Starting phenix.real_space_refine on Sun Sep 13 01:58:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6bqw_7134/09_2026/6bqw_7134.cif Found real_map, /net/cci-nas-00/data/ceres_data/6bqw_7134/09_2026/6bqw_7134.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6bqw_7134/09_2026/6bqw_7134.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6bqw_7134/09_2026/6bqw_7134.cif" model { file = "/net/cci-nas-00/data/ceres_data/6bqw_7134/09_2026/6bqw_7134.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6bqw_7134/09_2026/6bqw_7134.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6bqw_7134/09_2026/6bqw_7134.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6bqw_7134/09_2026/6bqw_7134.map" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 27 5.49 5 S 135 5.16 5 C 12681 2.51 5 N 3168 2.21 5 O 3942 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 153 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19953 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2186 Classifications: {'peptide': 275} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 5, 'TRANS': 267} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B, C, D, E, F, G, H, I Time building chain proxies: 2.70, per 1000 atoms: 0.14 Number of scatterers: 19953 At special positions: 0 Unit cell: (100, 100, 270, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 135 16.00 P 27 15.00 O 3942 8.00 N 3168 7.00 C 12681 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 - 3.00 Amino acid : True - 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: 1.80 Conformation dependent library (CDL) restraints added in 822.1 milliseconds 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4518 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 54 sheets defined 36.0% alpha, 25.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.75 Creating SS restraints... Processing helix chain 'A' and resid 60 through 65 Processing helix chain 'A' and resid 82 through 100 removed outlier: 4.051A pdb=" N ILE A 86 " --> pdb=" O MET A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 113 No H-bonds generated for 'chain 'A' and resid 111 through 113' Processing helix chain 'A' and resid 114 through 127 Processing helix chain 'A' and resid 152 through 158 Processing helix chain 'A' and resid 200 through 212 Processing helix chain 'A' and resid 227 through 239 Processing helix chain 'A' and resid 253 through 255 No H-bonds generated for 'chain 'A' and resid 253 through 255' Processing helix chain 'A' and resid 256 through 267 removed outlier: 3.904A pdb=" N VAL A 260 " --> pdb=" O TYR A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 275 removed outlier: 3.572A pdb=" N ALA A 275 " --> pdb=" O GLU A 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 65 Processing helix chain 'B' and resid 82 through 100 removed outlier: 4.051A pdb=" N ILE B 86 " --> pdb=" O MET B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 113 No H-bonds generated for 'chain 'B' and resid 111 through 113' Processing helix chain 'B' and resid 114 through 127 Processing helix chain 'B' and resid 152 through 158 Processing helix chain 'B' and resid 200 through 212 Processing helix chain 'B' and resid 227 through 239 Processing helix chain 'B' and resid 253 through 255 No H-bonds generated for 'chain 'B' and resid 253 through 255' Processing helix chain 'B' and resid 256 through 267 removed outlier: 3.904A pdb=" N VAL B 260 " --> pdb=" O TYR B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 275 removed outlier: 3.572A pdb=" N ALA B 275 " --> pdb=" O GLU B 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 65 Processing helix chain 'C' and resid 82 through 100 removed outlier: 4.051A pdb=" N ILE C 86 " --> pdb=" O MET C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 113 No H-bonds generated for 'chain 'C' and resid 111 through 113' Processing helix chain 'C' and resid 114 through 127 Processing helix chain 'C' and resid 152 through 158 Processing helix chain 'C' and resid 200 through 212 Processing helix chain 'C' and resid 227 through 239 Processing helix chain 'C' and resid 253 through 255 No H-bonds generated for 'chain 'C' and resid 253 through 255' Processing helix chain 'C' and resid 256 through 267 removed outlier: 3.904A pdb=" N VAL C 260 " --> pdb=" O TYR C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 275 removed outlier: 3.573A pdb=" N ALA C 275 " --> pdb=" O GLU C 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 60 through 65 Processing helix chain 'D' and resid 82 through 100 removed outlier: 4.051A pdb=" N ILE D 86 " --> pdb=" O MET D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 113 No H-bonds generated for 'chain 'D' and resid 111 through 113' Processing helix chain 'D' and resid 114 through 127 Processing helix chain 'D' and resid 152 through 158 Processing helix chain 'D' and resid 200 through 212 Processing helix chain 'D' and resid 227 through 239 Processing helix chain 'D' and resid 253 through 255 No H-bonds generated for 'chain 'D' and resid 253 through 255' Processing helix chain 'D' and resid 256 through 267 removed outlier: 3.904A pdb=" N VAL D 260 " --> pdb=" O TYR D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 275 removed outlier: 3.572A pdb=" N ALA D 275 " --> pdb=" O GLU D 271 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 65 Processing helix chain 'E' and resid 82 through 100 removed outlier: 4.050A pdb=" N ILE E 86 " --> pdb=" O MET E 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 113 No H-bonds generated for 'chain 'E' and resid 111 through 113' Processing helix chain 'E' and resid 114 through 127 Processing helix chain 'E' and resid 152 through 158 Processing helix chain 'E' and resid 200 through 212 Processing helix chain 'E' and resid 227 through 239 Processing helix chain 'E' and resid 253 through 255 No H-bonds generated for 'chain 'E' and resid 253 through 255' Processing helix chain 'E' and resid 256 through 267 removed outlier: 3.904A pdb=" N VAL E 260 " --> pdb=" O TYR E 256 " (cutoff:3.500A) Processing helix chain 'E' and resid 267 through 275 removed outlier: 3.572A pdb=" N ALA E 275 " --> pdb=" O GLU E 271 " (cutoff:3.500A) Processing helix chain 'F' and resid 60 through 65 Processing helix chain 'F' and resid 82 through 100 removed outlier: 4.050A pdb=" N ILE F 86 " --> pdb=" O MET F 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 111 through 113 No H-bonds generated for 'chain 'F' and resid 111 through 113' Processing helix chain 'F' and resid 114 through 127 Processing helix chain 'F' and resid 152 through 158 Processing helix chain 'F' and resid 200 through 212 Processing helix chain 'F' and resid 227 through 239 Processing helix chain 'F' and resid 253 through 255 No H-bonds generated for 'chain 'F' and resid 253 through 255' Processing helix chain 'F' and resid 256 through 267 removed outlier: 3.903A pdb=" N VAL F 260 " --> pdb=" O TYR F 256 " (cutoff:3.500A) Processing helix chain 'F' and resid 267 through 275 removed outlier: 3.572A pdb=" N ALA F 275 " --> pdb=" O GLU F 271 " (cutoff:3.500A) Processing helix chain 'G' and resid 60 through 65 Processing helix chain 'G' and resid 82 through 100 removed outlier: 4.051A pdb=" N ILE G 86 " --> pdb=" O MET G 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 113 No H-bonds generated for 'chain 'G' and resid 111 through 113' Processing helix chain 'G' and resid 114 through 127 Processing helix chain 'G' and resid 152 through 158 Processing helix chain 'G' and resid 200 through 212 Processing helix chain 'G' and resid 227 through 239 Processing helix chain 'G' and resid 253 through 255 No H-bonds generated for 'chain 'G' and resid 253 through 255' Processing helix chain 'G' and resid 256 through 267 removed outlier: 3.905A pdb=" N VAL G 260 " --> pdb=" O TYR G 256 " (cutoff:3.500A) Processing helix chain 'G' and resid 267 through 275 removed outlier: 3.572A pdb=" N ALA G 275 " --> pdb=" O GLU G 271 " (cutoff:3.500A) Processing helix chain 'H' and resid 60 through 65 Processing helix chain 'H' and resid 82 through 100 removed outlier: 4.050A pdb=" N ILE H 86 " --> pdb=" O MET H 82 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 113 No H-bonds generated for 'chain 'H' and resid 111 through 113' Processing helix chain 'H' and resid 114 through 127 Processing helix chain 'H' and resid 152 through 158 Processing helix chain 'H' and resid 200 through 212 Processing helix chain 'H' and resid 227 through 239 Processing helix chain 'H' and resid 253 through 255 No H-bonds generated for 'chain 'H' and resid 253 through 255' Processing helix chain 'H' and resid 256 through 267 removed outlier: 3.904A pdb=" N VAL H 260 " --> pdb=" O TYR H 256 " (cutoff:3.500A) Processing helix chain 'H' and resid 267 through 275 removed outlier: 3.572A pdb=" N ALA H 275 " --> pdb=" O GLU H 271 " (cutoff:3.500A) Processing helix chain 'I' and resid 60 through 65 Processing helix chain 'I' and resid 82 through 100 removed outlier: 4.050A pdb=" N ILE I 86 " --> pdb=" O MET I 82 " (cutoff:3.500A) Processing helix chain 'I' and resid 111 through 113 No H-bonds generated for 'chain 'I' and resid 111 through 113' Processing helix chain 'I' and resid 114 through 127 Processing helix chain 'I' and resid 152 through 158 Processing helix chain 'I' and resid 200 through 212 Processing helix chain 'I' and resid 227 through 239 Processing helix chain 'I' and resid 253 through 255 No H-bonds generated for 'chain 'I' and resid 253 through 255' Processing helix chain 'I' and resid 256 through 267 removed outlier: 3.904A pdb=" N VAL I 260 " --> pdb=" O TYR I 256 " (cutoff:3.500A) Processing helix chain 'I' and resid 267 through 275 removed outlier: 3.573A pdb=" N ALA I 275 " --> pdb=" O GLU I 271 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 26 Processing sheet with id=AA2, first strand: chain 'A' and resid 25 through 26 removed outlier: 4.633A pdb=" N VAL A 6 " --> pdb=" O ALA A 17 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N THR A 5 " --> pdb=" O ILE A 107 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N THR A 109 " --> pdb=" O THR A 5 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N ILE A 7 " --> pdb=" O THR A 109 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 33 through 35 Processing sheet with id=AA4, first strand: chain 'A' and resid 128 through 131 Processing sheet with id=AA5, first strand: chain 'A' and resid 183 through 184 Processing sheet with id=AA6, first strand: chain 'A' and resid 183 through 184 removed outlier: 6.787A pdb=" N VAL A 165 " --> pdb=" O VAL A 222 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N THR A 224 " --> pdb=" O VAL A 165 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N VAL A 167 " --> pdb=" O THR A 224 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 25 through 26 Processing sheet with id=AA8, first strand: chain 'B' and resid 25 through 26 removed outlier: 4.633A pdb=" N VAL B 6 " --> pdb=" O ALA B 17 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N THR B 5 " --> pdb=" O ILE B 107 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N THR B 109 " --> pdb=" O THR B 5 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N ILE B 7 " --> pdb=" O THR B 109 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 33 through 35 Processing sheet with id=AB1, first strand: chain 'B' and resid 128 through 131 Processing sheet with id=AB2, first strand: chain 'B' and resid 183 through 184 Processing sheet with id=AB3, first strand: chain 'B' and resid 183 through 184 removed outlier: 6.787A pdb=" N VAL B 165 " --> pdb=" O VAL B 222 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N THR B 224 " --> pdb=" O VAL B 165 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N VAL B 167 " --> pdb=" O THR B 224 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 25 through 26 Processing sheet with id=AB5, first strand: chain 'C' and resid 25 through 26 removed outlier: 4.633A pdb=" N VAL C 6 " --> pdb=" O ALA C 17 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N THR C 5 " --> pdb=" O ILE C 107 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N THR C 109 " --> pdb=" O THR C 5 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N ILE C 7 " --> pdb=" O THR C 109 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 33 through 35 Processing sheet with id=AB7, first strand: chain 'C' and resid 128 through 131 Processing sheet with id=AB8, first strand: chain 'C' and resid 183 through 184 Processing sheet with id=AB9, first strand: chain 'C' and resid 183 through 184 removed outlier: 6.787A pdb=" N VAL C 165 " --> pdb=" O VAL C 222 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N THR C 224 " --> pdb=" O VAL C 165 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N VAL C 167 " --> pdb=" O THR C 224 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 25 through 26 Processing sheet with id=AC2, first strand: chain 'D' and resid 25 through 26 removed outlier: 4.633A pdb=" N VAL D 6 " --> pdb=" O ALA D 17 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N THR D 5 " --> pdb=" O ILE D 107 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N THR D 109 " --> pdb=" O THR D 5 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N ILE D 7 " --> pdb=" O THR D 109 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 33 through 35 Processing sheet with id=AC4, first strand: chain 'D' and resid 128 through 131 Processing sheet with id=AC5, first strand: chain 'D' and resid 183 through 184 Processing sheet with id=AC6, first strand: chain 'D' and resid 183 through 184 removed outlier: 6.787A pdb=" N VAL D 165 " --> pdb=" O VAL D 222 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N THR D 224 " --> pdb=" O VAL D 165 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N VAL D 167 " --> pdb=" O THR D 224 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 25 through 26 Processing sheet with id=AC8, first strand: chain 'E' and resid 25 through 26 removed outlier: 4.632A pdb=" N VAL E 6 " --> pdb=" O ALA E 17 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N THR E 5 " --> pdb=" O ILE E 107 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N THR E 109 " --> pdb=" O THR E 5 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N ILE E 7 " --> pdb=" O THR E 109 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 33 through 35 Processing sheet with id=AD1, first strand: chain 'E' and resid 128 through 131 Processing sheet with id=AD2, first strand: chain 'E' and resid 183 through 184 Processing sheet with id=AD3, first strand: chain 'E' and resid 183 through 184 removed outlier: 6.787A pdb=" N VAL E 165 " --> pdb=" O VAL E 222 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N THR E 224 " --> pdb=" O VAL E 165 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N VAL E 167 " --> pdb=" O THR E 224 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 25 through 26 Processing sheet with id=AD5, first strand: chain 'F' and resid 25 through 26 removed outlier: 4.633A pdb=" N VAL F 6 " --> pdb=" O ALA F 17 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N THR F 5 " --> pdb=" O ILE F 107 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N THR F 109 " --> pdb=" O THR F 5 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N ILE F 7 " --> pdb=" O THR F 109 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 33 through 35 Processing sheet with id=AD7, first strand: chain 'F' and resid 128 through 131 Processing sheet with id=AD8, first strand: chain 'F' and resid 183 through 184 Processing sheet with id=AD9, first strand: chain 'F' and resid 183 through 184 removed outlier: 6.787A pdb=" N VAL F 165 " --> pdb=" O VAL F 222 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N THR F 224 " --> pdb=" O VAL F 165 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N VAL F 167 " --> pdb=" O THR F 224 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 25 through 26 Processing sheet with id=AE2, first strand: chain 'G' and resid 25 through 26 removed outlier: 4.633A pdb=" N VAL G 6 " --> pdb=" O ALA G 17 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N THR G 5 " --> pdb=" O ILE G 107 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N THR G 109 " --> pdb=" O THR G 5 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N ILE G 7 " --> pdb=" O THR G 109 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 33 through 35 Processing sheet with id=AE4, first strand: chain 'G' and resid 128 through 131 Processing sheet with id=AE5, first strand: chain 'G' and resid 183 through 184 Processing sheet with id=AE6, first strand: chain 'G' and resid 183 through 184 removed outlier: 6.787A pdb=" N VAL G 165 " --> pdb=" O VAL G 222 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N THR G 224 " --> pdb=" O VAL G 165 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N VAL G 167 " --> pdb=" O THR G 224 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'H' and resid 25 through 26 Processing sheet with id=AE8, first strand: chain 'H' and resid 25 through 26 removed outlier: 4.633A pdb=" N VAL H 6 " --> pdb=" O ALA H 17 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N THR H 5 " --> pdb=" O ILE H 107 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N THR H 109 " --> pdb=" O THR H 5 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N ILE H 7 " --> pdb=" O THR H 109 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'H' and resid 33 through 35 Processing sheet with id=AF1, first strand: chain 'H' and resid 128 through 131 Processing sheet with id=AF2, first strand: chain 'H' and resid 183 through 184 Processing sheet with id=AF3, first strand: chain 'H' and resid 183 through 184 removed outlier: 6.787A pdb=" N VAL H 165 " --> pdb=" O VAL H 222 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N THR H 224 " --> pdb=" O VAL H 165 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N VAL H 167 " --> pdb=" O THR H 224 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'I' and resid 25 through 26 Processing sheet with id=AF5, first strand: chain 'I' and resid 25 through 26 removed outlier: 4.633A pdb=" N VAL I 6 " --> pdb=" O ALA I 17 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N THR I 5 " --> pdb=" O ILE I 107 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N THR I 109 " --> pdb=" O THR I 5 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N ILE I 7 " --> pdb=" O THR I 109 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'I' and resid 33 through 35 Processing sheet with id=AF7, first strand: chain 'I' and resid 128 through 131 Processing sheet with id=AF8, first strand: chain 'I' and resid 183 through 184 Processing sheet with id=AF9, first strand: chain 'I' and resid 183 through 184 removed outlier: 6.787A pdb=" N VAL I 165 " --> pdb=" O VAL I 222 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N THR I 224 " --> pdb=" O VAL I 165 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N VAL I 167 " --> pdb=" O THR I 224 " (cutoff:3.500A) 918 hydrogen bonds defined for protein. 2322 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: 3.71 Time building geometry restraints manager: 2.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 5496 1.33 - 1.45: 4579 1.45 - 1.57: 10049 1.57 - 1.69: 18 1.69 - 1.82: 225 Bond restraints: 20367 Sorted by residual: bond pdb=" N3B ANP G 301 " pdb=" PG ANP G 301 " ideal model delta sigma weight residual 1.795 1.627 0.168 2.00e-02 2.50e+03 7.07e+01 bond pdb=" N3B ANP A 301 " pdb=" PG ANP A 301 " ideal model delta sigma weight residual 1.795 1.627 0.168 2.00e-02 2.50e+03 7.07e+01 bond pdb=" N3B ANP C 301 " pdb=" PG ANP C 301 " ideal model delta sigma weight residual 1.795 1.627 0.168 2.00e-02 2.50e+03 7.05e+01 bond pdb=" N3B ANP H 301 " pdb=" PG ANP H 301 " ideal model delta sigma weight residual 1.795 1.627 0.168 2.00e-02 2.50e+03 7.03e+01 bond pdb=" N3B ANP B 301 " pdb=" PG ANP B 301 " ideal model delta sigma weight residual 1.795 1.627 0.168 2.00e-02 2.50e+03 7.03e+01 ... (remaining 20362 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.81: 24313 1.81 - 3.61: 2610 3.61 - 5.42: 428 5.42 - 7.22: 57 7.22 - 9.03: 78 Bond angle restraints: 27486 Sorted by residual: angle pdb=" C LYS A 252 " pdb=" N PRO A 253 " pdb=" CA PRO A 253 " ideal model delta sigma weight residual 119.93 128.43 -8.50 1.07e+00 8.73e-01 6.31e+01 angle pdb=" C LYS E 252 " pdb=" N PRO E 253 " pdb=" CA PRO E 253 " ideal model delta sigma weight residual 119.93 128.43 -8.50 1.07e+00 8.73e-01 6.30e+01 angle pdb=" C LYS G 252 " pdb=" N PRO G 253 " pdb=" CA PRO G 253 " ideal model delta sigma weight residual 119.93 128.42 -8.49 1.07e+00 8.73e-01 6.30e+01 angle pdb=" C LYS I 252 " pdb=" N PRO I 253 " pdb=" CA PRO I 253 " ideal model delta sigma weight residual 119.93 128.41 -8.48 1.07e+00 8.73e-01 6.28e+01 angle pdb=" C LYS H 252 " pdb=" N PRO H 253 " pdb=" CA PRO H 253 " ideal model delta sigma weight residual 119.93 128.40 -8.47 1.07e+00 8.73e-01 6.27e+01 ... (remaining 27481 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.79: 11808 35.79 - 71.58: 126 71.58 - 107.37: 9 107.37 - 143.16: 0 143.16 - 178.95: 9 Dihedral angle restraints: 11952 sinusoidal: 4788 harmonic: 7164 Sorted by residual: dihedral pdb=" CA CYS H 164 " pdb=" C CYS H 164 " pdb=" N VAL H 165 " pdb=" CA VAL H 165 " ideal model delta harmonic sigma weight residual -180.00 -155.75 -24.25 0 5.00e+00 4.00e-02 2.35e+01 dihedral pdb=" CA CYS E 164 " pdb=" C CYS E 164 " pdb=" N VAL E 165 " pdb=" CA VAL E 165 " ideal model delta harmonic sigma weight residual 180.00 -155.76 -24.24 0 5.00e+00 4.00e-02 2.35e+01 dihedral pdb=" CA CYS D 164 " pdb=" C CYS D 164 " pdb=" N VAL D 165 " pdb=" CA VAL D 165 " ideal model delta harmonic sigma weight residual 180.00 -155.78 -24.22 0 5.00e+00 4.00e-02 2.35e+01 ... (remaining 11949 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 1739 0.061 - 0.123: 1002 0.123 - 0.184: 198 0.184 - 0.245: 22 0.245 - 0.307: 9 Chirality restraints: 2970 Sorted by residual: chirality pdb=" C2' ANP E 301 " pdb=" C1' ANP E 301 " pdb=" C3' ANP E 301 " pdb=" O2' ANP E 301 " both_signs ideal model delta sigma weight residual False -2.72 -2.42 -0.31 2.00e-01 2.50e+01 2.35e+00 chirality pdb=" C2' ANP D 301 " pdb=" C1' ANP D 301 " pdb=" C3' ANP D 301 " pdb=" O2' ANP D 301 " both_signs ideal model delta sigma weight residual False -2.72 -2.42 -0.31 2.00e-01 2.50e+01 2.35e+00 chirality pdb=" C2' ANP H 301 " pdb=" C1' ANP H 301 " pdb=" C3' ANP H 301 " pdb=" O2' ANP H 301 " both_signs ideal model delta sigma weight residual False -2.72 -2.42 -0.31 2.00e-01 2.50e+01 2.34e+00 ... (remaining 2967 not shown) Planarity restraints: 3447 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS A 164 " 0.012 2.00e-02 2.50e+03 2.49e-02 6.19e+00 pdb=" C CYS A 164 " -0.043 2.00e-02 2.50e+03 pdb=" O CYS A 164 " 0.016 2.00e-02 2.50e+03 pdb=" N VAL A 165 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS C 164 " -0.012 2.00e-02 2.50e+03 2.49e-02 6.19e+00 pdb=" C CYS C 164 " 0.043 2.00e-02 2.50e+03 pdb=" O CYS C 164 " -0.016 2.00e-02 2.50e+03 pdb=" N VAL C 165 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS D 164 " 0.012 2.00e-02 2.50e+03 2.48e-02 6.15e+00 pdb=" C CYS D 164 " -0.043 2.00e-02 2.50e+03 pdb=" O CYS D 164 " 0.016 2.00e-02 2.50e+03 pdb=" N VAL D 165 " 0.014 2.00e-02 2.50e+03 ... (remaining 3444 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 7458 2.83 - 3.34: 21057 3.34 - 3.86: 36382 3.86 - 4.38: 44731 4.38 - 4.90: 67976 Nonbonded interactions: 177604 Sorted by model distance: nonbonded pdb=" OG SER H 171 " pdb=" N LYS H 172 " model vdw 2.307 3.120 nonbonded pdb=" OG SER F 171 " pdb=" N LYS F 172 " model vdw 2.307 3.120 nonbonded pdb=" OG SER G 171 " pdb=" N LYS G 172 " model vdw 2.307 3.120 nonbonded pdb=" OG SER A 171 " pdb=" N LYS A 172 " model vdw 2.307 3.120 nonbonded pdb=" OG SER D 171 " pdb=" N LYS D 172 " model vdw 2.307 3.120 ... (remaining 177599 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.670 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: 0.020 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.030 Process input model: 17.420 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 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:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6781 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 : 0.016 0.168 20367 Z= 0.983 Angle : 1.278 9.026 27486 Z= 0.807 Chirality : 0.073 0.307 2970 Planarity : 0.006 0.025 3447 Dihedral : 13.449 178.952 7434 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 5.86 % Allowed : 10.26 % Favored : 83.88 % Rotamer: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.74 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.51 (0.14), residues: 2457 helix: -1.08 (0.16), residues: 747 sheet: -2.61 (0.17), residues: 432 loop : -3.07 (0.15), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 130 TYR 0.032 0.006 TYR G 56 PHE 0.010 0.003 PHE A 64 HIS 0.005 0.002 HIS A 34 Details of bonding type rmsd/Z covalent geometry : bond 0.01604 / 0.98 (20367) covalent geometry : angle 1.27816 / 0.81 (27486) hydrogen bonds : bond 0.15728 / 9.87 ( 882) hydrogen bonds : angle 9.90130 / 6.89 ( 2322) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 660 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 660 time to evaluate : 0.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 MET cc_start: 0.7448 (mmm) cc_final: 0.7104 (tpp) REVERT: B 48 VAL cc_start: 0.8139 (t) cc_final: 0.7653 (p) REVERT: B 88 LEU cc_start: 0.8119 (tp) cc_final: 0.7904 (tp) REVERT: B 95 ILE cc_start: 0.8275 (pt) cc_final: 0.7857 (pt) REVERT: C 187 MET cc_start: 0.5628 (ptt) cc_final: 0.5055 (ptp) REVERT: C 201 ILE cc_start: 0.8640 (mt) cc_final: 0.8393 (tp) REVERT: C 211 THR cc_start: 0.8373 (p) cc_final: 0.8057 (p) REVERT: C 235 LEU cc_start: 0.8170 (mt) cc_final: 0.7671 (mm) REVERT: C 259 SER cc_start: 0.8407 (p) cc_final: 0.8201 (t) REVERT: D 5 THR cc_start: 0.7657 (p) cc_final: 0.7451 (p) REVERT: D 32 ILE cc_start: 0.9129 (mt) cc_final: 0.7754 (mt) REVERT: D 180 ILE cc_start: 0.8687 (mt) cc_final: 0.8416 (pt) REVERT: D 202 MET cc_start: 0.7947 (mmm) cc_final: 0.7689 (tpp) REVERT: E 99 THR cc_start: 0.8487 (p) cc_final: 0.8171 (p) REVERT: E 159 SER cc_start: 0.8344 (m) cc_final: 0.8063 (p) REVERT: E 184 ILE cc_start: 0.8997 (mt) cc_final: 0.8776 (mt) REVERT: F 95 ILE cc_start: 0.8715 (pt) cc_final: 0.8253 (pt) REVERT: F 108 LEU cc_start: 0.8473 (mt) cc_final: 0.8124 (mt) REVERT: F 115 MET cc_start: 0.7695 (mtp) cc_final: 0.7297 (mtm) REVERT: F 159 SER cc_start: 0.8623 (m) cc_final: 0.8311 (p) REVERT: F 187 MET cc_start: 0.6185 (ptt) cc_final: 0.5636 (ptt) REVERT: F 259 SER cc_start: 0.8797 (p) cc_final: 0.8553 (p) REVERT: G 5 THR cc_start: 0.7288 (p) cc_final: 0.7019 (p) REVERT: G 95 ILE cc_start: 0.8708 (pt) cc_final: 0.8325 (pt) REVERT: H 88 LEU cc_start: 0.7980 (tp) cc_final: 0.7687 (tp) REVERT: H 222 VAL cc_start: 0.7908 (t) cc_final: 0.7682 (t) REVERT: H 235 LEU cc_start: 0.8311 (mt) cc_final: 0.7363 (mt) REVERT: I 211 THR cc_start: 0.8198 (p) cc_final: 0.7541 (p) outliers start: 0 outliers final: 0 residues processed: 660 average time/residue: 0.1772 time to fit residues: 169.7970 Evaluate side-chains 373 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 373 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 216 optimal weight: 0.9980 chunk 98 optimal weight: 6.9990 chunk 194 optimal weight: 2.9990 chunk 227 optimal weight: 3.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.9990 chunk 235 optimal weight: 0.9980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 105 ASN A 144 HIS A 163 ASN ** B 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 34 HIS ** C 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 105 ASN ** D 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 105 ASN ** D 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 34 HIS ** E 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 105 ASN E 144 HIS E 163 ASN ** F 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 63 ASN ** F 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 105 ASN G 23 GLN G 34 HIS ** G 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 105 ASN H 34 HIS ** H 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 105 ASN H 163 ASN ** I 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.065057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.051912 restraints weight = 96401.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.053929 restraints weight = 49513.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.055288 restraints weight = 30250.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.056211 restraints weight = 20573.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.056865 restraints weight = 15220.115| |-----------------------------------------------------------------------------| r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.3801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20367 Z= 0.170 Angle : 0.778 8.988 27486 Z= 0.424 Chirality : 0.048 0.193 2970 Planarity : 0.004 0.033 3447 Dihedral : 12.184 179.948 2745 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 19.38 Ramachandran Plot: Outliers : 2.44 % Allowed : 11.64 % Favored : 85.92 % Rotamer: Outliers : 0.14 % Allowed : 3.29 % Favored : 96.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.74 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.99 (0.16), residues: 2457 helix: 0.39 (0.18), residues: 693 sheet: -2.53 (0.18), residues: 549 loop : -1.70 (0.18), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 87 TYR 0.023 0.002 TYR E 256 PHE 0.028 0.002 PHE E 158 HIS 0.005 0.001 HIS I 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.17 (20367) covalent geometry : angle 0.77761 / 0.42 (27486) hydrogen bonds : bond 0.04728 / 3.00 ( 882) hydrogen bonds : angle 7.15263 / 5.02 ( 2322) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 486 time to evaluate : 0.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 GLN cc_start: 0.9117 (tt0) cc_final: 0.8899 (tt0) REVERT: A 73 TYR cc_start: 0.8169 (m-80) cc_final: 0.7966 (m-80) REVERT: A 186 LYS cc_start: 0.9351 (tttt) cc_final: 0.9143 (tttm) REVERT: A 202 MET cc_start: 0.6852 (mmm) cc_final: 0.6579 (tpp) REVERT: A 227 LYS cc_start: 0.9368 (mmtt) cc_final: 0.9151 (mmmm) REVERT: A 231 MET cc_start: 0.8859 (tpp) cc_final: 0.8600 (tpp) REVERT: B 98 GLU cc_start: 0.8742 (mt-10) cc_final: 0.8295 (pt0) REVERT: B 115 MET cc_start: 0.8803 (ttm) cc_final: 0.8370 (tpp) REVERT: B 141 PHE cc_start: 0.9013 (p90) cc_final: 0.8575 (p90) REVERT: C 46 GLU cc_start: 0.8024 (mp0) cc_final: 0.7732 (mp0) REVERT: C 63 ASN cc_start: 0.8863 (m110) cc_final: 0.8423 (t0) REVERT: C 98 GLU cc_start: 0.8678 (pt0) cc_final: 0.8332 (pt0) REVERT: C 151 GLU cc_start: 0.7711 (tt0) cc_final: 0.7509 (mt-10) REVERT: C 177 LEU cc_start: 0.8956 (tp) cc_final: 0.8654 (tp) REVERT: C 259 SER cc_start: 0.9286 (p) cc_final: 0.8694 (t) REVERT: D 46 GLU cc_start: 0.8592 (mp0) cc_final: 0.8052 (mp0) REVERT: D 88 LEU cc_start: 0.9767 (tp) cc_final: 0.9555 (tp) REVERT: D 106 LEU cc_start: 0.8735 (tp) cc_final: 0.8487 (tp) REVERT: D 124 GLN cc_start: 0.9195 (tm-30) cc_final: 0.8947 (tm-30) REVERT: D 148 MET cc_start: 0.7368 (tpt) cc_final: 0.6897 (mmm) REVERT: D 153 LEU cc_start: 0.9195 (mt) cc_final: 0.8977 (mt) REVERT: D 204 LEU cc_start: 0.8946 (mt) cc_final: 0.8582 (mt) REVERT: E 68 ARG cc_start: 0.8512 (mmt90) cc_final: 0.8108 (mmt90) REVERT: E 87 ARG cc_start: 0.9223 (mtt-85) cc_final: 0.8976 (ptp-110) REVERT: E 88 LEU cc_start: 0.9740 (tp) cc_final: 0.9479 (tp) REVERT: E 95 ILE cc_start: 0.9283 (pt) cc_final: 0.9004 (mt) REVERT: E 148 MET cc_start: 0.8033 (mmm) cc_final: 0.6985 (mmm) REVERT: E 159 SER cc_start: 0.8266 (m) cc_final: 0.7891 (p) REVERT: E 163 ASN cc_start: 0.6819 (m110) cc_final: 0.5649 (m110) REVERT: E 202 MET cc_start: 0.7361 (mmm) cc_final: 0.6872 (mmm) REVERT: E 248 LEU cc_start: 0.9057 (tp) cc_final: 0.8817 (tp) REVERT: E 259 SER cc_start: 0.9105 (p) cc_final: 0.8773 (t) REVERT: F 23 GLN cc_start: 0.8471 (tt0) cc_final: 0.8214 (tt0) REVERT: F 46 GLU cc_start: 0.8500 (mp0) cc_final: 0.8195 (mp0) REVERT: F 73 TYR cc_start: 0.7887 (m-80) cc_final: 0.7264 (m-80) REVERT: F 98 GLU cc_start: 0.8474 (pt0) cc_final: 0.8207 (pt0) REVERT: F 106 LEU cc_start: 0.8663 (tp) cc_final: 0.8401 (tp) REVERT: F 108 LEU cc_start: 0.9092 (mt) cc_final: 0.8783 (mt) REVERT: F 118 ASP cc_start: 0.8172 (m-30) cc_final: 0.7622 (m-30) REVERT: F 126 PHE cc_start: 0.8340 (m-80) cc_final: 0.8108 (m-80) REVERT: F 159 SER cc_start: 0.8798 (m) cc_final: 0.8447 (p) REVERT: F 187 MET cc_start: 0.6323 (ptt) cc_final: 0.6092 (ptt) REVERT: F 259 SER cc_start: 0.9367 (p) cc_final: 0.8973 (t) REVERT: G 1 MET cc_start: 0.7423 (mtm) cc_final: 0.6568 (mpp) REVERT: G 46 GLU cc_start: 0.8993 (mp0) cc_final: 0.8582 (mp0) REVERT: G 83 GLU cc_start: 0.8153 (pt0) cc_final: 0.7587 (pt0) REVERT: G 98 GLU cc_start: 0.8676 (pt0) cc_final: 0.8058 (pt0) REVERT: G 108 LEU cc_start: 0.9451 (mt) cc_final: 0.9214 (mt) REVERT: G 116 VAL cc_start: 0.8958 (t) cc_final: 0.8634 (m) REVERT: G 124 GLN cc_start: 0.8958 (tm-30) cc_final: 0.8623 (tm-30) REVERT: H 47 ARG cc_start: 0.7790 (mtt90) cc_final: 0.7537 (mpt180) REVERT: H 82 MET cc_start: 0.9428 (ttm) cc_final: 0.9074 (ttm) REVERT: H 83 GLU cc_start: 0.8869 (mp0) cc_final: 0.8572 (mp0) REVERT: H 88 LEU cc_start: 0.9292 (tp) cc_final: 0.8970 (tp) REVERT: H 126 PHE cc_start: 0.8131 (m-80) cc_final: 0.7894 (m-10) REVERT: H 231 MET cc_start: 0.9207 (tpt) cc_final: 0.8567 (tpp) REVERT: H 266 TYR cc_start: 0.9035 (m-10) cc_final: 0.8669 (m-10) REVERT: I 47 ARG cc_start: 0.8363 (mtm180) cc_final: 0.8070 (mtt180) REVERT: I 179 LEU cc_start: 0.9224 (tt) cc_final: 0.8773 (mm) outliers start: 3 outliers final: 0 residues processed: 487 average time/residue: 0.1556 time to fit residues: 112.3479 Evaluate side-chains 340 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 340 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 238 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 54 optimal weight: 10.0000 chunk 76 optimal weight: 9.9990 chunk 24 optimal weight: 6.9990 chunk 171 optimal weight: 0.9990 chunk 83 optimal weight: 0.9980 chunk 43 optimal weight: 30.0000 chunk 227 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 61 optimal weight: 5.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 144 HIS B 63 ASN C 63 ASN ** C 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 144 HIS ** D 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 144 HIS ** E 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 163 ASN ** F 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 144 HIS ** H 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.063031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.050360 restraints weight = 98854.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.052260 restraints weight = 52351.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.053530 restraints weight = 32572.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.054396 restraints weight = 22498.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.054974 restraints weight = 16824.672| |-----------------------------------------------------------------------------| r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.4750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 20367 Z= 0.183 Angle : 0.718 6.595 27486 Z= 0.392 Chirality : 0.047 0.169 2970 Planarity : 0.004 0.074 3447 Dihedral : 11.880 178.563 2745 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 19.83 Ramachandran Plot: Outliers : 2.32 % Allowed : 11.64 % Favored : 86.04 % Rotamer: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.74 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.95 (0.16), residues: 2457 helix: 0.08 (0.18), residues: 756 sheet: -2.27 (0.20), residues: 450 loop : -1.77 (0.18), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 87 TYR 0.023 0.002 TYR H 56 PHE 0.026 0.002 PHE E 104 HIS 0.008 0.001 HIS I 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.18 (20367) covalent geometry : angle 0.71792 / 0.39 (27486) hydrogen bonds : bond 0.04227 / 2.65 ( 882) hydrogen bonds : angle 6.61237 / 4.64 ( 2322) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 417 time to evaluate : 0.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 GLN cc_start: 0.9092 (tt0) cc_final: 0.8869 (tt0) REVERT: A 87 ARG cc_start: 0.9172 (mtt-85) cc_final: 0.8821 (ptp-110) REVERT: A 115 MET cc_start: 0.8422 (mtp) cc_final: 0.8043 (mtt) REVERT: A 211 THR cc_start: 0.8875 (p) cc_final: 0.8156 (p) REVERT: A 231 MET cc_start: 0.8849 (tpp) cc_final: 0.8609 (tpp) REVERT: A 259 SER cc_start: 0.9241 (p) cc_final: 0.9029 (p) REVERT: B 7 ILE cc_start: 0.8471 (mp) cc_final: 0.8265 (mm) REVERT: B 73 TYR cc_start: 0.7892 (m-80) cc_final: 0.7286 (m-80) REVERT: B 88 LEU cc_start: 0.9517 (tp) cc_final: 0.9253 (tp) REVERT: B 98 GLU cc_start: 0.8770 (mt-10) cc_final: 0.8365 (pt0) REVERT: B 109 THR cc_start: 0.8324 (p) cc_final: 0.8044 (t) REVERT: B 115 MET cc_start: 0.8904 (ttm) cc_final: 0.8425 (tpp) REVERT: B 126 PHE cc_start: 0.9164 (m-80) cc_final: 0.8933 (m-80) REVERT: B 139 PHE cc_start: 0.7806 (t80) cc_final: 0.7055 (t80) REVERT: B 141 PHE cc_start: 0.9047 (p90) cc_final: 0.7700 (p90) REVERT: C 46 GLU cc_start: 0.8022 (mp0) cc_final: 0.7702 (mp0) REVERT: C 63 ASN cc_start: 0.8998 (m-40) cc_final: 0.8511 (t0) REVERT: C 73 TYR cc_start: 0.8105 (m-80) cc_final: 0.7580 (m-80) REVERT: C 88 LEU cc_start: 0.9698 (tp) cc_final: 0.9394 (tp) REVERT: C 98 GLU cc_start: 0.8712 (pt0) cc_final: 0.8508 (pt0) REVERT: C 115 MET cc_start: 0.8647 (mmm) cc_final: 0.8319 (mmm) REVERT: C 177 LEU cc_start: 0.9025 (tp) cc_final: 0.8736 (tp) REVERT: C 259 SER cc_start: 0.9191 (p) cc_final: 0.8575 (t) REVERT: D 46 GLU cc_start: 0.8593 (mp0) cc_final: 0.8212 (mp0) REVERT: D 47 ARG cc_start: 0.6932 (mpt180) cc_final: 0.6731 (mpt180) REVERT: D 98 GLU cc_start: 0.8582 (tp30) cc_final: 0.8212 (tm-30) REVERT: D 124 GLN cc_start: 0.9201 (tm-30) cc_final: 0.8919 (tm-30) REVERT: E 1 MET cc_start: 0.8542 (mtp) cc_final: 0.8293 (ttp) REVERT: E 62 LYS cc_start: 0.9286 (mmmm) cc_final: 0.8889 (mptt) REVERT: E 88 LEU cc_start: 0.9677 (tp) cc_final: 0.9469 (tp) REVERT: E 108 LEU cc_start: 0.9596 (mt) cc_final: 0.9390 (mt) REVERT: E 115 MET cc_start: 0.8214 (tpp) cc_final: 0.7599 (tpp) REVERT: E 148 MET cc_start: 0.8066 (mmm) cc_final: 0.7360 (mmm) REVERT: E 259 SER cc_start: 0.9109 (p) cc_final: 0.8813 (t) REVERT: F 23 GLN cc_start: 0.8390 (tt0) cc_final: 0.8084 (tt0) REVERT: F 46 GLU cc_start: 0.8368 (mp0) cc_final: 0.8072 (mp0) REVERT: F 73 TYR cc_start: 0.8060 (m-80) cc_final: 0.7508 (m-80) REVERT: F 108 LEU cc_start: 0.9183 (mt) cc_final: 0.8860 (mt) REVERT: F 115 MET cc_start: 0.8912 (tpp) cc_final: 0.8438 (tpp) REVERT: F 139 PHE cc_start: 0.8412 (t80) cc_final: 0.8077 (t80) REVERT: F 159 SER cc_start: 0.8817 (m) cc_final: 0.8482 (p) REVERT: F 259 SER cc_start: 0.9329 (p) cc_final: 0.8994 (t) REVERT: G 46 GLU cc_start: 0.8881 (mp0) cc_final: 0.8643 (mp0) REVERT: G 106 LEU cc_start: 0.8640 (tp) cc_final: 0.8406 (tp) REVERT: G 107 ILE cc_start: 0.9291 (mt) cc_final: 0.9003 (mm) REVERT: G 108 LEU cc_start: 0.9477 (mt) cc_final: 0.8572 (mt) REVERT: G 115 MET cc_start: 0.7862 (tpp) cc_final: 0.7601 (tpp) REVERT: G 124 GLN cc_start: 0.9155 (tm-30) cc_final: 0.8758 (tm-30) REVERT: G 231 MET cc_start: 0.9106 (tpp) cc_final: 0.8804 (tpp) REVERT: H 47 ARG cc_start: 0.7947 (mtt90) cc_final: 0.7591 (mpt180) REVERT: H 82 MET cc_start: 0.9312 (ttm) cc_final: 0.8985 (ttm) REVERT: H 88 LEU cc_start: 0.9321 (tp) cc_final: 0.9020 (tp) REVERT: H 148 MET cc_start: 0.7534 (tpt) cc_final: 0.6852 (tpp) REVERT: H 231 MET cc_start: 0.9196 (tpt) cc_final: 0.8946 (tpt) REVERT: I 115 MET cc_start: 0.8502 (mmm) cc_final: 0.8074 (mpp) REVERT: I 179 LEU cc_start: 0.9154 (tt) cc_final: 0.8744 (mm) REVERT: I 231 MET cc_start: 0.9349 (tpp) cc_final: 0.9123 (mmm) outliers start: 0 outliers final: 0 residues processed: 417 average time/residue: 0.1617 time to fit residues: 101.1658 Evaluate side-chains 298 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 298 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 69 optimal weight: 0.9990 chunk 19 optimal weight: 10.0000 chunk 202 optimal weight: 0.0980 chunk 98 optimal weight: 9.9990 chunk 91 optimal weight: 4.9990 chunk 30 optimal weight: 10.0000 chunk 230 optimal weight: 9.9990 chunk 104 optimal weight: 4.9990 chunk 74 optimal weight: 0.2980 chunk 77 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 23 GLN C 63 ASN ** D 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 163 ASN ** F 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 144 HIS ** G 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 163 ASN ** H 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 144 HIS ** H 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.065145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.052422 restraints weight = 96574.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.054383 restraints weight = 51633.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.055657 restraints weight = 32234.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.056594 restraints weight = 22478.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.057239 restraints weight = 16759.794| |-----------------------------------------------------------------------------| r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.5367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 20367 Z= 0.141 Angle : 0.677 7.671 27486 Z= 0.368 Chirality : 0.046 0.168 2970 Planarity : 0.004 0.037 3447 Dihedral : 11.764 179.066 2745 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 17.80 Ramachandran Plot: Outliers : 1.75 % Allowed : 11.76 % Favored : 86.49 % Rotamer: Outliers : 0.05 % Allowed : 2.18 % Favored : 97.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.74 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.82 (0.16), residues: 2457 helix: 0.16 (0.18), residues: 783 sheet: -2.00 (0.21), residues: 450 loop : -1.79 (0.18), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 87 TYR 0.027 0.002 TYR G 56 PHE 0.027 0.002 PHE F 270 HIS 0.008 0.001 HIS F 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.14 (20367) covalent geometry : angle 0.67696 / 0.37 (27486) hydrogen bonds : bond 0.03976 / 2.51 ( 882) hydrogen bonds : angle 6.29750 / 4.44 ( 2322) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 402 time to evaluate : 0.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 TYR cc_start: 0.7990 (m-80) cc_final: 0.7354 (m-80) REVERT: A 211 THR cc_start: 0.8687 (p) cc_final: 0.8245 (p) REVERT: A 231 MET cc_start: 0.8855 (tpp) cc_final: 0.8586 (tpp) REVERT: B 1 MET cc_start: 0.8727 (mtm) cc_final: 0.8331 (mtm) REVERT: B 63 ASN cc_start: 0.8575 (m-40) cc_final: 0.8308 (t0) REVERT: B 73 TYR cc_start: 0.7756 (m-80) cc_final: 0.7530 (m-80) REVERT: B 88 LEU cc_start: 0.9489 (tp) cc_final: 0.9268 (tp) REVERT: B 98 GLU cc_start: 0.8782 (mt-10) cc_final: 0.8396 (pt0) REVERT: B 109 THR cc_start: 0.8317 (p) cc_final: 0.8088 (t) REVERT: B 115 MET cc_start: 0.8936 (ttm) cc_final: 0.8466 (tpp) REVERT: B 139 PHE cc_start: 0.7632 (t80) cc_final: 0.7004 (t80) REVERT: B 141 PHE cc_start: 0.8987 (p90) cc_final: 0.7767 (p90) REVERT: C 63 ASN cc_start: 0.8820 (m110) cc_final: 0.8373 (m-40) REVERT: C 88 LEU cc_start: 0.9657 (tp) cc_final: 0.9437 (tp) REVERT: C 177 LEU cc_start: 0.9148 (tp) cc_final: 0.8888 (tp) REVERT: C 202 MET cc_start: 0.7802 (mmm) cc_final: 0.6190 (mmm) REVERT: C 259 SER cc_start: 0.9259 (p) cc_final: 0.8798 (t) REVERT: D 46 GLU cc_start: 0.8524 (mp0) cc_final: 0.8120 (mp0) REVERT: D 98 GLU cc_start: 0.8471 (tp30) cc_final: 0.8159 (tt0) REVERT: D 124 GLN cc_start: 0.9214 (tm-30) cc_final: 0.8951 (tm-30) REVERT: D 145 ASN cc_start: 0.8218 (m-40) cc_final: 0.7968 (t0) REVERT: D 148 MET cc_start: 0.7656 (tpt) cc_final: 0.7408 (mmm) REVERT: D 268 ARG cc_start: 0.8645 (mmm-85) cc_final: 0.8393 (mmm160) REVERT: E 46 GLU cc_start: 0.7766 (mm-30) cc_final: 0.7451 (mm-30) REVERT: E 88 LEU cc_start: 0.9709 (tp) cc_final: 0.9494 (tp) REVERT: E 115 MET cc_start: 0.8383 (tpp) cc_final: 0.7865 (tpp) REVERT: E 148 MET cc_start: 0.8057 (mmm) cc_final: 0.7341 (mmm) REVERT: E 202 MET cc_start: 0.7310 (mmm) cc_final: 0.6996 (mmm) REVERT: F 8 ASP cc_start: 0.8698 (t0) cc_final: 0.8396 (t0) REVERT: F 73 TYR cc_start: 0.8100 (m-80) cc_final: 0.7404 (m-80) REVERT: F 108 LEU cc_start: 0.9137 (mt) cc_final: 0.8870 (mt) REVERT: F 115 MET cc_start: 0.9018 (tpp) cc_final: 0.8360 (tpp) REVERT: F 118 ASP cc_start: 0.8041 (m-30) cc_final: 0.7831 (m-30) REVERT: F 139 PHE cc_start: 0.8339 (t80) cc_final: 0.7991 (t80) REVERT: F 159 SER cc_start: 0.8794 (m) cc_final: 0.8514 (p) REVERT: F 184 ILE cc_start: 0.9418 (mp) cc_final: 0.9089 (tt) REVERT: F 259 SER cc_start: 0.9229 (p) cc_final: 0.9003 (t) REVERT: G 62 LYS cc_start: 0.9040 (mttt) cc_final: 0.8748 (mmmt) REVERT: G 78 ARG cc_start: 0.6640 (pmt170) cc_final: 0.6378 (pmt170) REVERT: G 98 GLU cc_start: 0.8740 (pt0) cc_final: 0.8448 (pt0) REVERT: G 108 LEU cc_start: 0.9075 (mt) cc_final: 0.8627 (mt) REVERT: G 115 MET cc_start: 0.8167 (tpp) cc_final: 0.6345 (tpp) REVERT: G 124 GLN cc_start: 0.9146 (tm-30) cc_final: 0.8778 (tm-30) REVERT: G 148 MET cc_start: 0.7849 (mmm) cc_final: 0.7558 (ttm) REVERT: G 231 MET cc_start: 0.9184 (tpp) cc_final: 0.8566 (tpp) REVERT: H 47 ARG cc_start: 0.7985 (mtt90) cc_final: 0.7569 (mpt180) REVERT: H 83 GLU cc_start: 0.8812 (mp0) cc_final: 0.8242 (mp0) REVERT: H 88 LEU cc_start: 0.9344 (tp) cc_final: 0.9136 (tp) REVERT: H 101 LYS cc_start: 0.6011 (mptt) cc_final: 0.5630 (mptt) REVERT: H 115 MET cc_start: 0.8218 (tpp) cc_final: 0.6798 (tpp) REVERT: H 151 GLU cc_start: 0.8569 (mt-10) cc_final: 0.8295 (mt-10) REVERT: H 266 TYR cc_start: 0.8883 (m-10) cc_final: 0.8616 (m-10) REVERT: I 1 MET cc_start: 0.3270 (tpt) cc_final: 0.1490 (tmm) REVERT: I 45 MET cc_start: 0.3069 (mtm) cc_final: 0.2738 (mtm) REVERT: I 148 MET cc_start: 0.6239 (tpp) cc_final: 0.5829 (tpt) REVERT: I 179 LEU cc_start: 0.9067 (tt) cc_final: 0.8768 (mm) outliers start: 1 outliers final: 0 residues processed: 402 average time/residue: 0.1597 time to fit residues: 97.5989 Evaluate side-chains 301 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 301 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 180 optimal weight: 5.9990 chunk 65 optimal weight: 3.9990 chunk 241 optimal weight: 8.9990 chunk 70 optimal weight: 10.0000 chunk 26 optimal weight: 6.9990 chunk 93 optimal weight: 8.9990 chunk 101 optimal weight: 0.7980 chunk 2 optimal weight: 10.0000 chunk 16 optimal weight: 10.0000 chunk 136 optimal weight: 5.9990 chunk 88 optimal weight: 0.6980 overall best weight: 3.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 163 ASN ** F 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.061748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.049215 restraints weight = 99834.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.051031 restraints weight = 53746.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.052284 restraints weight = 33897.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.053124 restraints weight = 23609.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.053718 restraints weight = 17809.884| |-----------------------------------------------------------------------------| r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.5768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 20367 Z= 0.230 Angle : 0.735 7.407 27486 Z= 0.397 Chirality : 0.047 0.244 2970 Planarity : 0.004 0.042 3447 Dihedral : 11.627 171.590 2745 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 20.83 Ramachandran Plot: Outliers : 1.59 % Allowed : 13.02 % Favored : 85.39 % Rotamer: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.74 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.62 (0.16), residues: 2457 helix: 0.67 (0.19), residues: 684 sheet: -1.81 (0.22), residues: 495 loop : -1.76 (0.17), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 87 TYR 0.030 0.002 TYR G 90 PHE 0.027 0.002 PHE E 270 HIS 0.008 0.002 HIS C 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00489 / 0.23 (20367) covalent geometry : angle 0.73477 / 0.40 (27486) hydrogen bonds : bond 0.04149 / 2.62 ( 882) hydrogen bonds : angle 6.28586 / 4.39 ( 2322) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 357 time to evaluate : 0.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7838 (mtm) cc_final: 0.7588 (mtm) REVERT: A 22 LYS cc_start: 0.9249 (mppt) cc_final: 0.9016 (mptt) REVERT: A 23 GLN cc_start: 0.9110 (tt0) cc_final: 0.8899 (tt0) REVERT: A 231 MET cc_start: 0.8893 (tpp) cc_final: 0.8598 (tpp) REVERT: B 72 MET cc_start: 0.8721 (mpp) cc_final: 0.8468 (mpp) REVERT: B 98 GLU cc_start: 0.8876 (mt-10) cc_final: 0.8501 (pt0) REVERT: B 109 THR cc_start: 0.8364 (p) cc_final: 0.8140 (t) REVERT: B 115 MET cc_start: 0.9000 (ttm) cc_final: 0.8480 (tpp) REVERT: C 1 MET cc_start: 0.8463 (ttt) cc_final: 0.7914 (tmm) REVERT: C 63 ASN cc_start: 0.8988 (m110) cc_final: 0.8495 (m-40) REVERT: C 72 MET cc_start: 0.8834 (mtm) cc_final: 0.8350 (mpp) REVERT: C 73 TYR cc_start: 0.8063 (m-80) cc_final: 0.7357 (m-80) REVERT: C 115 MET cc_start: 0.8433 (mmm) cc_final: 0.8212 (mmm) REVERT: C 177 LEU cc_start: 0.9217 (tp) cc_final: 0.8980 (tp) REVERT: C 259 SER cc_start: 0.9297 (p) cc_final: 0.8893 (t) REVERT: D 78 ARG cc_start: 0.7068 (tpp80) cc_final: 0.6849 (tmm-80) REVERT: D 98 GLU cc_start: 0.8600 (tp30) cc_final: 0.8295 (tm-30) REVERT: D 115 MET cc_start: 0.9125 (tpp) cc_final: 0.8882 (tpp) REVERT: D 124 GLN cc_start: 0.9235 (tm-30) cc_final: 0.8937 (tm-30) REVERT: D 145 ASN cc_start: 0.8326 (m-40) cc_final: 0.8112 (t0) REVERT: D 151 GLU cc_start: 0.8376 (mt-10) cc_final: 0.7739 (mt-10) REVERT: D 268 ARG cc_start: 0.8643 (mmm-85) cc_final: 0.8411 (mmm160) REVERT: E 46 GLU cc_start: 0.8017 (mm-30) cc_final: 0.7766 (mm-30) REVERT: E 115 MET cc_start: 0.8320 (tpp) cc_final: 0.7654 (tpp) REVERT: E 148 MET cc_start: 0.8085 (mmm) cc_final: 0.7434 (mmm) REVERT: F 45 MET cc_start: 0.7643 (tpp) cc_final: 0.6945 (tpp) REVERT: F 106 LEU cc_start: 0.8693 (tp) cc_final: 0.8477 (tp) REVERT: F 108 LEU cc_start: 0.9313 (mt) cc_final: 0.8995 (mt) REVERT: F 115 MET cc_start: 0.9027 (tpp) cc_final: 0.8359 (tpp) REVERT: F 118 ASP cc_start: 0.8139 (m-30) cc_final: 0.7894 (m-30) REVERT: F 139 PHE cc_start: 0.8528 (t80) cc_final: 0.8319 (t80) REVERT: F 159 SER cc_start: 0.8947 (m) cc_final: 0.8618 (p) REVERT: F 259 SER cc_start: 0.9197 (p) cc_final: 0.8966 (t) REVERT: G 68 ARG cc_start: 0.8317 (mmp80) cc_final: 0.8087 (mmp80) REVERT: G 98 GLU cc_start: 0.8795 (pt0) cc_final: 0.8562 (pt0) REVERT: G 101 LYS cc_start: 0.8215 (mmtt) cc_final: 0.8006 (mmtt) REVERT: G 124 GLN cc_start: 0.9232 (tm-30) cc_final: 0.8837 (tm-30) REVERT: G 231 MET cc_start: 0.9193 (tpp) cc_final: 0.8633 (tpp) REVERT: H 1 MET cc_start: 0.8421 (ttm) cc_final: 0.6642 (tpt) REVERT: H 88 LEU cc_start: 0.9395 (tp) cc_final: 0.9144 (tp) REVERT: H 101 LYS cc_start: 0.5945 (mptt) cc_final: 0.5376 (mptt) REVERT: H 126 PHE cc_start: 0.8341 (m-80) cc_final: 0.7979 (m-10) REVERT: I 1 MET cc_start: 0.3279 (tpt) cc_final: 0.1829 (tmm) REVERT: I 125 HIS cc_start: 0.7844 (m170) cc_final: 0.7497 (m170) REVERT: I 179 LEU cc_start: 0.9122 (tt) cc_final: 0.8788 (mm) REVERT: I 187 MET cc_start: 0.6511 (mtm) cc_final: 0.6136 (mtm) REVERT: I 219 TYR cc_start: 0.8626 (m-10) cc_final: 0.8138 (m-80) REVERT: I 231 MET cc_start: 0.9369 (mmm) cc_final: 0.8990 (mmm) outliers start: 0 outliers final: 0 residues processed: 357 average time/residue: 0.1707 time to fit residues: 91.3019 Evaluate side-chains 272 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 272 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 13 optimal weight: 7.9990 chunk 37 optimal weight: 10.0000 chunk 237 optimal weight: 0.9990 chunk 157 optimal weight: 8.9990 chunk 168 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 207 optimal weight: 9.9990 chunk 20 optimal weight: 0.9980 chunk 22 optimal weight: 10.0000 chunk 171 optimal weight: 0.9990 chunk 233 optimal weight: 2.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 163 ASN ** F 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.064328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.051799 restraints weight = 96463.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.053694 restraints weight = 51646.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.054966 restraints weight = 32257.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.055845 restraints weight = 22373.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.056455 restraints weight = 16743.455| |-----------------------------------------------------------------------------| r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.6094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 20367 Z= 0.137 Angle : 0.675 11.511 27486 Z= 0.364 Chirality : 0.046 0.168 2970 Planarity : 0.004 0.034 3447 Dihedral : 11.267 172.930 2745 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 17.85 Ramachandran Plot: Outliers : 1.55 % Allowed : 11.52 % Favored : 86.94 % Rotamer: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.74 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.54 (0.17), residues: 2457 helix: 0.61 (0.19), residues: 720 sheet: -1.80 (0.22), residues: 513 loop : -1.65 (0.18), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 87 TYR 0.036 0.002 TYR F 90 PHE 0.025 0.001 PHE E 270 HIS 0.006 0.001 HIS H 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.14 (20367) covalent geometry : angle 0.67459 / 0.36 (27486) hydrogen bonds : bond 0.03717 / 2.35 ( 882) hydrogen bonds : angle 6.06889 / 4.28 ( 2322) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 373 time to evaluate : 0.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 GLN cc_start: 0.9087 (tt0) cc_final: 0.8858 (tt0) REVERT: A 202 MET cc_start: 0.6859 (tpp) cc_final: 0.6592 (tpp) REVERT: A 231 MET cc_start: 0.8953 (tpp) cc_final: 0.8579 (tpp) REVERT: B 1 MET cc_start: 0.8781 (mtm) cc_final: 0.8200 (ttp) REVERT: B 72 MET cc_start: 0.8663 (mpp) cc_final: 0.8376 (mpp) REVERT: B 88 LEU cc_start: 0.9495 (tp) cc_final: 0.9294 (tp) REVERT: B 98 GLU cc_start: 0.8822 (mt-10) cc_final: 0.8560 (pt0) REVERT: B 115 MET cc_start: 0.8947 (ttm) cc_final: 0.8479 (tpp) REVERT: B 139 PHE cc_start: 0.7856 (t80) cc_final: 0.7630 (t80) REVERT: C 63 ASN cc_start: 0.9024 (m110) cc_final: 0.8467 (m-40) REVERT: C 73 TYR cc_start: 0.8036 (m-80) cc_final: 0.7430 (m-80) REVERT: C 115 MET cc_start: 0.8608 (mmm) cc_final: 0.8399 (mmm) REVERT: C 202 MET cc_start: 0.7793 (mmm) cc_final: 0.7590 (mmm) REVERT: C 259 SER cc_start: 0.9180 (p) cc_final: 0.8761 (t) REVERT: D 46 GLU cc_start: 0.8371 (mp0) cc_final: 0.8013 (mp0) REVERT: D 98 GLU cc_start: 0.8517 (tp30) cc_final: 0.8304 (tt0) REVERT: D 124 GLN cc_start: 0.9244 (tm-30) cc_final: 0.8923 (tm-30) REVERT: D 148 MET cc_start: 0.7413 (tpt) cc_final: 0.7065 (mmm) REVERT: D 240 TYR cc_start: 0.9177 (m-80) cc_final: 0.8635 (m-10) REVERT: D 268 ARG cc_start: 0.8624 (mmm-85) cc_final: 0.8398 (mmm160) REVERT: E 46 GLU cc_start: 0.8140 (mm-30) cc_final: 0.7900 (mm-30) REVERT: E 83 GLU cc_start: 0.9012 (mp0) cc_final: 0.8497 (mp0) REVERT: E 88 LEU cc_start: 0.9788 (tp) cc_final: 0.9538 (tp) REVERT: E 115 MET cc_start: 0.8315 (tpp) cc_final: 0.7710 (tpp) REVERT: E 148 MET cc_start: 0.8098 (mmm) cc_final: 0.7398 (mmm) REVERT: F 45 MET cc_start: 0.8216 (tpp) cc_final: 0.7132 (tpp) REVERT: F 115 MET cc_start: 0.9126 (tpp) cc_final: 0.8896 (tpp) REVERT: F 118 ASP cc_start: 0.8163 (m-30) cc_final: 0.7939 (m-30) REVERT: F 139 PHE cc_start: 0.8545 (t80) cc_final: 0.8285 (t80) REVERT: F 159 SER cc_start: 0.8832 (m) cc_final: 0.8564 (p) REVERT: G 78 ARG cc_start: 0.6931 (pmt170) cc_final: 0.6581 (pmt170) REVERT: G 101 LYS cc_start: 0.8153 (mmtt) cc_final: 0.7950 (mmtt) REVERT: G 115 MET cc_start: 0.7915 (tpp) cc_final: 0.6051 (tpp) REVERT: G 124 GLN cc_start: 0.9194 (tm-30) cc_final: 0.8777 (tm-30) REVERT: G 202 MET cc_start: 0.7964 (tpt) cc_final: 0.7283 (tpt) REVERT: G 227 LYS cc_start: 0.9454 (mttm) cc_final: 0.9132 (mtpp) REVERT: G 231 MET cc_start: 0.9189 (tpp) cc_final: 0.8552 (tpp) REVERT: H 1 MET cc_start: 0.8542 (ttm) cc_final: 0.7784 (ttp) REVERT: H 88 LEU cc_start: 0.9363 (tp) cc_final: 0.9037 (tp) REVERT: H 126 PHE cc_start: 0.8304 (m-80) cc_final: 0.7975 (m-10) REVERT: H 268 ARG cc_start: 0.8913 (mpp80) cc_final: 0.8428 (tpm170) REVERT: I 1 MET cc_start: 0.3237 (tpt) cc_final: 0.1148 (tmm) REVERT: I 45 MET cc_start: 0.2564 (mtm) cc_final: 0.1838 (mtm) REVERT: I 125 HIS cc_start: 0.7711 (m170) cc_final: 0.7494 (m170) outliers start: 0 outliers final: 0 residues processed: 373 average time/residue: 0.1638 time to fit residues: 92.2955 Evaluate side-chains 279 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 279 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 241 optimal weight: 9.9990 chunk 203 optimal weight: 7.9990 chunk 198 optimal weight: 0.9990 chunk 164 optimal weight: 3.9990 chunk 144 optimal weight: 3.9990 chunk 233 optimal weight: 20.0000 chunk 216 optimal weight: 20.0000 chunk 188 optimal weight: 0.8980 chunk 208 optimal weight: 10.0000 chunk 15 optimal weight: 5.9990 chunk 186 optimal weight: 9.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 34 HIS ** G 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.061963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.049553 restraints weight = 99651.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.051363 restraints weight = 53964.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.052585 restraints weight = 34055.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.053428 restraints weight = 23864.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.054042 restraints weight = 18067.703| |-----------------------------------------------------------------------------| r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.6287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 20367 Z= 0.209 Angle : 0.718 8.118 27486 Z= 0.386 Chirality : 0.047 0.185 2970 Planarity : 0.004 0.041 3447 Dihedral : 11.145 164.174 2745 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 20.77 Ramachandran Plot: Outliers : 1.55 % Allowed : 12.09 % Favored : 86.37 % Rotamer: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.74 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.00 (0.16), residues: 2457 helix: 0.07 (0.18), residues: 783 sheet: -1.88 (0.21), residues: 513 loop : -2.03 (0.18), residues: 1161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 87 TYR 0.026 0.002 TYR F 90 PHE 0.018 0.002 PHE G 74 HIS 0.011 0.001 HIS B 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.21 (20367) covalent geometry : angle 0.71816 / 0.39 (27486) hydrogen bonds : bond 0.03811 / 2.41 ( 882) hydrogen bonds : angle 6.18068 / 4.34 ( 2322) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 335 time to evaluate : 0.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 GLN cc_start: 0.9107 (tt0) cc_final: 0.8885 (tt0) REVERT: A 101 LYS cc_start: 0.6766 (mmtt) cc_final: 0.6451 (mmmt) REVERT: A 231 MET cc_start: 0.8944 (tpp) cc_final: 0.8677 (tpp) REVERT: B 1 MET cc_start: 0.8884 (mtm) cc_final: 0.8477 (mtm) REVERT: B 72 MET cc_start: 0.8601 (mpp) cc_final: 0.8305 (mpp) REVERT: B 98 GLU cc_start: 0.8892 (mt-10) cc_final: 0.8616 (pt0) REVERT: B 115 MET cc_start: 0.8988 (ttm) cc_final: 0.8525 (tpp) REVERT: B 139 PHE cc_start: 0.7949 (t80) cc_final: 0.7700 (t80) REVERT: C 63 ASN cc_start: 0.8994 (m110) cc_final: 0.8567 (m-40) REVERT: C 71 GLN cc_start: 0.8711 (mp10) cc_final: 0.8382 (mp10) REVERT: C 72 MET cc_start: 0.8714 (mtm) cc_final: 0.8449 (mpp) REVERT: C 73 TYR cc_start: 0.8124 (m-80) cc_final: 0.7422 (m-80) REVERT: C 88 LEU cc_start: 0.9725 (tp) cc_final: 0.9504 (tp) REVERT: C 259 SER cc_start: 0.9194 (p) cc_final: 0.8867 (t) REVERT: D 1 MET cc_start: 0.8073 (ttt) cc_final: 0.7806 (tmm) REVERT: D 46 GLU cc_start: 0.8461 (mp0) cc_final: 0.7915 (mp0) REVERT: D 124 GLN cc_start: 0.9211 (tm-30) cc_final: 0.8932 (tm-30) REVERT: D 151 GLU cc_start: 0.8276 (mt-10) cc_final: 0.7549 (mt-10) REVERT: D 202 MET cc_start: 0.6933 (tpp) cc_final: 0.6559 (mmm) REVERT: D 240 TYR cc_start: 0.9150 (m-80) cc_final: 0.8720 (m-10) REVERT: E 88 LEU cc_start: 0.9749 (tp) cc_final: 0.9548 (tp) REVERT: E 115 MET cc_start: 0.8280 (tpp) cc_final: 0.7647 (tpp) REVERT: E 148 MET cc_start: 0.8036 (mmm) cc_final: 0.7412 (mmm) REVERT: F 45 MET cc_start: 0.8357 (tpp) cc_final: 0.7185 (tpp) REVERT: F 115 MET cc_start: 0.9057 (tpp) cc_final: 0.8346 (tpp) REVERT: F 118 ASP cc_start: 0.8137 (m-30) cc_final: 0.7892 (m-30) REVERT: G 72 MET cc_start: 0.7904 (ptp) cc_final: 0.7667 (ptt) REVERT: G 101 LYS cc_start: 0.8156 (mmtt) cc_final: 0.7942 (mmtt) REVERT: G 124 GLN cc_start: 0.9246 (tm-30) cc_final: 0.8796 (tm-30) REVERT: G 202 MET cc_start: 0.8164 (tpt) cc_final: 0.7376 (tpt) REVERT: G 231 MET cc_start: 0.9165 (tpp) cc_final: 0.8668 (tpp) REVERT: H 88 LEU cc_start: 0.9403 (tp) cc_final: 0.9171 (tp) REVERT: H 126 PHE cc_start: 0.8393 (m-80) cc_final: 0.8099 (m-10) REVERT: I 1 MET cc_start: 0.3165 (tpt) cc_final: 0.0481 (tmm) REVERT: I 125 HIS cc_start: 0.7859 (m170) cc_final: 0.7410 (m170) REVERT: I 179 LEU cc_start: 0.9072 (tt) cc_final: 0.8744 (mm) outliers start: 0 outliers final: 0 residues processed: 335 average time/residue: 0.1580 time to fit residues: 80.4264 Evaluate side-chains 253 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 253 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 38 optimal weight: 8.9990 chunk 223 optimal weight: 30.0000 chunk 161 optimal weight: 0.7980 chunk 204 optimal weight: 9.9990 chunk 241 optimal weight: 8.9990 chunk 49 optimal weight: 9.9990 chunk 147 optimal weight: 5.9990 chunk 29 optimal weight: 0.0000 chunk 150 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 227 optimal weight: 6.9990 overall best weight: 1.9590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 63 ASN ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.063037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.050531 restraints weight = 98032.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.052367 restraints weight = 52957.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.053632 restraints weight = 33474.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.054483 restraints weight = 23343.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.055126 restraints weight = 17649.536| |-----------------------------------------------------------------------------| r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.6543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20367 Z= 0.158 Angle : 0.694 9.087 27486 Z= 0.372 Chirality : 0.047 0.166 2970 Planarity : 0.004 0.038 3447 Dihedral : 11.041 165.638 2745 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 18.67 Ramachandran Plot: Outliers : 1.51 % Allowed : 11.64 % Favored : 86.85 % Rotamer: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.74 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.69 (0.16), residues: 2457 helix: 0.60 (0.19), residues: 711 sheet: -1.87 (0.21), residues: 513 loop : -1.82 (0.17), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 87 TYR 0.031 0.002 TYR H 56 PHE 0.025 0.002 PHE E 270 HIS 0.008 0.001 HIS F 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.16 (20367) covalent geometry : angle 0.69368 / 0.37 (27486) hydrogen bonds : bond 0.03676 / 2.33 ( 882) hydrogen bonds : angle 6.06503 / 4.28 ( 2322) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 340 time to evaluate : 0.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 GLN cc_start: 0.9117 (tt0) cc_final: 0.8898 (tt0) REVERT: A 101 LYS cc_start: 0.6704 (mmtt) cc_final: 0.6380 (mmmt) REVERT: A 231 MET cc_start: 0.8979 (tpp) cc_final: 0.8675 (tpp) REVERT: B 1 MET cc_start: 0.8757 (mtm) cc_final: 0.8246 (ttm) REVERT: B 72 MET cc_start: 0.8578 (mpp) cc_final: 0.8324 (mpp) REVERT: B 98 GLU cc_start: 0.8907 (mt-10) cc_final: 0.8666 (pt0) REVERT: B 115 MET cc_start: 0.8898 (ttm) cc_final: 0.8471 (tpp) REVERT: C 63 ASN cc_start: 0.8992 (m-40) cc_final: 0.8538 (m-40) REVERT: C 71 GLN cc_start: 0.8651 (mp10) cc_final: 0.8271 (mp10) REVERT: C 73 TYR cc_start: 0.8035 (m-80) cc_final: 0.7381 (m-80) REVERT: C 88 LEU cc_start: 0.9745 (tp) cc_final: 0.9517 (tp) REVERT: C 259 SER cc_start: 0.9198 (p) cc_final: 0.8910 (t) REVERT: D 1 MET cc_start: 0.8089 (ttt) cc_final: 0.7851 (tmm) REVERT: D 46 GLU cc_start: 0.8422 (mp0) cc_final: 0.7775 (mp0) REVERT: D 73 TYR cc_start: 0.8439 (m-80) cc_final: 0.8058 (m-80) REVERT: D 124 GLN cc_start: 0.9284 (tm-30) cc_final: 0.8965 (tm-30) REVERT: D 240 TYR cc_start: 0.9207 (m-80) cc_final: 0.8798 (m-10) REVERT: D 268 ARG cc_start: 0.9287 (mtm-85) cc_final: 0.8688 (mmm160) REVERT: E 83 GLU cc_start: 0.8952 (mp0) cc_final: 0.8464 (mp0) REVERT: E 115 MET cc_start: 0.8289 (tpp) cc_final: 0.7697 (tpp) REVERT: E 124 GLN cc_start: 0.9437 (tt0) cc_final: 0.9221 (tm-30) REVERT: E 148 MET cc_start: 0.8100 (mmm) cc_final: 0.7387 (mmm) REVERT: F 3 LEU cc_start: 0.9349 (tp) cc_final: 0.9121 (tp) REVERT: F 45 MET cc_start: 0.8430 (tpp) cc_final: 0.7053 (tpp) REVERT: F 105 ASN cc_start: 0.8495 (m110) cc_final: 0.7635 (t0) REVERT: F 115 MET cc_start: 0.9140 (tpp) cc_final: 0.8412 (tpp) REVERT: F 118 ASP cc_start: 0.8188 (m-30) cc_final: 0.7971 (m-30) REVERT: G 39 LEU cc_start: 0.8044 (tp) cc_final: 0.7822 (tp) REVERT: G 72 MET cc_start: 0.8196 (ptp) cc_final: 0.7846 (ptt) REVERT: G 78 ARG cc_start: 0.7439 (pmt170) cc_final: 0.7111 (pmt170) REVERT: G 101 LYS cc_start: 0.8069 (mmtt) cc_final: 0.7850 (mmtt) REVERT: G 124 GLN cc_start: 0.9275 (tm-30) cc_final: 0.8833 (tm-30) REVERT: G 202 MET cc_start: 0.8089 (tpt) cc_final: 0.7440 (tpt) REVERT: G 227 LYS cc_start: 0.9434 (mttm) cc_final: 0.9133 (mtpp) REVERT: G 231 MET cc_start: 0.9218 (tpp) cc_final: 0.8739 (tpp) REVERT: H 45 MET cc_start: 0.7690 (tpp) cc_final: 0.7390 (tpp) REVERT: H 231 MET cc_start: 0.9210 (tpt) cc_final: 0.8925 (tpp) REVERT: H 268 ARG cc_start: 0.8941 (mpp80) cc_final: 0.8396 (tpm170) REVERT: I 1 MET cc_start: 0.3251 (tpt) cc_final: 0.0635 (tmm) REVERT: I 45 MET cc_start: 0.1817 (mtm) cc_final: 0.0446 (ttp) REVERT: I 125 HIS cc_start: 0.7775 (m170) cc_final: 0.7394 (m170) REVERT: I 131 GLU cc_start: 0.8113 (pp20) cc_final: 0.7706 (tm-30) REVERT: I 179 LEU cc_start: 0.9019 (tt) cc_final: 0.8753 (mm) REVERT: I 231 MET cc_start: 0.9377 (mmm) cc_final: 0.9154 (mmm) outliers start: 0 outliers final: 0 residues processed: 340 average time/residue: 0.1588 time to fit residues: 82.2485 Evaluate side-chains 264 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 264 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 123 optimal weight: 0.9980 chunk 22 optimal weight: 10.0000 chunk 195 optimal weight: 10.0000 chunk 14 optimal weight: 8.9990 chunk 127 optimal weight: 2.9990 chunk 73 optimal weight: 10.0000 chunk 83 optimal weight: 4.9990 chunk 175 optimal weight: 10.0000 chunk 140 optimal weight: 3.9990 chunk 9 optimal weight: 5.9990 chunk 241 optimal weight: 0.9980 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 51 ASN ** E 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.062088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.049702 restraints weight = 98902.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.051530 restraints weight = 53562.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.052769 restraints weight = 33735.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.053630 restraints weight = 23590.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.054237 restraints weight = 17751.240| |-----------------------------------------------------------------------------| r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.6720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 20367 Z= 0.194 Angle : 0.721 9.365 27486 Z= 0.386 Chirality : 0.048 0.168 2970 Planarity : 0.004 0.047 3447 Dihedral : 11.022 162.230 2745 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 20.98 Ramachandran Plot: Outliers : 1.30 % Allowed : 12.25 % Favored : 86.45 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.74 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.07 (0.16), residues: 2457 helix: -0.01 (0.18), residues: 783 sheet: -1.84 (0.21), residues: 504 loop : -2.11 (0.17), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 87 TYR 0.029 0.002 TYR H 56 PHE 0.030 0.002 PHE E 270 HIS 0.007 0.001 HIS F 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.19 (20367) covalent geometry : angle 0.72129 / 0.39 (27486) hydrogen bonds : bond 0.03748 / 2.38 ( 882) hydrogen bonds : angle 6.14581 / 4.32 ( 2322) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 331 time to evaluate : 0.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 GLN cc_start: 0.9091 (tt0) cc_final: 0.8874 (tt0) REVERT: A 101 LYS cc_start: 0.6958 (mmtt) cc_final: 0.6639 (mmmt) REVERT: A 211 THR cc_start: 0.8867 (p) cc_final: 0.8628 (p) REVERT: A 215 ILE cc_start: 0.9436 (mm) cc_final: 0.9128 (tp) REVERT: A 231 MET cc_start: 0.8953 (tpp) cc_final: 0.8672 (tpp) REVERT: B 1 MET cc_start: 0.8703 (mtm) cc_final: 0.8255 (ttm) REVERT: B 3 LEU cc_start: 0.9579 (mt) cc_final: 0.9371 (mt) REVERT: B 71 GLN cc_start: 0.8858 (mp10) cc_final: 0.8418 (mp-120) REVERT: B 72 MET cc_start: 0.8495 (mpp) cc_final: 0.8163 (mpp) REVERT: B 115 MET cc_start: 0.8961 (ttm) cc_final: 0.8447 (tpp) REVERT: C 63 ASN cc_start: 0.8972 (m-40) cc_final: 0.8529 (m-40) REVERT: C 71 GLN cc_start: 0.8700 (mp10) cc_final: 0.8322 (mp10) REVERT: C 73 TYR cc_start: 0.8039 (m-80) cc_final: 0.7445 (m-80) REVERT: C 88 LEU cc_start: 0.9708 (tp) cc_final: 0.9504 (tp) REVERT: C 259 SER cc_start: 0.9148 (p) cc_final: 0.8893 (t) REVERT: D 46 GLU cc_start: 0.8434 (mp0) cc_final: 0.7764 (mp0) REVERT: D 124 GLN cc_start: 0.9244 (tm-30) cc_final: 0.8941 (tm-30) REVERT: D 151 GLU cc_start: 0.8177 (mt-10) cc_final: 0.7527 (mt-10) REVERT: D 191 THR cc_start: 0.8553 (m) cc_final: 0.8323 (p) REVERT: D 240 TYR cc_start: 0.9203 (m-80) cc_final: 0.8810 (m-10) REVERT: E 83 GLU cc_start: 0.8906 (mp0) cc_final: 0.8404 (mp0) REVERT: E 115 MET cc_start: 0.8341 (tpp) cc_final: 0.7680 (tpp) REVERT: E 148 MET cc_start: 0.8092 (mmm) cc_final: 0.7396 (mmm) REVERT: E 211 THR cc_start: 0.9042 (p) cc_final: 0.8694 (p) REVERT: F 2 THR cc_start: 0.8870 (p) cc_final: 0.8508 (p) REVERT: F 45 MET cc_start: 0.8440 (tpp) cc_final: 0.7060 (tpp) REVERT: F 105 ASN cc_start: 0.8467 (m110) cc_final: 0.7701 (t0) REVERT: F 106 LEU cc_start: 0.8656 (tp) cc_final: 0.8421 (tp) REVERT: F 115 MET cc_start: 0.9083 (tpp) cc_final: 0.8384 (tpp) REVERT: G 72 MET cc_start: 0.8146 (ptp) cc_final: 0.7770 (ptt) REVERT: G 101 LYS cc_start: 0.8004 (mmtt) cc_final: 0.7790 (mmtt) REVERT: G 124 GLN cc_start: 0.9270 (tm-30) cc_final: 0.8798 (tm-30) REVERT: G 202 MET cc_start: 0.8186 (tpt) cc_final: 0.7515 (tpt) REVERT: G 231 MET cc_start: 0.9160 (tpp) cc_final: 0.8753 (tpp) REVERT: G 273 MET cc_start: 0.8334 (ptm) cc_final: 0.8102 (ptp) REVERT: H 45 MET cc_start: 0.7784 (tpp) cc_final: 0.7463 (tpp) REVERT: H 231 MET cc_start: 0.9129 (tpt) cc_final: 0.8903 (tpt) REVERT: H 268 ARG cc_start: 0.8942 (mpp80) cc_final: 0.8413 (tpm170) REVERT: I 1 MET cc_start: 0.3002 (tpt) cc_final: 0.0552 (tmm) REVERT: I 131 GLU cc_start: 0.8090 (pp20) cc_final: 0.7692 (tm-30) REVERT: I 179 LEU cc_start: 0.8982 (tt) cc_final: 0.8706 (mm) REVERT: I 231 MET cc_start: 0.9372 (mmm) cc_final: 0.9136 (mmm) outliers start: 0 outliers final: 0 residues processed: 331 average time/residue: 0.1568 time to fit residues: 78.1029 Evaluate side-chains 264 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 264 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 117 optimal weight: 0.7980 chunk 221 optimal weight: 3.9990 chunk 136 optimal weight: 9.9990 chunk 237 optimal weight: 10.0000 chunk 123 optimal weight: 2.9990 chunk 145 optimal weight: 0.3980 chunk 196 optimal weight: 0.9980 chunk 111 optimal weight: 6.9990 chunk 219 optimal weight: 10.0000 chunk 229 optimal weight: 5.9990 chunk 52 optimal weight: 9.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 81 HIS ** 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 = 0.3415 r_free = 0.3415 target = 0.062999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.050596 restraints weight = 97506.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.052454 restraints weight = 52963.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.053722 restraints weight = 33455.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.054555 restraints weight = 23366.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.055180 restraints weight = 17714.430| |-----------------------------------------------------------------------------| r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.6899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 20367 Z= 0.156 Angle : 0.701 9.685 27486 Z= 0.375 Chirality : 0.047 0.181 2970 Planarity : 0.004 0.036 3447 Dihedral : 10.987 164.611 2745 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 19.71 Ramachandran Plot: Outliers : 1.26 % Allowed : 11.88 % Favored : 86.85 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.74 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.87 (0.16), residues: 2457 helix: 0.39 (0.19), residues: 711 sheet: -1.76 (0.20), residues: 621 loop : -1.97 (0.18), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 268 TYR 0.043 0.002 TYR A 219 PHE 0.029 0.002 PHE E 270 HIS 0.004 0.001 HIS F 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.16 (20367) covalent geometry : angle 0.70086 / 0.37 (27486) hydrogen bonds : bond 0.03632 / 2.30 ( 882) hydrogen bonds : angle 6.08984 / 4.29 ( 2322) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4914 Ramachandran restraints generated. 2457 Oldfield, 0 Emsley, 2457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 333 time to evaluate : 0.962 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 GLN cc_start: 0.9106 (tt0) cc_final: 0.8888 (tt0) REVERT: A 45 MET cc_start: 0.7832 (mpp) cc_final: 0.6896 (mpp) REVERT: A 215 ILE cc_start: 0.9563 (mm) cc_final: 0.9344 (mp) REVERT: A 231 MET cc_start: 0.9012 (tpp) cc_final: 0.8724 (tpp) REVERT: B 1 MET cc_start: 0.8690 (mtm) cc_final: 0.8213 (ttm) REVERT: B 3 LEU cc_start: 0.9546 (mt) cc_final: 0.9331 (mt) REVERT: B 7 ILE cc_start: 0.7885 (tp) cc_final: 0.7571 (mm) REVERT: B 71 GLN cc_start: 0.8825 (mp10) cc_final: 0.8388 (mp10) REVERT: B 72 MET cc_start: 0.8465 (mpp) cc_final: 0.8187 (mpp) REVERT: B 115 MET cc_start: 0.8953 (ttm) cc_final: 0.8421 (tpp) REVERT: B 202 MET cc_start: 0.8512 (mmp) cc_final: 0.8303 (mmp) REVERT: C 63 ASN cc_start: 0.9006 (m-40) cc_final: 0.8505 (m-40) REVERT: C 71 GLN cc_start: 0.8646 (mp10) cc_final: 0.8278 (mp10) REVERT: C 73 TYR cc_start: 0.8049 (m-80) cc_final: 0.7377 (m-80) REVERT: C 88 LEU cc_start: 0.9738 (tp) cc_final: 0.9530 (tp) REVERT: C 109 THR cc_start: 0.9362 (p) cc_final: 0.9067 (t) REVERT: C 115 MET cc_start: 0.8390 (mmm) cc_final: 0.7894 (mmm) REVERT: C 202 MET cc_start: 0.7770 (mmm) cc_final: 0.7523 (mmm) REVERT: C 259 SER cc_start: 0.9123 (p) cc_final: 0.8877 (t) REVERT: D 45 MET cc_start: 0.8106 (mpp) cc_final: 0.6923 (tpp) REVERT: D 46 GLU cc_start: 0.8414 (mp0) cc_final: 0.7813 (mp0) REVERT: D 107 ILE cc_start: 0.9382 (mm) cc_final: 0.9153 (mm) REVERT: D 124 GLN cc_start: 0.9291 (tm-30) cc_final: 0.8963 (tm-30) REVERT: D 148 MET cc_start: 0.7563 (tpt) cc_final: 0.6423 (tpt) REVERT: D 151 GLU cc_start: 0.8095 (mt-10) cc_final: 0.7751 (mt-10) REVERT: D 240 TYR cc_start: 0.9248 (m-80) cc_final: 0.8844 (m-10) REVERT: D 268 ARG cc_start: 0.9241 (mtm-85) cc_final: 0.8617 (mmm160) REVERT: E 83 GLU cc_start: 0.8926 (mp0) cc_final: 0.8354 (mp0) REVERT: E 108 LEU cc_start: 0.9677 (mm) cc_final: 0.9270 (mp) REVERT: E 115 MET cc_start: 0.8362 (tpp) cc_final: 0.7848 (tpp) REVERT: E 148 MET cc_start: 0.8155 (mmm) cc_final: 0.7369 (mmm) REVERT: F 2 THR cc_start: 0.8884 (p) cc_final: 0.8505 (p) REVERT: F 3 LEU cc_start: 0.9365 (tp) cc_final: 0.9140 (tp) REVERT: F 45 MET cc_start: 0.8436 (tpp) cc_final: 0.7053 (tpp) REVERT: F 73 TYR cc_start: 0.8453 (m-10) cc_final: 0.7964 (m-10) REVERT: F 105 ASN cc_start: 0.8583 (m110) cc_final: 0.7730 (t0) REVERT: F 106 LEU cc_start: 0.8775 (tp) cc_final: 0.8540 (tp) REVERT: F 115 MET cc_start: 0.9105 (tpp) cc_final: 0.8343 (tpp) REVERT: F 148 MET cc_start: 0.8231 (mpp) cc_final: 0.8006 (mtt) REVERT: F 268 ARG cc_start: 0.8812 (mmm160) cc_final: 0.8325 (mmp80) REVERT: G 39 LEU cc_start: 0.8516 (tp) cc_final: 0.8295 (tp) REVERT: G 72 MET cc_start: 0.8083 (ptp) cc_final: 0.7641 (ptt) REVERT: G 73 TYR cc_start: 0.7911 (m-80) cc_final: 0.7437 (m-80) REVERT: G 101 LYS cc_start: 0.8012 (mmtt) cc_final: 0.7807 (mmtt) REVERT: G 124 GLN cc_start: 0.9277 (tm-30) cc_final: 0.8829 (tm-30) REVERT: G 202 MET cc_start: 0.8132 (tpt) cc_final: 0.7505 (tpt) REVERT: G 227 LYS cc_start: 0.9409 (mttm) cc_final: 0.9150 (mtpp) REVERT: G 231 MET cc_start: 0.9202 (tpp) cc_final: 0.8782 (tpp) REVERT: H 45 MET cc_start: 0.7690 (tpp) cc_final: 0.7320 (tpp) REVERT: H 163 ASN cc_start: 0.7221 (m-40) cc_final: 0.6907 (m-40) REVERT: H 231 MET cc_start: 0.9215 (tpt) cc_final: 0.8910 (tpp) REVERT: H 268 ARG cc_start: 0.8954 (mpp80) cc_final: 0.8373 (tpm170) REVERT: I 1 MET cc_start: 0.2950 (tpt) cc_final: 0.0586 (tmm) REVERT: I 45 MET cc_start: 0.0762 (ttt) cc_final: 0.0391 (ttt) REVERT: I 125 HIS cc_start: 0.7734 (m170) cc_final: 0.7260 (m170) REVERT: I 131 GLU cc_start: 0.8094 (pp20) cc_final: 0.7708 (tm-30) REVERT: I 231 MET cc_start: 0.9402 (mmm) cc_final: 0.9192 (mmm) outliers start: 0 outliers final: 0 residues processed: 333 average time/residue: 0.1637 time to fit residues: 82.4387 Evaluate side-chains 266 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 266 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 207 optimal weight: 0.9980 chunk 183 optimal weight: 2.9990 chunk 115 optimal weight: 9.9990 chunk 187 optimal weight: 8.9990 chunk 69 optimal weight: 6.9990 chunk 100 optimal weight: 10.0000 chunk 1 optimal weight: 9.9990 chunk 66 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 179 optimal weight: 10.0000 chunk 163 optimal weight: 10.0000 overall best weight: 3.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 51 ASN ** E 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 23 GLN ** F 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.061237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.048903 restraints weight = 98290.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.050728 restraints weight = 53219.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.051963 restraints weight = 33567.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.052768 restraints weight = 23410.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.053404 restraints weight = 17744.510| |-----------------------------------------------------------------------------| r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.7062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 20367 Z= 0.213 Angle : 0.742 9.743 27486 Z= 0.395 Chirality : 0.048 0.170 2970 Planarity : 0.004 0.040 3447 Dihedral : 11.012 161.501 2745 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 22.30 Ramachandran Plot: Outliers : 1.14 % Allowed : 12.78 % Favored : 86.08 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.74 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.30 (0.16), residues: 2457 helix: -0.10 (0.18), residues: 765 sheet: -1.91 (0.20), residues: 630 loop : -2.29 (0.18), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 78 TYR 0.027 0.002 TYR H 56 PHE 0.030 0.002 PHE E 270 HIS 0.006 0.001 HIS F 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00459 / 0.21 (20367) covalent geometry : angle 0.74185 / 0.40 (27486) hydrogen bonds : bond 0.03826 / 2.43 ( 882) hydrogen bonds : angle 6.22071 / 4.35 ( 2322) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3479.82 seconds wall clock time: 61 minutes 54.57 seconds (3714.57 seconds total)