Starting phenix.real_space_refine on Thu Sep 18 20:42:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6bqw_7134/09_2025/6bqw_7134.cif Found real_map, /net/cci-nas-00/data/ceres_data/6bqw_7134/09_2025/6bqw_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 { model { file = "/net/cci-nas-00/data/ceres_data/6bqw_7134/09_2025/6bqw_7134.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6bqw_7134/09_2025/6bqw_7134.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6bqw_7134/09_2025/6bqw_7134.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6bqw_7134/09_2025/6bqw_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-2.0-5805/lib/python3.9/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: 2.49, per 1000 atoms: 0.12 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: 2.07 Conformation dependent library (CDL) restraints added in 612.0 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.97 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: 4.08 Time building geometry restraints manager: 2.61 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: 12024 35.79 - 71.58: 153 71.58 - 107.37: 18 107.37 - 143.16: 0 143.16 - 178.95: 9 Dihedral angle restraints: 12204 sinusoidal: 5040 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 12201 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: 2.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 17.390 Find NCS groups from input model: 0.180 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:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7024 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 : 13.915 178.952 7686 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 aren 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 covalent geometry : bond 0.01604 (20367) covalent geometry : angle 1.27816 (27486) hydrogen bonds : bond 0.15728 ( 882) hydrogen bonds : angle 9.90130 ( 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 : 0.804 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: 0.7452 (p) REVERT: D 32 ILE cc_start: 0.9133 (mt) cc_final: 0.7761 (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: 0.8488 (p) cc_final: 0.8171 (p) REVERT: E 159 SER cc_start: 0.8344 (m) cc_final: 0.8062 (p) REVERT: E 184 ILE cc_start: 0.8996 (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: 0.8312 (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: 0.7364 (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: 0.1842 time to fit residues: 174.8701 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 : 0.556 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3471 r_free = 0.3471 target = 0.064883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.051991 restraints weight = 96505.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.053953 restraints weight = 50283.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.055278 restraints weight = 30959.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.056158 restraints weight = 21101.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.056698 restraints weight = 15770.766| |-----------------------------------------------------------------------------| r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.3783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 20367 Z= 0.168 Angle : 0.776 8.795 27486 Z= 0.423 Chirality : 0.048 0.197 2970 Planarity : 0.004 0.034 3447 Dihedral : 13.301 179.190 2997 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 19.30 Ramachandran Plot: Outliers : 2.40 % Allowed : 11.80 % Favored : 85.80 % Rotamer: Outliers : 0.14 % Allowed : 3.19 % Favored : 96.67 % 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 aren not related in a simple way. whole: -2.00 (0.16), residues: 2457 helix: 0.37 (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 A 87 TYR 0.024 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 covalent geometry : bond 0.00345 (20367) covalent geometry : angle 0.77589 (27486) hydrogen bonds : bond 0.04769 ( 882) hydrogen bonds : angle 7.16529 ( 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 487 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 484 time to evaluate : 0.840 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: A 23 GLN cc_start: 0.9066 (tt0) cc_final: 0.8853 (tt0) REVERT: A 73 TYR cc_start: 0.8141 (m-80) cc_final: 0.7428 (m-80) REVERT: A 115 MET cc_start: 0.8516 (mtm) cc_final: 0.8098 (mtt) REVERT: A 186 LYS cc_start: 0.9352 (tttt) cc_final: 0.9136 (tttm) REVERT: A 202 MET cc_start: 0.6923 (mmm) cc_final: 0.6636 (tpp) REVERT: A 231 MET cc_start: 0.8760 (tpp) cc_final: 0.8544 (tpp) REVERT: B 98 GLU cc_start: 0.8734 (mt-10) cc_final: 0.8287 (pt0) REVERT: B 115 MET cc_start: 0.8806 (ttm) cc_final: 0.8387 (tpp) REVERT: B 141 PHE cc_start: 0.8965 (p90) cc_final: 0.8547 (p90) REVERT: C 46 GLU cc_start: 0.7998 (mp0) cc_final: 0.7712 (mp0) REVERT: C 63 ASN cc_start: 0.8831 (m110) cc_final: 0.8374 (t0) REVERT: C 98 GLU cc_start: 0.8667 (pt0) cc_final: 0.8376 (pt0) REVERT: C 177 LEU cc_start: 0.8961 (tp) cc_final: 0.8661 (tp) REVERT: C 259 SER cc_start: 0.9292 (p) cc_final: 0.8709 (t) REVERT: D 46 GLU cc_start: 0.8575 (mp0) cc_final: 0.8045 (mp0) REVERT: D 88 LEU cc_start: 0.9757 (tp) cc_final: 0.9548 (tp) REVERT: D 102 LYS cc_start: 0.7987 (tmmt) cc_final: 0.7686 (ttpt) REVERT: D 106 LEU cc_start: 0.8669 (tp) cc_final: 0.8409 (tp) REVERT: D 124 GLN cc_start: 0.9163 (tm-30) cc_final: 0.8926 (tm-30) REVERT: D 148 MET cc_start: 0.7380 (tpt) cc_final: 0.6929 (mmm) REVERT: D 153 LEU cc_start: 0.9145 (mt) cc_final: 0.8932 (mt) REVERT: D 204 LEU cc_start: 0.8939 (mt) cc_final: 0.8583 (mt) REVERT: E 46 GLU cc_start: 0.8099 (mp0) cc_final: 0.7532 (mp0) REVERT: E 68 ARG cc_start: 0.8518 (mmt90) cc_final: 0.8168 (mmt90) REVERT: E 88 LEU cc_start: 0.9720 (tp) cc_final: 0.9474 (tp) REVERT: E 148 MET cc_start: 0.8017 (mmm) cc_final: 0.6949 (mmm) REVERT: E 159 SER cc_start: 0.8258 (m) cc_final: 0.7893 (p) REVERT: E 163 ASN cc_start: 0.6679 (m110) cc_final: 0.5515 (m110) REVERT: E 202 MET cc_start: 0.7408 (mmm) cc_final: 0.6915 (mmm) REVERT: E 248 LEU cc_start: 0.9008 (tp) cc_final: 0.8784 (tp) REVERT: E 259 SER cc_start: 0.9101 (p) cc_final: 0.8766 (t) REVERT: F 23 GLN cc_start: 0.8419 (tt0) cc_final: 0.8152 (tt0) REVERT: F 46 GLU cc_start: 0.8465 (mp0) cc_final: 0.8183 (mp0) REVERT: F 95 ILE cc_start: 0.9427 (pt) cc_final: 0.9221 (mm) REVERT: F 98 GLU cc_start: 0.8442 (pt0) cc_final: 0.8187 (pt0) REVERT: F 106 LEU cc_start: 0.8622 (tp) cc_final: 0.8353 (tp) REVERT: F 108 LEU cc_start: 0.9043 (mt) cc_final: 0.8745 (mt) REVERT: F 118 ASP cc_start: 0.8126 (m-30) cc_final: 0.7588 (m-30) REVERT: F 126 PHE cc_start: 0.8298 (m-80) cc_final: 0.8094 (m-80) REVERT: F 159 SER cc_start: 0.8794 (m) cc_final: 0.8445 (p) REVERT: F 187 MET cc_start: 0.6385 (ptt) cc_final: 0.6164 (ptt) REVERT: F 259 SER cc_start: 0.9364 (p) cc_final: 0.8972 (t) REVERT: G 1 MET cc_start: 0.7395 (mtm) cc_final: 0.6709 (mpp) REVERT: G 46 GLU cc_start: 0.8955 (mp0) cc_final: 0.8561 (mp0) REVERT: G 83 GLU cc_start: 0.8120 (pt0) cc_final: 0.7569 (pt0) REVERT: G 98 GLU cc_start: 0.8669 (pt0) cc_final: 0.8191 (pt0) REVERT: G 101 LYS cc_start: 0.8478 (mmtt) cc_final: 0.8166 (mmtt) REVERT: G 108 LEU cc_start: 0.9408 (mt) cc_final: 0.9190 (mt) REVERT: G 116 VAL cc_start: 0.8960 (t) cc_final: 0.8636 (m) REVERT: G 124 GLN cc_start: 0.8939 (tm-30) cc_final: 0.8607 (tm-30) REVERT: H 82 MET cc_start: 0.9399 (ttm) cc_final: 0.9045 (ttm) REVERT: H 88 LEU cc_start: 0.9272 (tp) cc_final: 0.8947 (tp) REVERT: H 126 PHE cc_start: 0.8099 (m-80) cc_final: 0.7862 (m-10) REVERT: H 231 MET cc_start: 0.9101 (tpt) cc_final: 0.8465 (tpp) REVERT: H 266 TYR cc_start: 0.8981 (m-10) cc_final: 0.8639 (m-10) REVERT: I 47 ARG cc_start: 0.8403 (mtm180) cc_final: 0.8110 (mtt180) REVERT: I 179 LEU cc_start: 0.9207 (tt) cc_final: 0.8720 (mm) outliers start: 3 outliers final: 0 residues processed: 485 average time/residue: 0.1811 time to fit residues: 128.9223 Evaluate side-chains 336 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 336 time to evaluate : 0.807 ------------------------------------------------------------------------------- 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: 2.9990 chunk 0 optimal weight: 7.9990 chunk 54 optimal weight: 9.9990 chunk 76 optimal weight: 10.0000 chunk 24 optimal weight: 9.9990 chunk 171 optimal weight: 0.9990 chunk 83 optimal weight: 5.9990 chunk 43 optimal weight: 10.0000 chunk 227 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 61 optimal weight: 6.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 HIS ** B 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 63 ASN ** C 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 144 HIS ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 125 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 ** G 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 144 HIS ** 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 = 0.3407 r_free = 0.3407 target = 0.062594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.049987 restraints weight = 99288.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.051867 restraints weight = 52530.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.053129 restraints weight = 32659.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.053929 restraints weight = 22564.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.054566 restraints weight = 17075.269| |-----------------------------------------------------------------------------| r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.4636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 20367 Z= 0.200 Angle : 0.728 6.715 27486 Z= 0.396 Chirality : 0.047 0.181 2970 Planarity : 0.004 0.065 3447 Dihedral : 13.016 179.554 2997 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 21.36 Ramachandran Plot: Outliers : 2.40 % Allowed : 11.64 % Favored : 85.96 % Rotamer: Outliers : 0.05 % Allowed : 2.31 % Favored : 97.64 % 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 aren not related in a simple way. whole: -2.02 (0.16), residues: 2457 helix: 0.04 (0.17), residues: 756 sheet: -2.31 (0.19), residues: 549 loop : -1.71 (0.19), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 78 TYR 0.024 0.002 TYR H 217 PHE 0.021 0.002 PHE E 104 HIS 0.008 0.001 HIS I 34 Details of bonding type rmsd covalent geometry : bond 0.00424 (20367) covalent geometry : angle 0.72805 (27486) hydrogen bonds : bond 0.04320 ( 882) hydrogen bonds : angle 6.69170 ( 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 407 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 406 time to evaluate : 0.877 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: 0.9095 (tt0) cc_final: 0.8874 (tt0) REVERT: A 115 MET cc_start: 0.8613 (mtm) cc_final: 0.8220 (mtt) REVERT: A 202 MET cc_start: 0.7176 (mmm) cc_final: 0.6927 (tpp) REVERT: A 211 THR cc_start: 0.8894 (p) cc_final: 0.8169 (p) REVERT: A 231 MET cc_start: 0.8859 (tpp) cc_final: 0.8611 (tpp) REVERT: B 7 ILE cc_start: 0.8505 (mp) cc_final: 0.8281 (mm) REVERT: B 73 TYR cc_start: 0.7932 (m-80) cc_final: 0.7370 (m-80) REVERT: B 88 LEU cc_start: 0.9496 (tp) cc_final: 0.9224 (tp) REVERT: B 98 GLU cc_start: 0.8785 (mt-10) cc_final: 0.8378 (pt0) REVERT: B 109 THR cc_start: 0.8372 (p) cc_final: 0.8092 (t) REVERT: B 115 MET cc_start: 0.8883 (ttm) cc_final: 0.8423 (tpp) REVERT: B 139 PHE cc_start: 0.7828 (t80) cc_final: 0.7052 (t80) REVERT: B 141 PHE cc_start: 0.9052 (p90) cc_final: 0.7694 (p90) REVERT: C 46 GLU cc_start: 0.7930 (mp0) cc_final: 0.7531 (mp0) REVERT: C 63 ASN cc_start: 0.8975 (m-40) cc_final: 0.8508 (t0) REVERT: C 73 TYR cc_start: 0.7997 (m-80) cc_final: 0.7474 (m-80) REVERT: C 88 LEU cc_start: 0.9717 (tp) cc_final: 0.9460 (tp) REVERT: C 98 GLU cc_start: 0.8711 (pt0) cc_final: 0.8480 (pt0) REVERT: C 115 MET cc_start: 0.8601 (mmm) cc_final: 0.8098 (mmm) REVERT: C 177 LEU cc_start: 0.9058 (tp) cc_final: 0.8760 (tp) REVERT: C 259 SER cc_start: 0.9252 (p) cc_final: 0.8695 (t) REVERT: D 46 GLU cc_start: 0.8606 (mp0) cc_final: 0.8111 (mp0) REVERT: D 47 ARG cc_start: 0.6752 (mpt180) cc_final: 0.6543 (mpt180) REVERT: D 68 ARG cc_start: 0.7490 (mmm160) cc_final: 0.7192 (mmm160) REVERT: D 98 GLU cc_start: 0.8612 (tp30) cc_final: 0.8214 (tm-30) REVERT: D 102 LYS cc_start: 0.8019 (tmmt) cc_final: 0.7720 (ttpt) REVERT: D 118 ASP cc_start: 0.7948 (m-30) cc_final: 0.7562 (m-30) REVERT: D 124 GLN cc_start: 0.9212 (tm-30) cc_final: 0.8932 (tm-30) REVERT: E 62 LYS cc_start: 0.9278 (mmmm) cc_final: 0.8889 (mptt) REVERT: E 88 LEU cc_start: 0.9688 (tp) cc_final: 0.9481 (tp) REVERT: E 108 LEU cc_start: 0.9590 (mt) cc_final: 0.9390 (mt) REVERT: E 115 MET cc_start: 0.8213 (tpp) cc_final: 0.7642 (tpp) REVERT: E 148 MET cc_start: 0.7992 (mmm) cc_final: 0.7262 (mmm) REVERT: E 240 TYR cc_start: 0.9212 (m-80) cc_final: 0.8718 (m-10) REVERT: E 259 SER cc_start: 0.9111 (p) cc_final: 0.8832 (t) REVERT: F 46 GLU cc_start: 0.8394 (mp0) cc_final: 0.8090 (mp0) REVERT: F 73 TYR cc_start: 0.7927 (m-80) cc_final: 0.7503 (m-80) REVERT: F 95 ILE cc_start: 0.9405 (pt) cc_final: 0.9135 (mm) REVERT: F 98 GLU cc_start: 0.8519 (pt0) cc_final: 0.8152 (pt0) REVERT: F 108 LEU cc_start: 0.9181 (mt) cc_final: 0.8862 (mt) REVERT: F 115 MET cc_start: 0.8779 (tpp) cc_final: 0.8211 (tpp) REVERT: F 159 SER cc_start: 0.8892 (m) cc_final: 0.8576 (p) REVERT: F 259 SER cc_start: 0.9328 (p) cc_final: 0.8949 (t) REVERT: G 46 GLU cc_start: 0.8902 (mp0) cc_final: 0.8395 (mp0) REVERT: G 107 ILE cc_start: 0.9257 (mt) cc_final: 0.8929 (mm) REVERT: G 108 LEU cc_start: 0.9491 (mt) cc_final: 0.8564 (mt) REVERT: G 124 GLN cc_start: 0.9151 (tm-30) cc_final: 0.8760 (tm-30) REVERT: G 211 THR cc_start: 0.8592 (p) cc_final: 0.8366 (p) REVERT: G 231 MET cc_start: 0.9090 (tpp) cc_final: 0.8680 (tpp) REVERT: H 47 ARG cc_start: 0.8165 (mpt180) cc_final: 0.7746 (mpt180) REVERT: H 83 GLU cc_start: 0.8888 (mp0) cc_final: 0.8181 (mp0) REVERT: H 88 LEU cc_start: 0.9326 (tp) cc_final: 0.9024 (tp) REVERT: H 148 MET cc_start: 0.7558 (tpt) cc_final: 0.7108 (tpp) REVERT: H 231 MET cc_start: 0.9202 (tpt) cc_final: 0.8935 (tpt) REVERT: H 268 ARG cc_start: 0.8985 (mpp-170) cc_final: 0.8503 (tpm170) REVERT: I 45 MET cc_start: 0.3943 (mtm) cc_final: 0.3698 (mtm) REVERT: I 179 LEU cc_start: 0.9180 (tt) cc_final: 0.8736 (mm) outliers start: 1 outliers final: 0 residues processed: 407 average time/residue: 0.1670 time to fit residues: 101.1003 Evaluate side-chains 300 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 300 time to evaluate : 0.757 ------------------------------------------------------------------------------- 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: 0.4980 chunk 19 optimal weight: 9.9990 chunk 202 optimal weight: 7.9990 chunk 98 optimal weight: 8.9990 chunk 91 optimal weight: 2.9990 chunk 30 optimal weight: 10.0000 chunk 230 optimal weight: 8.9990 chunk 104 optimal weight: 4.9990 chunk 74 optimal weight: 0.8980 chunk 77 optimal weight: 0.9980 chunk 63 optimal weight: 0.8980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 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 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 163 ASN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.064362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.051688 restraints weight = 96974.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.053611 restraints weight = 51625.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.054909 restraints weight = 32234.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.055750 restraints weight = 22297.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.056410 restraints weight = 16806.504| |-----------------------------------------------------------------------------| r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.5311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20367 Z= 0.148 Angle : 0.683 8.909 27486 Z= 0.371 Chirality : 0.046 0.168 2970 Planarity : 0.004 0.039 3447 Dihedral : 12.909 178.703 2997 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 18.49 Ramachandran Plot: Outliers : 1.79 % Allowed : 11.52 % Favored : 86.69 % Rotamer: Outliers : 0.09 % Allowed : 1.94 % Favored : 97.96 % 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 aren not related in a simple way. whole: -1.91 (0.17), residues: 2457 helix: 0.14 (0.18), residues: 783 sheet: -2.21 (0.19), residues: 567 loop : -1.70 (0.19), residues: 1107 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 87 TYR 0.027 0.002 TYR G 56 PHE 0.026 0.002 PHE D 96 HIS 0.007 0.001 HIS F 125 Details of bonding type rmsd covalent geometry : bond 0.00306 (20367) covalent geometry : angle 0.68251 (27486) hydrogen bonds : bond 0.04047 ( 882) hydrogen bonds : angle 6.38247 ( 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: 2 poor density : 401 time to evaluate : 0.816 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 211 THR cc_start: 0.8696 (p) cc_final: 0.8263 (p) REVERT: A 231 MET cc_start: 0.8853 (tpp) cc_final: 0.8527 (tpp) REVERT: B 1 MET cc_start: 0.8734 (mtp) cc_final: 0.8393 (ttp) REVERT: B 98 GLU cc_start: 0.8783 (mt-10) cc_final: 0.8387 (pt0) REVERT: B 115 MET cc_start: 0.8989 (ttm) cc_final: 0.8482 (tpp) REVERT: B 139 PHE cc_start: 0.7668 (t80) cc_final: 0.7036 (t80) REVERT: B 141 PHE cc_start: 0.9032 (p90) cc_final: 0.7751 (p90) REVERT: C 63 ASN cc_start: 0.8824 (m110) cc_final: 0.8406 (m-40) REVERT: C 73 TYR cc_start: 0.8039 (m-80) cc_final: 0.7519 (m-80) REVERT: C 88 LEU cc_start: 0.9693 (tp) cc_final: 0.9480 (tp) REVERT: C 115 MET cc_start: 0.8646 (mmm) cc_final: 0.8399 (mmm) REVERT: C 259 SER cc_start: 0.9277 (p) cc_final: 0.8831 (t) REVERT: D 46 GLU cc_start: 0.8519 (mp0) cc_final: 0.8118 (mp0) REVERT: D 68 ARG cc_start: 0.7493 (mmm160) cc_final: 0.6849 (mmm160) REVERT: D 98 GLU cc_start: 0.8448 (tp30) cc_final: 0.8141 (tt0) REVERT: D 102 LYS cc_start: 0.8079 (tmmt) cc_final: 0.7726 (ttpt) REVERT: D 124 GLN cc_start: 0.9194 (tm-30) cc_final: 0.8960 (tm-30) REVERT: D 145 ASN cc_start: 0.8280 (m-40) cc_final: 0.8020 (t0) REVERT: D 202 MET cc_start: 0.7255 (mmm) cc_final: 0.7045 (mmm) REVERT: D 268 ARG cc_start: 0.8601 (mmm-85) cc_final: 0.8372 (mmm160) REVERT: E 88 LEU cc_start: 0.9702 (tp) cc_final: 0.9494 (tp) REVERT: E 115 MET cc_start: 0.8339 (tpp) cc_final: 0.7630 (tpp) REVERT: E 148 MET cc_start: 0.8043 (mmm) cc_final: 0.7322 (mmm) REVERT: E 202 MET cc_start: 0.7305 (mmm) cc_final: 0.7005 (mmm) REVERT: F 8 ASP cc_start: 0.8688 (t0) cc_final: 0.8383 (t0) REVERT: F 73 TYR cc_start: 0.8057 (m-80) cc_final: 0.7381 (m-80) REVERT: F 108 LEU cc_start: 0.9181 (mt) cc_final: 0.8865 (mt) REVERT: F 115 MET cc_start: 0.8949 (tpp) cc_final: 0.8293 (tpp) REVERT: F 118 ASP cc_start: 0.8084 (m-30) cc_final: 0.7821 (m-30) REVERT: F 159 SER cc_start: 0.8818 (m) cc_final: 0.8516 (p) REVERT: G 62 LYS cc_start: 0.9069 (mttt) cc_final: 0.8789 (mmmt) REVERT: G 83 GLU cc_start: 0.8556 (pm20) cc_final: 0.8266 (pm20) REVERT: G 98 GLU cc_start: 0.8756 (pt0) cc_final: 0.8479 (pt0) REVERT: G 115 MET cc_start: 0.7966 (tpp) cc_final: 0.7751 (tpp) REVERT: G 124 GLN cc_start: 0.9163 (tm-30) cc_final: 0.8787 (tm-30) REVERT: G 231 MET cc_start: 0.9239 (tpp) cc_final: 0.8656 (tpp) REVERT: H 47 ARG cc_start: 0.8089 (mpt180) cc_final: 0.7763 (mpt180) REVERT: H 83 GLU cc_start: 0.8805 (mp0) cc_final: 0.8242 (mp0) REVERT: H 115 MET cc_start: 0.8253 (tpp) cc_final: 0.6805 (tpp) REVERT: H 231 MET cc_start: 0.9168 (tpt) cc_final: 0.8905 (tpt) REVERT: H 268 ARG cc_start: 0.9005 (mpp-170) cc_final: 0.8406 (tpm170) REVERT: I 1 MET cc_start: 0.3500 (tpt) cc_final: 0.1681 (tmm) REVERT: I 179 LEU cc_start: 0.9148 (tt) cc_final: 0.8849 (mm) outliers start: 2 outliers final: 0 residues processed: 402 average time/residue: 0.1617 time to fit residues: 97.9686 Evaluate side-chains 291 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 291 time to evaluate : 0.785 ------------------------------------------------------------------------------- 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: 8.9990 chunk 65 optimal weight: 6.9990 chunk 241 optimal weight: 9.9990 chunk 70 optimal weight: 8.9990 chunk 26 optimal weight: 6.9990 chunk 93 optimal weight: 0.9980 chunk 101 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 chunk 16 optimal weight: 0.8980 chunk 136 optimal weight: 10.0000 chunk 88 optimal weight: 3.9990 overall best weight: 1.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 ** 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 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** ** 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 = 0.3453 r_free = 0.3453 target = 0.064289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.051718 restraints weight = 97276.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.053600 restraints weight = 52201.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.054877 restraints weight = 32845.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.055701 restraints weight = 22829.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.056355 restraints weight = 17273.279| |-----------------------------------------------------------------------------| r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.5725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 20367 Z= 0.151 Angle : 0.678 7.145 27486 Z= 0.369 Chirality : 0.046 0.168 2970 Planarity : 0.004 0.074 3447 Dihedral : 12.779 175.725 2997 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 18.01 Ramachandran Plot: Outliers : 1.55 % Allowed : 12.33 % Favored : 86.12 % Rotamer: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % 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 aren not related in a simple way. whole: -1.54 (0.17), residues: 2457 helix: 0.69 (0.19), residues: 711 sheet: -1.81 (0.20), residues: 603 loop : -1.64 (0.18), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 87 TYR 0.039 0.002 TYR A 219 PHE 0.023 0.002 PHE E 270 HIS 0.006 0.001 HIS C 125 Details of bonding type rmsd covalent geometry : bond 0.00320 (20367) covalent geometry : angle 0.67791 (27486) hydrogen bonds : bond 0.03907 ( 882) hydrogen bonds : angle 6.21516 ( 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 369 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 369 time to evaluate : 0.951 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: 0.9071 (tt0) cc_final: 0.8836 (tt0) REVERT: A 45 MET cc_start: 0.7806 (mpp) cc_final: 0.7398 (mpp) REVERT: A 211 THR cc_start: 0.8796 (p) cc_final: 0.8287 (p) REVERT: A 231 MET cc_start: 0.8938 (tpp) cc_final: 0.8601 (tpp) REVERT: B 1 MET cc_start: 0.8717 (mtp) cc_final: 0.8213 (ttp) REVERT: B 72 MET cc_start: 0.8750 (mpp) cc_final: 0.8468 (mpp) REVERT: B 73 TYR cc_start: 0.7678 (m-80) cc_final: 0.6794 (m-80) REVERT: B 98 GLU cc_start: 0.8817 (mt-10) cc_final: 0.8447 (pt0) REVERT: B 115 MET cc_start: 0.8965 (ttm) cc_final: 0.8549 (tpp) REVERT: B 139 PHE cc_start: 0.7776 (t80) cc_final: 0.7166 (t80) REVERT: B 141 PHE cc_start: 0.9075 (p90) cc_final: 0.7791 (p90) REVERT: C 63 ASN cc_start: 0.8890 (m110) cc_final: 0.8365 (m-40) REVERT: C 73 TYR cc_start: 0.8022 (m-80) cc_final: 0.7366 (m-80) REVERT: C 115 MET cc_start: 0.8804 (mmm) cc_final: 0.8418 (mmm) REVERT: C 151 GLU cc_start: 0.7853 (mp0) cc_final: 0.7413 (mp0) REVERT: C 202 MET cc_start: 0.7462 (mmm) cc_final: 0.7232 (mmm) REVERT: C 259 SER cc_start: 0.9223 (p) cc_final: 0.8743 (t) REVERT: D 46 GLU cc_start: 0.8427 (mp0) cc_final: 0.7878 (mp0) REVERT: D 62 LYS cc_start: 0.9559 (mptt) cc_final: 0.9353 (mptt) REVERT: D 68 ARG cc_start: 0.7256 (mmm160) cc_final: 0.6990 (mmm160) REVERT: D 102 LYS cc_start: 0.7919 (tmmt) cc_final: 0.7675 (ttpt) REVERT: D 124 GLN cc_start: 0.9226 (tm-30) cc_final: 0.9002 (tm-30) REVERT: D 145 ASN cc_start: 0.8313 (m-40) cc_final: 0.8057 (t0) REVERT: D 268 ARG cc_start: 0.8684 (mmm-85) cc_final: 0.8431 (mmm160) REVERT: E 1 MET cc_start: 0.8736 (mtp) cc_final: 0.8353 (ttm) REVERT: E 46 GLU cc_start: 0.7892 (mp0) cc_final: 0.7587 (mp0) REVERT: E 88 LEU cc_start: 0.9754 (tp) cc_final: 0.9537 (tp) REVERT: E 115 MET cc_start: 0.8309 (tpp) cc_final: 0.7582 (tpp) REVERT: E 148 MET cc_start: 0.8102 (mmm) cc_final: 0.7317 (mmm) REVERT: F 45 MET cc_start: 0.7038 (tpp) cc_final: 0.6388 (tpp) REVERT: F 106 LEU cc_start: 0.8645 (tp) cc_final: 0.8354 (tp) REVERT: F 108 LEU cc_start: 0.9270 (mt) cc_final: 0.8972 (mt) REVERT: F 115 MET cc_start: 0.9089 (tpp) cc_final: 0.8431 (tpp) REVERT: F 118 ASP cc_start: 0.8108 (m-30) cc_final: 0.7811 (m-30) REVERT: F 159 SER cc_start: 0.8879 (m) cc_final: 0.8563 (p) REVERT: G 46 GLU cc_start: 0.8826 (mp0) cc_final: 0.8484 (mp0) REVERT: G 57 VAL cc_start: 0.8710 (m) cc_final: 0.8161 (p) REVERT: G 62 LYS cc_start: 0.9067 (mttt) cc_final: 0.8803 (mmmt) REVERT: G 73 TYR cc_start: 0.8301 (m-80) cc_final: 0.7926 (m-80) REVERT: G 98 GLU cc_start: 0.8798 (pt0) cc_final: 0.8537 (pt0) REVERT: G 108 LEU cc_start: 0.9512 (mt) cc_final: 0.9084 (mt) REVERT: G 124 GLN cc_start: 0.9219 (tm-30) cc_final: 0.8798 (tm-30) REVERT: G 231 MET cc_start: 0.9244 (tpp) cc_final: 0.8518 (tpp) REVERT: H 88 LEU cc_start: 0.9382 (tp) cc_final: 0.9104 (tp) REVERT: H 106 LEU cc_start: 0.8788 (tp) cc_final: 0.8573 (tp) REVERT: H 126 PHE cc_start: 0.8265 (m-80) cc_final: 0.7825 (m-10) REVERT: H 268 ARG cc_start: 0.9094 (mpp-170) cc_final: 0.8416 (tpm170) REVERT: I 1 MET cc_start: 0.3317 (tpt) cc_final: 0.1867 (tmm) REVERT: I 45 MET cc_start: 0.2860 (mtm) cc_final: -0.1225 (mtm) REVERT: I 115 MET cc_start: 0.8528 (mmt) cc_final: 0.7563 (mmm) REVERT: I 131 GLU cc_start: 0.8183 (pm20) cc_final: 0.7850 (tm-30) REVERT: I 179 LEU cc_start: 0.9085 (tt) cc_final: 0.8859 (mm) outliers start: 0 outliers final: 0 residues processed: 369 average time/residue: 0.1673 time to fit residues: 92.6132 Evaluate side-chains 288 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 288 time to evaluate : 0.763 ------------------------------------------------------------------------------- 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: 7.9990 chunk 237 optimal weight: 10.0000 chunk 157 optimal weight: 7.9990 chunk 168 optimal weight: 9.9990 chunk 58 optimal weight: 0.9980 chunk 207 optimal weight: 10.0000 chunk 20 optimal weight: 2.9990 chunk 22 optimal weight: 10.0000 chunk 171 optimal weight: 0.9980 chunk 233 optimal weight: 8.9990 overall best weight: 4.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** E 81 HIS ** 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** F 163 ASN ** 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 = 0.3360 r_free = 0.3360 target = 0.060636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.048305 restraints weight = 100016.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.050088 restraints weight = 54076.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.051296 restraints weight = 34188.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.052139 restraints weight = 23903.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.052676 restraints weight = 18028.069| |-----------------------------------------------------------------------------| r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.6087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 20367 Z= 0.261 Angle : 0.776 11.887 27486 Z= 0.414 Chirality : 0.048 0.175 2970 Planarity : 0.004 0.053 3447 Dihedral : 12.558 177.108 2997 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 23.52 Ramachandran Plot: Outliers : 1.42 % Allowed : 12.78 % Favored : 85.80 % Rotamer: Outliers : 0.05 % Allowed : 2.82 % Favored : 97.13 % 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 aren not related in a simple way. whole: -2.06 (0.16), residues: 2457 helix: 0.02 (0.18), residues: 756 sheet: -1.97 (0.20), residues: 612 loop : -1.92 (0.18), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 87 TYR 0.024 0.003 TYR F 65 PHE 0.029 0.002 PHE F 270 HIS 0.008 0.002 HIS H 125 Details of bonding type rmsd covalent geometry : bond 0.00556 (20367) covalent geometry : angle 0.77624 (27486) hydrogen bonds : bond 0.04155 ( 882) hydrogen bonds : angle 6.44213 ( 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 325 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 324 time to evaluate : 0.813 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: 0.9115 (tt0) cc_final: 0.8887 (tt0) REVERT: A 231 MET cc_start: 0.8934 (tpp) cc_final: 0.8631 (tpp) REVERT: B 1 MET cc_start: 0.8873 (mtp) cc_final: 0.8588 (ttm) REVERT: B 72 MET cc_start: 0.8642 (mpp) cc_final: 0.8325 (mpp) REVERT: B 98 GLU cc_start: 0.8933 (mt-10) cc_final: 0.8649 (pt0) REVERT: B 115 MET cc_start: 0.8987 (ttm) cc_final: 0.8374 (tpp) REVERT: C 1 MET cc_start: 0.8431 (ttt) cc_final: 0.7949 (tmm) REVERT: C 63 ASN cc_start: 0.8969 (m110) cc_final: 0.8525 (m-40) REVERT: C 73 TYR cc_start: 0.8167 (m-80) cc_final: 0.7475 (m-80) REVERT: C 88 LEU cc_start: 0.9723 (tp) cc_final: 0.9505 (tp) REVERT: C 115 MET cc_start: 0.8763 (mmm) cc_final: 0.8436 (mmm) REVERT: C 259 SER cc_start: 0.9257 (p) cc_final: 0.8866 (t) REVERT: D 46 GLU cc_start: 0.8460 (mp0) cc_final: 0.8024 (mp0) REVERT: D 124 GLN cc_start: 0.9192 (tm-30) cc_final: 0.8939 (tm-30) REVERT: D 145 ASN cc_start: 0.8438 (m-40) cc_final: 0.8205 (t0) REVERT: D 240 TYR cc_start: 0.9152 (m-80) cc_final: 0.8798 (m-10) REVERT: E 115 MET cc_start: 0.8241 (tpp) cc_final: 0.7552 (tpp) REVERT: E 148 MET cc_start: 0.8059 (mmm) cc_final: 0.7404 (mmm) REVERT: E 202 MET cc_start: 0.7334 (mmm) cc_final: 0.7057 (mmm) REVERT: F 106 LEU cc_start: 0.8675 (tp) cc_final: 0.8424 (tp) REVERT: F 108 LEU cc_start: 0.9324 (mt) cc_final: 0.9024 (mt) REVERT: F 115 MET cc_start: 0.9031 (tpp) cc_final: 0.8335 (tpp) REVERT: F 118 ASP cc_start: 0.8212 (m-30) cc_final: 0.7967 (m-30) REVERT: G 57 VAL cc_start: 0.8906 (m) cc_final: 0.8246 (p) REVERT: G 101 LYS cc_start: 0.8299 (mmtt) cc_final: 0.8065 (mmtt) REVERT: G 108 LEU cc_start: 0.9186 (mt) cc_final: 0.8659 (mt) REVERT: G 124 GLN cc_start: 0.9289 (tm-30) cc_final: 0.8850 (tm-30) REVERT: G 231 MET cc_start: 0.9128 (tpp) cc_final: 0.8523 (tpp) REVERT: H 47 ARG cc_start: 0.8194 (mpt180) cc_final: 0.7808 (mpt180) REVERT: H 115 MET cc_start: 0.8806 (tpp) cc_final: 0.8256 (mmm) REVERT: H 256 TYR cc_start: 0.8818 (m-80) cc_final: 0.8539 (m-80) REVERT: I 1 MET cc_start: 0.3340 (tpt) cc_final: 0.0757 (tmm) REVERT: I 125 HIS cc_start: 0.7853 (m170) cc_final: 0.7450 (m170) REVERT: I 179 LEU cc_start: 0.9089 (tt) cc_final: 0.8831 (mm) outliers start: 1 outliers final: 0 residues processed: 325 average time/residue: 0.1704 time to fit residues: 82.5645 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 : 0.782 ------------------------------------------------------------------------------- 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: 20.0000 chunk 203 optimal weight: 4.9990 chunk 198 optimal weight: 1.9990 chunk 164 optimal weight: 9.9990 chunk 144 optimal weight: 0.8980 chunk 233 optimal weight: 10.0000 chunk 216 optimal weight: 20.0000 chunk 188 optimal weight: 8.9990 chunk 208 optimal weight: 10.0000 chunk 15 optimal weight: 0.8980 chunk 186 optimal weight: 8.9990 overall best weight: 3.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 81 HIS ** 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 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 81 HIS ** 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** ** 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 = 0.3372 r_free = 0.3372 target = 0.061177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.048707 restraints weight = 100010.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.050538 restraints weight = 54294.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.051729 restraints weight = 34247.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 62)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.052599 restraints weight = 24108.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.053193 restraints weight = 18154.557| |-----------------------------------------------------------------------------| r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.6386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.113 20367 Z= 0.230 Angle : 0.744 8.970 27486 Z= 0.398 Chirality : 0.048 0.155 2970 Planarity : 0.004 0.047 3447 Dihedral : 12.357 166.111 2997 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 22.45 Ramachandran Plot: Outliers : 1.47 % Allowed : 12.74 % Favored : 85.80 % Rotamer: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % 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 aren not related in a simple way. whole: -2.18 (0.16), residues: 2457 helix: -0.09 (0.18), residues: 756 sheet: -1.99 (0.20), residues: 621 loop : -2.02 (0.18), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 87 TYR 0.040 0.002 TYR E 90 PHE 0.023 0.002 PHE F 270 HIS 0.006 0.002 HIS H 125 Details of bonding type rmsd covalent geometry : bond 0.00495 (20367) covalent geometry : angle 0.74385 (27486) hydrogen bonds : bond 0.04009 ( 882) hydrogen bonds : angle 6.43349 ( 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 326 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 326 time to evaluate : 0.840 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: A 23 GLN cc_start: 0.9086 (tt0) cc_final: 0.8856 (tt0) REVERT: A 45 MET cc_start: 0.7844 (mpp) cc_final: 0.7539 (mpp) REVERT: A 101 LYS cc_start: 0.6998 (mmtt) cc_final: 0.6669 (mmmt) REVERT: A 211 THR cc_start: 0.8901 (p) cc_final: 0.8700 (p) REVERT: A 231 MET cc_start: 0.8926 (tpp) cc_final: 0.8599 (tpp) REVERT: B 72 MET cc_start: 0.8524 (mpp) cc_final: 0.7209 (pmm) REVERT: B 115 MET cc_start: 0.9015 (ttm) cc_final: 0.8467 (tpp) REVERT: B 126 PHE cc_start: 0.8695 (m-80) cc_final: 0.8487 (m-80) REVERT: C 63 ASN cc_start: 0.9030 (m-40) cc_final: 0.8562 (m-40) REVERT: C 71 GLN cc_start: 0.8771 (mp10) cc_final: 0.8331 (mp10) REVERT: C 73 TYR cc_start: 0.8121 (m-80) cc_final: 0.7710 (m-80) REVERT: C 115 MET cc_start: 0.8744 (mmm) cc_final: 0.8366 (mmm) REVERT: C 259 SER cc_start: 0.9171 (p) cc_final: 0.8829 (t) REVERT: D 1 MET cc_start: 0.8188 (ttt) cc_final: 0.7988 (tmm) REVERT: D 46 GLU cc_start: 0.8394 (mp0) cc_final: 0.8008 (mp0) REVERT: D 95 ILE cc_start: 0.9646 (tt) cc_final: 0.9213 (tt) REVERT: D 107 ILE cc_start: 0.9367 (mm) cc_final: 0.9167 (mm) REVERT: D 124 GLN cc_start: 0.9188 (tm-30) cc_final: 0.8974 (tm-30) REVERT: D 175 ASN cc_start: 0.8307 (m-40) cc_final: 0.7946 (m-40) REVERT: D 240 TYR cc_start: 0.9166 (m-80) cc_final: 0.8800 (m-10) REVERT: D 256 TYR cc_start: 0.8160 (m-10) cc_final: 0.7095 (m-10) REVERT: E 83 GLU cc_start: 0.8901 (mp0) cc_final: 0.8311 (mp0) REVERT: E 115 MET cc_start: 0.8251 (tpp) cc_final: 0.7583 (tpp) REVERT: E 148 MET cc_start: 0.8066 (mmm) cc_final: 0.7381 (mmm) REVERT: F 73 TYR cc_start: 0.8454 (m-10) cc_final: 0.8012 (m-80) REVERT: F 106 LEU cc_start: 0.8653 (tp) cc_final: 0.8419 (tp) REVERT: F 108 LEU cc_start: 0.9302 (mt) cc_final: 0.9017 (mt) REVERT: F 115 MET cc_start: 0.9106 (tpp) cc_final: 0.8414 (tpp) REVERT: F 118 ASP cc_start: 0.8166 (m-30) cc_final: 0.7894 (m-30) REVERT: G 57 VAL cc_start: 0.8799 (m) cc_final: 0.8269 (p) REVERT: G 73 TYR cc_start: 0.8310 (m-80) cc_final: 0.7848 (m-80) REVERT: G 101 LYS cc_start: 0.8231 (mmtt) cc_final: 0.8001 (mmtt) REVERT: G 108 LEU cc_start: 0.9273 (mt) cc_final: 0.8644 (mt) REVERT: G 115 MET cc_start: 0.7862 (mmp) cc_final: 0.7391 (mmp) REVERT: G 124 GLN cc_start: 0.9255 (tm-30) cc_final: 0.8826 (tm-30) REVERT: G 148 MET cc_start: 0.8164 (mmm) cc_final: 0.7615 (ttm) REVERT: G 202 MET cc_start: 0.7909 (mmt) cc_final: 0.7614 (mmt) REVERT: G 227 LYS cc_start: 0.9443 (mttm) cc_final: 0.9164 (mtpp) REVERT: G 231 MET cc_start: 0.9167 (tpp) cc_final: 0.8680 (tpp) REVERT: H 88 LEU cc_start: 0.9403 (tp) cc_final: 0.9186 (tp) REVERT: H 115 MET cc_start: 0.8746 (tpp) cc_final: 0.8521 (tpp) REVERT: H 262 LEU cc_start: 0.9444 (mt) cc_final: 0.9211 (mt) REVERT: I 1 MET cc_start: 0.3358 (tpt) cc_final: 0.0746 (tmm) REVERT: I 125 HIS cc_start: 0.7899 (m170) cc_final: 0.7474 (m170) outliers start: 0 outliers final: 0 residues processed: 326 average time/residue: 0.1667 time to fit residues: 81.4911 Evaluate side-chains 248 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 248 time to evaluate : 0.785 ------------------------------------------------------------------------------- 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: 7.9990 chunk 223 optimal weight: 20.0000 chunk 161 optimal weight: 0.9990 chunk 204 optimal weight: 9.9990 chunk 241 optimal weight: 8.9990 chunk 49 optimal weight: 7.9990 chunk 147 optimal weight: 0.8980 chunk 29 optimal weight: 3.9990 chunk 150 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 227 optimal weight: 7.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 ASN ** 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 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.062534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.050087 restraints weight = 98203.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.051929 restraints weight = 53406.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.053190 restraints weight = 33826.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.054030 restraints weight = 23571.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.054668 restraints weight = 17820.587| |-----------------------------------------------------------------------------| r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.6576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 20367 Z= 0.166 Angle : 0.690 8.871 27486 Z= 0.373 Chirality : 0.047 0.162 2970 Planarity : 0.004 0.039 3447 Dihedral : 12.262 163.301 2997 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 20.32 Ramachandran Plot: Outliers : 1.38 % Allowed : 12.17 % Favored : 86.45 % Rotamer: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % 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 aren not related in a simple way. whole: -2.15 (0.17), residues: 2457 helix: 0.10 (0.19), residues: 747 sheet: -1.94 (0.20), residues: 639 loop : -2.15 (0.18), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 87 TYR 0.033 0.002 TYR E 90 PHE 0.029 0.002 PHE F 270 HIS 0.005 0.001 HIS H 125 Details of bonding type rmsd covalent geometry : bond 0.00363 (20367) covalent geometry : angle 0.68983 (27486) hydrogen bonds : bond 0.03770 ( 882) hydrogen bonds : angle 6.28348 ( 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 336 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 336 time to evaluate : 0.878 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: A 23 GLN cc_start: 0.9092 (tt0) cc_final: 0.8864 (tt0) REVERT: A 101 LYS cc_start: 0.7060 (mmtt) cc_final: 0.6751 (mmmt) REVERT: A 211 THR cc_start: 0.8821 (p) cc_final: 0.8595 (p) REVERT: A 231 MET cc_start: 0.8970 (tpp) cc_final: 0.8666 (tpp) REVERT: B 72 MET cc_start: 0.8473 (mpp) cc_final: 0.7209 (pmm) REVERT: B 98 GLU cc_start: 0.8906 (mt-10) cc_final: 0.8705 (mt-10) REVERT: B 115 MET cc_start: 0.8843 (ttm) cc_final: 0.8430 (tpp) REVERT: C 63 ASN cc_start: 0.8979 (m-40) cc_final: 0.8504 (m-40) REVERT: C 71 GLN cc_start: 0.8605 (mp10) cc_final: 0.8249 (mp10) REVERT: C 115 MET cc_start: 0.8840 (mmm) cc_final: 0.8564 (mmm) REVERT: C 259 SER cc_start: 0.9078 (p) cc_final: 0.8756 (t) REVERT: D 1 MET cc_start: 0.8280 (ttt) cc_final: 0.7949 (tmm) REVERT: D 46 GLU cc_start: 0.8463 (mp0) cc_final: 0.8018 (mp0) REVERT: D 124 GLN cc_start: 0.9214 (tm-30) cc_final: 0.9002 (tm-30) REVERT: D 175 ASN cc_start: 0.8347 (m-40) cc_final: 0.7870 (m-40) REVERT: D 240 TYR cc_start: 0.9199 (m-80) cc_final: 0.8801 (m-10) REVERT: E 83 GLU cc_start: 0.8892 (mp0) cc_final: 0.8227 (mp0) REVERT: E 115 MET cc_start: 0.8227 (tpp) cc_final: 0.7619 (tpp) REVERT: E 124 GLN cc_start: 0.9436 (tt0) cc_final: 0.9218 (tm-30) REVERT: E 148 MET cc_start: 0.8065 (mmm) cc_final: 0.7393 (mmm) REVERT: F 73 TYR cc_start: 0.8514 (m-10) cc_final: 0.7891 (m-10) REVERT: F 115 MET cc_start: 0.9120 (tpp) cc_final: 0.8389 (tpp) REVERT: F 118 ASP cc_start: 0.8172 (m-30) cc_final: 0.7900 (m-30) REVERT: G 57 VAL cc_start: 0.8744 (m) cc_final: 0.8309 (p) REVERT: G 73 TYR cc_start: 0.8271 (m-80) cc_final: 0.7752 (m-80) REVERT: G 101 LYS cc_start: 0.8179 (mmtt) cc_final: 0.7961 (mmtt) REVERT: G 108 LEU cc_start: 0.9332 (mt) cc_final: 0.8594 (mt) REVERT: G 115 MET cc_start: 0.7816 (mmp) cc_final: 0.7394 (mmm) REVERT: G 124 GLN cc_start: 0.9264 (tm-30) cc_final: 0.8821 (tm-30) REVERT: G 148 MET cc_start: 0.8190 (mmm) cc_final: 0.7769 (ttm) REVERT: G 202 MET cc_start: 0.7831 (mmt) cc_final: 0.7605 (mmt) REVERT: G 227 LYS cc_start: 0.9464 (mttm) cc_final: 0.9175 (mtpp) REVERT: G 231 MET cc_start: 0.9247 (tpp) cc_final: 0.8772 (tpp) REVERT: I 1 MET cc_start: 0.3292 (tpt) cc_final: 0.0736 (tmm) REVERT: I 125 HIS cc_start: 0.7845 (m170) cc_final: 0.7378 (m170) outliers start: 0 outliers final: 0 residues processed: 336 average time/residue: 0.1760 time to fit residues: 88.6539 Evaluate side-chains 255 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 255 time to evaluate : 0.849 ------------------------------------------------------------------------------- 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: 0.5980 chunk 22 optimal weight: 3.9990 chunk 195 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 127 optimal weight: 0.2980 chunk 73 optimal weight: 5.9990 chunk 83 optimal weight: 0.3980 chunk 175 optimal weight: 3.9990 chunk 140 optimal weight: 10.0000 chunk 9 optimal weight: 5.9990 chunk 241 optimal weight: 20.0000 overall best weight: 0.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 51 ASN ** 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 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 ASN ** 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** G 11 ASN ** 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** I 163 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.064945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.052126 restraints weight = 95743.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.054113 restraints weight = 50710.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.055479 restraints weight = 31571.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.056412 restraints weight = 21728.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.057086 restraints weight = 16136.613| |-----------------------------------------------------------------------------| r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.6874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20367 Z= 0.129 Angle : 0.677 9.269 27486 Z= 0.365 Chirality : 0.046 0.173 2970 Planarity : 0.004 0.052 3447 Dihedral : 12.169 163.784 2997 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 17.47 Ramachandran Plot: Outliers : 1.26 % Allowed : 11.44 % Favored : 87.30 % Rotamer: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % 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 aren not related in a simple way. whole: -1.60 (0.17), residues: 2457 helix: 0.67 (0.19), residues: 675 sheet: -1.88 (0.22), residues: 549 loop : -1.64 (0.18), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 268 TYR 0.031 0.002 TYR E 90 PHE 0.028 0.001 PHE E 270 HIS 0.006 0.001 HIS G 34 Details of bonding type rmsd covalent geometry : bond 0.00271 (20367) covalent geometry : angle 0.67743 (27486) hydrogen bonds : bond 0.03624 ( 882) hydrogen bonds : angle 6.06605 ( 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 359 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 359 time to evaluate : 0.800 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: A 23 GLN cc_start: 0.9042 (tt0) cc_final: 0.8800 (tt0) REVERT: A 45 MET cc_start: 0.7818 (mpp) cc_final: 0.6962 (mpp) REVERT: A 187 MET cc_start: 0.7188 (mtm) cc_final: 0.6900 (mtm) REVERT: A 211 THR cc_start: 0.8862 (p) cc_final: 0.8631 (p) REVERT: A 231 MET cc_start: 0.9006 (tpp) cc_final: 0.8703 (tpp) REVERT: A 266 TYR cc_start: 0.8384 (m-80) cc_final: 0.8138 (m-80) REVERT: B 1 MET cc_start: 0.8540 (ttp) cc_final: 0.7580 (tmm) REVERT: B 3 LEU cc_start: 0.9491 (mt) cc_final: 0.9253 (mt) REVERT: B 72 MET cc_start: 0.8419 (mpp) cc_final: 0.7238 (pmm) REVERT: B 98 GLU cc_start: 0.8912 (mt-10) cc_final: 0.8699 (mt-10) REVERT: B 115 MET cc_start: 0.8883 (ttm) cc_final: 0.8511 (tpp) REVERT: C 63 ASN cc_start: 0.8972 (m-40) cc_final: 0.8530 (m-40) REVERT: C 259 SER cc_start: 0.9025 (p) cc_final: 0.8768 (t) REVERT: D 45 MET cc_start: 0.8144 (mpp) cc_final: 0.7266 (mpp) REVERT: D 46 GLU cc_start: 0.8459 (mp0) cc_final: 0.8056 (mp0) REVERT: D 124 GLN cc_start: 0.9239 (tm-30) cc_final: 0.8998 (tm-30) REVERT: D 175 ASN cc_start: 0.8261 (m-40) cc_final: 0.7668 (m-40) REVERT: D 191 THR cc_start: 0.8643 (m) cc_final: 0.8121 (p) REVERT: D 240 TYR cc_start: 0.9218 (m-80) cc_final: 0.8813 (m-10) REVERT: D 268 ARG cc_start: 0.9268 (mtm-85) cc_final: 0.8553 (mmm160) REVERT: E 83 GLU cc_start: 0.8894 (mp0) cc_final: 0.8333 (mp0) REVERT: E 108 LEU cc_start: 0.9647 (mm) cc_final: 0.9392 (mp) REVERT: E 115 MET cc_start: 0.8269 (tpp) cc_final: 0.7701 (tpp) REVERT: E 148 MET cc_start: 0.8164 (mmm) cc_final: 0.7362 (mmm) REVERT: F 45 MET cc_start: 0.8156 (tpp) cc_final: 0.7071 (tpp) REVERT: F 73 TYR cc_start: 0.8504 (m-10) cc_final: 0.7714 (m-10) REVERT: F 118 ASP cc_start: 0.8270 (m-30) cc_final: 0.8051 (m-30) REVERT: G 73 TYR cc_start: 0.8320 (m-80) cc_final: 0.7884 (m-80) REVERT: G 108 LEU cc_start: 0.9377 (mt) cc_final: 0.8673 (mt) REVERT: G 115 MET cc_start: 0.8009 (mmp) cc_final: 0.7574 (mmp) REVERT: G 124 GLN cc_start: 0.9246 (tm-30) cc_final: 0.8844 (tm-30) REVERT: G 227 LYS cc_start: 0.9464 (mttm) cc_final: 0.9183 (mtpp) REVERT: G 231 MET cc_start: 0.9281 (tpp) cc_final: 0.8781 (tpp) REVERT: H 1 MET cc_start: 0.7509 (ttt) cc_final: 0.7203 (ttt) REVERT: H 45 MET cc_start: 0.8894 (mtm) cc_final: 0.8630 (mtm) REVERT: H 47 ARG cc_start: 0.8588 (mpt180) cc_final: 0.8333 (mpt180) REVERT: H 88 LEU cc_start: 0.9374 (tp) cc_final: 0.9164 (tp) REVERT: H 163 ASN cc_start: 0.7302 (m-40) cc_final: 0.7077 (m-40) REVERT: I 1 MET cc_start: 0.3019 (tpt) cc_final: 0.0539 (tmm) REVERT: I 45 MET cc_start: 0.0858 (mtm) cc_final: 0.0267 (ttp) REVERT: I 125 HIS cc_start: 0.7774 (m170) cc_final: 0.7437 (m170) REVERT: I 231 MET cc_start: 0.9312 (mmt) cc_final: 0.8788 (mmm) outliers start: 0 outliers final: 0 residues processed: 359 average time/residue: 0.1628 time to fit residues: 88.6243 Evaluate side-chains 273 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 273 time to evaluate : 0.818 ------------------------------------------------------------------------------- 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: 0.9990 chunk 221 optimal weight: 9.9990 chunk 136 optimal weight: 7.9990 chunk 237 optimal weight: 9.9990 chunk 123 optimal weight: 0.8980 chunk 145 optimal weight: 3.9990 chunk 196 optimal weight: 5.9990 chunk 111 optimal weight: 8.9990 chunk 219 optimal weight: 9.9990 chunk 229 optimal weight: 0.8980 chunk 52 optimal weight: 0.0470 overall best weight: 1.3682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 63 ASN ** B 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 51 ASN ** 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 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 51 ASN ** E 76 ASN ** 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 23 GLN ** 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** F 163 ASN G 11 ASN ** 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** ** I 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.064445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.051985 restraints weight = 96800.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.053884 restraints weight = 52549.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.055180 restraints weight = 32991.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.056022 restraints weight = 22867.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.056682 restraints weight = 17206.439| |-----------------------------------------------------------------------------| r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.7052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20367 Z= 0.144 Angle : 0.693 9.530 27486 Z= 0.373 Chirality : 0.047 0.210 2970 Planarity : 0.004 0.068 3447 Dihedral : 12.072 162.854 2997 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 18.74 Ramachandran Plot: Outliers : 1.18 % Allowed : 11.36 % Favored : 87.46 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % 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 aren not related in a simple way. whole: -1.82 (0.17), residues: 2457 helix: 0.66 (0.19), residues: 675 sheet: -1.79 (0.20), residues: 639 loop : -1.98 (0.18), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 87 TYR 0.036 0.002 TYR G 90 PHE 0.032 0.002 PHE E 270 HIS 0.007 0.001 HIS F 125 Details of bonding type rmsd covalent geometry : bond 0.00312 (20367) covalent geometry : angle 0.69274 (27486) hydrogen bonds : bond 0.03682 ( 882) hydrogen bonds : angle 6.08507 ( 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 349 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 349 time to evaluate : 0.834 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: A 23 GLN cc_start: 0.9044 (tt0) cc_final: 0.8808 (tt0) REVERT: A 45 MET cc_start: 0.7876 (mpp) cc_final: 0.7102 (mpp) REVERT: A 215 ILE cc_start: 0.9479 (mm) cc_final: 0.9140 (tp) REVERT: A 216 ASP cc_start: 0.8882 (t70) cc_final: 0.8638 (p0) REVERT: A 231 MET cc_start: 0.9021 (tpp) cc_final: 0.8713 (tpp) REVERT: A 266 TYR cc_start: 0.8363 (m-80) cc_final: 0.7995 (m-80) REVERT: B 3 LEU cc_start: 0.9508 (mt) cc_final: 0.9305 (mt) REVERT: B 71 GLN cc_start: 0.8780 (mp10) cc_final: 0.8349 (mp-120) REVERT: B 98 GLU cc_start: 0.8918 (mt-10) cc_final: 0.8661 (mt-10) REVERT: B 115 MET cc_start: 0.8910 (ttm) cc_final: 0.8437 (tpp) REVERT: C 63 ASN cc_start: 0.8970 (m-40) cc_final: 0.8553 (m-40) REVERT: C 88 LEU cc_start: 0.9733 (tp) cc_final: 0.9527 (tp) REVERT: C 259 SER cc_start: 0.9004 (p) cc_final: 0.8742 (t) REVERT: D 1 MET cc_start: 0.7721 (ttt) cc_final: 0.7516 (tmm) REVERT: D 46 GLU cc_start: 0.8419 (mp0) cc_final: 0.7984 (mp0) REVERT: D 47 ARG cc_start: 0.6950 (mpt180) cc_final: 0.6635 (mpt180) REVERT: D 124 GLN cc_start: 0.9206 (tm-30) cc_final: 0.8956 (tm-30) REVERT: D 175 ASN cc_start: 0.8417 (m-40) cc_final: 0.7997 (m-40) REVERT: D 191 THR cc_start: 0.8611 (m) cc_final: 0.8327 (m) REVERT: D 240 TYR cc_start: 0.9214 (m-80) cc_final: 0.8805 (m-10) REVERT: D 268 ARG cc_start: 0.9235 (mtm-85) cc_final: 0.8498 (mmm160) REVERT: E 83 GLU cc_start: 0.8885 (mp0) cc_final: 0.8314 (mp0) REVERT: E 115 MET cc_start: 0.8193 (tpp) cc_final: 0.7676 (tpp) REVERT: E 148 MET cc_start: 0.8241 (mmm) cc_final: 0.7450 (mmm) REVERT: E 211 THR cc_start: 0.9023 (p) cc_final: 0.8497 (p) REVERT: F 45 MET cc_start: 0.8404 (tpp) cc_final: 0.7311 (tpp) REVERT: F 73 TYR cc_start: 0.8572 (m-10) cc_final: 0.7874 (m-10) REVERT: F 115 MET cc_start: 0.9234 (tpp) cc_final: 0.8906 (tpp) REVERT: F 268 ARG cc_start: 0.8460 (mmp80) cc_final: 0.8050 (mmp80) REVERT: G 73 TYR cc_start: 0.8363 (m-80) cc_final: 0.7900 (m-80) REVERT: G 115 MET cc_start: 0.8118 (mmp) cc_final: 0.7385 (mmm) REVERT: G 124 GLN cc_start: 0.9236 (tm-30) cc_final: 0.8820 (tm-30) REVERT: G 231 MET cc_start: 0.9294 (tpp) cc_final: 0.8783 (tpp) REVERT: H 47 ARG cc_start: 0.8631 (mpt180) cc_final: 0.8247 (mpt180) REVERT: H 88 LEU cc_start: 0.9380 (tp) cc_final: 0.9173 (tp) REVERT: H 179 LEU cc_start: 0.9352 (tt) cc_final: 0.9095 (tt) REVERT: I 1 MET cc_start: 0.3205 (tpt) cc_final: 0.0749 (tmm) REVERT: I 231 MET cc_start: 0.9307 (mmt) cc_final: 0.8802 (mmm) outliers start: 0 outliers final: 0 residues processed: 349 average time/residue: 0.1628 time to fit residues: 86.0550 Evaluate side-chains 270 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 270 time to evaluate : 0.845 ------------------------------------------------------------------------------- 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: 5.9990 chunk 183 optimal weight: 0.9980 chunk 115 optimal weight: 0.9990 chunk 187 optimal weight: 0.9990 chunk 69 optimal weight: 0.9990 chunk 100 optimal weight: 9.9990 chunk 1 optimal weight: 10.0000 chunk 66 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 chunk 179 optimal weight: 3.9990 chunk 163 optimal weight: 9.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 51 ASN ** 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 71 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 ASN ** 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** F 163 ASN G 11 ASN ** G 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 163 ASN ** H 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.065258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.052751 restraints weight = 96807.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.054666 restraints weight = 52579.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.055965 restraints weight = 33111.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.056862 restraints weight = 22979.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.057499 restraints weight = 17188.443| |-----------------------------------------------------------------------------| r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.7272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20367 Z= 0.134 Angle : 0.689 9.487 27486 Z= 0.371 Chirality : 0.047 0.177 2970 Planarity : 0.004 0.067 3447 Dihedral : 12.035 160.968 2997 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 17.70 Ramachandran Plot: Outliers : 1.06 % Allowed : 11.80 % Favored : 87.14 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % 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 aren not related in a simple way. whole: -1.74 (0.17), residues: 2457 helix: 0.62 (0.19), residues: 684 sheet: -1.62 (0.20), residues: 621 loop : -1.97 (0.18), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 87 TYR 0.033 0.002 TYR E 256 PHE 0.033 0.001 PHE F 270 HIS 0.009 0.001 HIS G 34 Details of bonding type rmsd covalent geometry : bond 0.00289 (20367) covalent geometry : angle 0.68857 (27486) hydrogen bonds : bond 0.03669 ( 882) hydrogen bonds : angle 6.00207 ( 2322) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3545.61 seconds wall clock time: 63 minutes 2.52 seconds (3782.52 seconds total)