARG C 42 *********************** 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 188 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 167 time to evaluate : 1.251 Fit side-chains REVERT: B 56 ARG cc_start: 0.7572 (ttp80) cc_final: 0.7338 (ttt-90) REVERT: B 250 MET cc_start: 0.7307 (tpp) cc_final: 0.6934 (tpt) REVERT: A 193 ASP cc_start: 0.8360 (m-30) cc_final: 0.7825 (p0) REVERT: A 250 MET cc_start: 0.7360 (tpp) cc_final: 0.6954 (tpt) REVERT: D 250 MET cc_start: 0.7333 (tpp) cc_final: 0.6959 (tpt) outliers start: 21 outliers final: 16 residues processed: 178 average time/residue: 0.2894 time to fit residues: 69.2411 Evaluate side-chains 164 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 148 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 193 ASP Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 308 SER Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain C residue 156 HIS Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 189 GLU Chi-restraints excluded: chain C residue 308 SER Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 189 GLU Chi-restraints excluded: chain D residue 193 ASP Chi-restraints excluded: chain D residue 308 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 118 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 77 optimal weight: 0.0670 chunk 32 optimal weight: 4.9990 chunk 131 optimal weight: 1.9990 chunk 109 optimal weight: 0.0980 chunk 60 optimal weight: 0.5980 chunk 10 optimal weight: 3.9990 chunk 43 optimal weight: 0.9980 chunk 69 optimal weight: 0.9990 chunk 126 optimal weight: 4.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.2494 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= 0.145 Angle : 0.436 5.628 14464 Z= 0.225 Chirality : 0.039 0.117 1644 Planarity : 0.003 0.032 1880 Dihedral : 3.737 15.024 1472 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.98 % Allowed : 13.67 % Favored : 84.35 % 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: 1.59 (0.24), residues: 1364 helix: 2.64 (0.19), residues: 688 sheet: -1.62 (0.34), residues: 204 loop : -0.00 (0.30), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 295 HIS 0.002 0.000 HIS D 219 PHE 0.009 0.001 PHE C 79 TYR 0.009 0.001 TYR A 213 ARG 0.005 0.000 ARG D 56 *********************** 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 193 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 171 time to evaluate : 1.171 Fit side-chains REVERT: B 42 ARG cc_start: 0.7146 (ttm-80) cc_final: 0.6687 (mtt90) REVERT: B 56 ARG cc_start: 0.7590 (ttp80) cc_final: 0.7341 (ttt-90) REVERT: B 250 MET cc_start: 0.7304 (tpp) cc_final: 0.6920 (tpt) REVERT: A 250 MET cc_start: 0.7355 (tpp) cc_final: 0.6954 (tpt) REVERT: D 42 ARG cc_start: 0.7131 (ttm-80) cc_final: 0.6721 (mtt90) REVERT: D 250 MET cc_start: 0.7291 (tpp) cc_final: 0.6895 (tpt) outliers start: 22 outliers final: 17 residues processed: 183 average time/residue: 0.2914 time to fit residues: 71.3037 Evaluate side-chains 167 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 150 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 193 ASP Chi-restraints excluded: chain B residue 308 SER Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain C residue 156 HIS Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 189 GLU Chi-restraints excluded: chain C residue 193 ASP Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 308 SER Chi-restraints excluded: chain D residue 45 SER Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 189 GLU Chi-restraints excluded: chain D residue 193 ASP Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 308 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 14 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 110 optimal weight: 0.1980 chunk 73 optimal weight: 0.9980 chunk 131 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 10672 Z= 0.247 Angle : 0.480 5.644 14464 Z= 0.248 Chirality : 0.040 0.122 1644 Planarity : 0.004 0.031 1880 Dihedral : 3.868 15.480 1472 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.34 % Allowed : 14.30 % Favored : 83.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.23), residues: 1364 helix: 2.54 (0.19), residues: 688 sheet: -1.59 (0.34), residues: 200 loop : -0.12 (0.30), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 147 HIS 0.002 0.001 HIS C 156 PHE 0.010 0.001 PHE C 79 TYR 0.015 0.001 TYR A 213 ARG 0.007 0.001 ARG D 56 *********************** 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 174 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 148 time to evaluate : 1.227 Fit side-chains REVERT: B 250 MET cc_start: 0.7330 (tpp) cc_final: 0.6983 (tpt) REVERT: B 338 CYS cc_start: 0.7689 (t) cc_final: 0.7149 (t) REVERT: A 250 MET cc_start: 0.7389 (tpp) cc_final: 0.7026 (tpt) REVERT: A 338 CYS cc_start: 0.7759 (t) cc_final: 0.7312 (t) REVERT: C 338 CYS cc_start: 0.7771 (t) cc_final: 0.7334 (t) REVERT: D 34 GLU cc_start: 0.8378 (mp0) cc_final: 0.8065 (mp0) REVERT: D 250 MET cc_start: 0.7330 (tpp) cc_final: 0.6978 (tpt) REVERT: D 338 CYS cc_start: 0.7793 (t) cc_final: 0.7347 (t) outliers start: 26 outliers final: 23 residues processed: 163 average time/residue: 0.2860 time to fit residues: 62.7808 Evaluate side-chains 167 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 144 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 193 ASP Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 308 SER Chi-restraints excluded: chain A residue 156 HIS Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 189 GLU Chi-restraints excluded: chain C residue 193 ASP Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 308 SER Chi-restraints excluded: chain D residue 45 SER Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 189 GLU Chi-restraints excluded: chain D residue 193 ASP Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 308 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 83 optimal weight: 0.7980 chunk 89 optimal weight: 3.9990 chunk 64 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 119 optimal weight: 0.5980 chunk 125 optimal weight: 0.4980 chunk 114 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 168 ASN ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.2647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 10672 Z= 0.163 Angle : 0.450 5.650 14464 Z= 0.232 Chirality : 0.039 0.117 1644 Planarity : 0.003 0.032 1880 Dihedral : 3.733 14.912 1472 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.07 % Allowed : 15.02 % Favored : 82.91 % 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 (0.24), residues: 1364 helix: 2.72 (0.19), residues: 688 sheet: -1.51 (0.34), residues: 200 loop : 0.02 (0.31), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 295 HIS 0.002 0.000 HIS D 219 PHE 0.008 0.001 PHE C 79 TYR 0.011 0.001 TYR B 213 ARG 0.005 0.000 ARG B 56 *********************** 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 176 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 153 time to evaluate : 0.960 Fit side-chains REVERT: B 250 MET cc_start: 0.7286 (tpp) cc_final: 0.6916 (tpt) REVERT: B 338 CYS cc_start: 0.7694 (t) cc_final: 0.7252 (t) REVERT: A 250 MET cc_start: 0.7325 (tpp) cc_final: 0.6943 (tpt) REVERT: A 338 CYS cc_start: 0.7706 (t) cc_final: 0.7297 (t) REVERT: C 338 CYS cc_start: 0.7690 (t) cc_final: 0.7243 (t) REVERT: D 250 MET cc_start: 0.7281 (tpp) cc_final: 0.6903 (tpt) REVERT: D 338 CYS cc_start: 0.7716 (t) cc_final: 0.7267 (t) outliers start: 23 outliers final: 22 residues processed: 166 average time/residue: 0.2874 time to fit residues: 63.8932 Evaluate side-chains 172 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 150 time to evaluate : 1.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 193 ASP Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 308 SER Chi-restraints excluded: chain A residue 156 HIS Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 156 HIS Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 189 GLU Chi-restraints excluded: chain C residue 193 ASP Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain C residue 308 SER Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 189 GLU Chi-restraints excluded: chain D residue 193 ASP Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 308 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 3.9990 chunk 125 optimal weight: 0.0170 chunk 73 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 95 optimal weight: 6.9990 chunk 37 optimal weight: 6.9990 chunk 110 optimal weight: 1.9990 chunk 115 optimal weight: 0.6980 chunk 121 optimal weight: 0.0770 chunk 80 optimal weight: 0.5980 chunk 129 optimal weight: 4.9990 overall best weight: 0.4776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10672 Z= 0.146 Angle : 0.443 5.783 14464 Z= 0.230 Chirality : 0.039 0.117 1644 Planarity : 0.003 0.031 1880 Dihedral : 3.603 14.669 1472 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.07 % Allowed : 15.11 % Favored : 82.82 % 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: 1.87 (0.24), residues: 1364 helix: 2.87 (0.19), residues: 692 sheet: -1.64 (0.34), residues: 200 loop : 0.15 (0.31), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 295 HIS 0.002 0.000 HIS D 219 PHE 0.007 0.001 PHE D 79 TYR 0.012 0.001 TYR B 213 ARG 0.005 0.000 ARG B 56 *********************** 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 178 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 155 time to evaluate : 1.241 Fit side-chains REVERT: B 250 MET cc_start: 0.7304 (tpp) cc_final: 0.6922 (tpt) REVERT: B 338 CYS cc_start: 0.7690 (t) cc_final: 0.7272 (t) REVERT: A 250 MET cc_start: 0.7339 (tpp) cc_final: 0.6971 (tpt) REVERT: A 338 CYS cc_start: 0.7687 (t) cc_final: 0.7273 (t) REVERT: C 338 CYS cc_start: 0.7685 (t) cc_final: 0.7279 (t) REVERT: D 250 MET cc_start: 0.7301 (tpp) cc_final: 0.6916 (tpt) REVERT: D 338 CYS cc_start: 0.7708 (t) cc_final: 0.7276 (t) outliers start: 23 outliers final: 22 residues processed: 166 average time/residue: 0.2710 time to fit residues: 60.8690 Evaluate side-chains 170 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 148 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 193 ASP Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 308 SER Chi-restraints excluded: chain A residue 156 HIS Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 189 GLU Chi-restraints excluded: chain C residue 193 ASP Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 308 SER Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 189 GLU Chi-restraints excluded: chain D residue 193 ASP Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 308 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 0.1980 chunk 61 optimal weight: 1.9990 chunk 89 optimal weight: 0.5980 chunk 135 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 107 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 83 optimal weight: 0.0060 chunk 66 optimal weight: 1.9990 chunk 85 optimal weight: 0.7980 chunk 114 optimal weight: 0.7980 overall best weight: 0.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.2815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10672 Z= 0.145 Angle : 0.451 6.057 14464 Z= 0.235 Chirality : 0.038 0.115 1644 Planarity : 0.003 0.031 1880 Dihedral : 3.558 14.357 1472 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.80 % Allowed : 16.01 % Favored : 82.19 % 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: 1.97 (0.24), residues: 1364 helix: 2.95 (0.19), residues: 692 sheet: -1.63 (0.34), residues: 200 loop : 0.22 (0.31), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 295 HIS 0.003 0.000 HIS A 219 PHE 0.007 0.001 PHE B 144 TYR 0.016 0.001 TYR B 213 ARG 0.006 0.000 ARG B 56 ********************** 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 172 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 152 time to evaluate : 1.266 Fit side-chains REVERT: B 250 MET cc_start: 0.7335 (tpp) cc_final: 0.6968 (tpt) REVERT: B 338 CYS cc_start: 0.7620 (t) cc_final: 0.7149 (t) REVERT: A 250 MET cc_start: 0.7323 (tpp) cc_final: 0.6950 (tpt) REVERT: A 338 CYS cc_start: 0.7678 (t) cc_final: 0.7269 (t) REVERT: C 338 CYS cc_start: 0.7729 (t) cc_final: 0.7311 (t) REVERT: D 338 CYS cc_start: 0.7674 (t) cc_final: 0.7256 (t) outliers start: 20 outliers final: 20 residues processed: 162 average time/residue: 0.2761 time to fit residues: 61.2319 Evaluate side-chains 163 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 143 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 193 ASP Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 308 SER Chi-restraints excluded: chain A residue 156 HIS Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 189 GLU Chi-restraints excluded: chain C residue 193 ASP Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 308 SER Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 189 GLU Chi-restraints excluded: chain D residue 193 ASP Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 308 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 33 optimal weight: 3.9990 chunk 99 optimal weight: 3.9990 chunk 15 optimal weight: 0.4980 chunk 29 optimal weight: 3.9990 chunk 108 optimal weight: 7.9990 chunk 45 optimal weight: 0.7980 chunk 110 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 94 optimal weight: 0.7980 chunk 6 optimal weight: 5.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.144835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.117396 restraints weight = 13006.372| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 1.99 r_work: 0.3297 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.2855 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= 0.200 Angle : 0.483 6.107 14464 Z= 0.252 Chirality : 0.040 0.120 1644 Planarity : 0.003 0.031 1880 Dihedral : 3.672 14.749 1472 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.07 % Allowed : 16.01 % Favored : 81.92 % 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: 1.91 (0.24), residues: 1364 helix: 2.90 (0.19), residues: 692 sheet: -1.42 (0.36), residues: 180 loop : -0.01 (0.31), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 147 HIS 0.002 0.001 HIS B 220 PHE 0.008 0.001 PHE C 79 TYR 0.020 0.001 TYR A 213 ARG 0.003 0.000 ARG C 56 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2486.47 seconds wall clock time: 45 minutes 33.94 seconds (2733.94 seconds total)