Starting phenix.real_space_refine on Tue Jun 17 14:17:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6bqw_7134/06_2025/6bqw_7134.cif Found real_map, /net/cci-nas-00/data/ceres_data/6bqw_7134/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6bqw_7134/06_2025/6bqw_7134.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6bqw_7134/06_2025/6bqw_7134.map" model { file = "/net/cci-nas-00/data/ceres_data/6bqw_7134/06_2025/6bqw_7134.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6bqw_7134/06_2025/6bqw_7134.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: C, B, E, D, G, F, I, H Time building chain proxies: 6.50, per 1000 atoms: 0.33 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: 5.64 Conformation dependent library (CDL) restraints added in 2.7 seconds 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: 3.28 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: 7.20 Time building geometry restraints manager: 6.53 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: 0.17 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' } 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: 3.480 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: 0.850 Check model and map are aligned: 0.140 Set scattering table: 0.190 Process input model: 41.980 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.940 ------------------------------------------------------------------------------- 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 : 8.25 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 HIS 0.005 0.002 HIS A 34 PHE 0.010 0.003 PHE A 64 TYR 0.032 0.006 TYR G 56 ARG 0.003 0.001 ARG C 130 Details of bonding type rmsd hydrogen bonds : bond 0.15728 ( 882) hydrogen bonds : angle 9.90130 ( 2322) covalent geometry : bond 0.01604 (20367) covalent geometry : angle 1.27816 (27486) *********************** 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 : 2.424 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: symmetry clash revert: symmetry clash REVERT: A 202 MET cc_start: 0.7448 (mmm) cc_final: 0.7098 (tpp) REVERT: B 48 VAL cc_start: 0.8139 (t) cc_final: 0.7654 (p) REVERT: B 88 LEU cc_start: 0.8119 (tp) cc_final: 0.7901 (tp) REVERT: B 95 ILE cc_start: 0.8275 (pt) cc_final: 0.7869 (pt) REVERT: C 187 MET cc_start: 0.5628 (ptt) cc_final: 0.5051 (ptp) REVERT: C 201 ILE cc_start: 0.8640 (mt) cc_final: 0.8402 (tp) REVERT: C 211 THR cc_start: 0.8373 (p) cc_final: 0.7331 (p) REVERT: C 235 LEU cc_start: 0.8170 (mt) cc_final: 0.7657 (mm) REVERT: C 259 SER cc_start: 0.8407 (p) cc_final: 0.8193 (t) REVERT: D 5 THR cc_start: 0.7657 (p) cc_final: 0.7449 (p) REVERT: D 32 ILE cc_start: 0.9133 (mt) cc_final: 0.7760 (mt) REVERT: D 180 ILE cc_start: 0.8687 (mt) cc_final: 0.8418 (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: 0.8173 (p) REVERT: E 159 SER cc_start: 0.8344 (m) cc_final: 0.8069 (p) REVERT: E 184 ILE cc_start: 0.8996 (mt) cc_final: 0.8779 (mt) REVERT: F 95 ILE cc_start: 0.8715 (pt) cc_final: 0.8266 (pt) REVERT: F 108 LEU cc_start: 0.8473 (mt) cc_final: 0.8115 (mt) REVERT: F 115 MET cc_start: 0.7695 (mtp) cc_final: 0.7292 (mtm) REVERT: F 159 SER cc_start: 0.8623 (m) cc_final: 0.8318 (p) REVERT: F 187 MET cc_start: 0.6185 (ptt) cc_final: 0.5641 (ptt) REVERT: F 259 SER cc_start: 0.8797 (p) cc_final: 0.8557 (p) REVERT: G 5 THR cc_start: 0.7288 (p) cc_final: 0.7022 (p) REVERT: G 95 ILE cc_start: 0.8708 (pt) cc_final: 0.8331 (pt) REVERT: H 88 LEU cc_start: 0.7980 (tp) cc_final: 0.7694 (tp) REVERT: H 222 VAL cc_start: 0.7908 (t) cc_final: 0.7691 (t) REVERT: H 235 LEU cc_start: 0.8311 (mt) cc_final: 0.7361 (mt) REVERT: I 211 THR cc_start: 0.8198 (p) cc_final: 0.7535 (p) outliers start: 0 outliers final: 0 residues processed: 660 average time/residue: 0.3938 time to fit residues: 371.0518 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 : 2.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 205 optimal weight: 5.9990 chunk 184 optimal weight: 5.9990 chunk 102 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 98 optimal weight: 8.9990 chunk 190 optimal weight: 6.9990 chunk 73 optimal weight: 4.9990 chunk 115 optimal weight: 0.9990 chunk 141 optimal weight: 0.9990 chunk 220 optimal weight: 9.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 144 HIS A 163 ASN ** B 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 144 HIS ** F 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 23 GLN ** G 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 105 ASN ** H 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.062610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.049858 restraints weight = 97683.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.051734 restraints weight = 51189.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.052996 restraints weight = 31579.580| |-----------------------------------------------------------------------------| r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.3823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 20367 Z= 0.208 Angle : 0.796 8.844 27486 Z= 0.432 Chirality : 0.049 0.195 2970 Planarity : 0.004 0.030 3447 Dihedral : 13.176 179.296 2997 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 20.77 Ramachandran Plot: Outliers : 2.56 % Allowed : 11.27 % Favored : 86.16 % Rotamer: Outliers : 0.09 % Allowed : 3.06 % Favored : 96.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.74 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.42 (0.16), residues: 2457 helix: -0.21 (0.17), residues: 756 sheet: -2.52 (0.17), residues: 603 loop : -1.96 (0.19), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS C 34 PHE 0.028 0.002 PHE E 158 TYR 0.021 0.002 TYR E 256 ARG 0.005 0.001 ARG I 78 Details of bonding type rmsd hydrogen bonds : bond 0.04733 ( 882) hydrogen bonds : angle 7.19296 ( 2322) covalent geometry : bond 0.00441 (20367) covalent geometry : angle 0.79649 (27486) *********************** 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 469 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 467 time to evaluate : 2.277 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: 0.9176 (tt0) cc_final: 0.8974 (tt0) REVERT: A 73 TYR cc_start: 0.8055 (m-80) cc_final: 0.7821 (m-80) REVERT: A 202 MET cc_start: 0.6997 (mmm) cc_final: 0.6719 (tpp) REVERT: A 211 THR cc_start: 0.8890 (p) cc_final: 0.8117 (p) REVERT: A 227 LYS cc_start: 0.9409 (mmtt) cc_final: 0.9086 (mmtm) REVERT: A 231 MET cc_start: 0.8891 (tpp) cc_final: 0.8601 (tpp) REVERT: B 115 MET cc_start: 0.8831 (ttm) cc_final: 0.8346 (tpp) REVERT: B 139 PHE cc_start: 0.7803 (t80) cc_final: 0.6865 (t80) REVERT: B 141 PHE cc_start: 0.9056 (p90) cc_final: 0.7599 (p90) REVERT: C 23 GLN cc_start: 0.8163 (tt0) cc_final: 0.7805 (pp30) REVERT: C 46 GLU cc_start: 0.8125 (mp0) cc_final: 0.7772 (mp0) REVERT: C 63 ASN cc_start: 0.8937 (m110) cc_final: 0.8574 (t0) REVERT: C 98 GLU cc_start: 0.8759 (pt0) cc_final: 0.8518 (pt0) REVERT: C 109 THR cc_start: 0.9088 (p) cc_final: 0.8842 (p) REVERT: C 174 LEU cc_start: 0.9457 (tp) cc_final: 0.9210 (mm) REVERT: C 177 LEU cc_start: 0.9003 (tp) cc_final: 0.8692 (tp) REVERT: C 187 MET cc_start: 0.3683 (ptt) cc_final: 0.3284 (ptp) REVERT: C 259 SER cc_start: 0.9329 (p) cc_final: 0.8820 (t) REVERT: D 46 GLU cc_start: 0.8731 (mp0) cc_final: 0.8269 (mp0) REVERT: D 88 LEU cc_start: 0.9755 (tp) cc_final: 0.9553 (tp) REVERT: D 106 LEU cc_start: 0.8764 (tp) cc_final: 0.8482 (tp) REVERT: D 124 GLN cc_start: 0.9218 (tm-30) cc_final: 0.8960 (tm-30) REVERT: D 148 MET cc_start: 0.7430 (tpt) cc_final: 0.6861 (mmm) REVERT: D 240 TYR cc_start: 0.9092 (m-80) cc_final: 0.8685 (m-10) REVERT: E 68 ARG cc_start: 0.8567 (mmt90) cc_final: 0.8252 (mmt90) REVERT: E 88 LEU cc_start: 0.9774 (tp) cc_final: 0.9537 (tp) REVERT: E 108 LEU cc_start: 0.9608 (mt) cc_final: 0.9220 (mt) REVERT: E 148 MET cc_start: 0.8071 (mmm) cc_final: 0.7148 (mmm) REVERT: E 211 THR cc_start: 0.8792 (p) cc_final: 0.7990 (p) REVERT: E 234 CYS cc_start: 0.8925 (m) cc_final: 0.8669 (p) REVERT: E 248 LEU cc_start: 0.9107 (tp) cc_final: 0.8856 (tp) REVERT: E 259 SER cc_start: 0.9083 (p) cc_final: 0.8790 (t) REVERT: F 45 MET cc_start: 0.8001 (mtm) cc_final: 0.7681 (mtm) REVERT: F 46 GLU cc_start: 0.8521 (mp0) cc_final: 0.8240 (mp0) REVERT: F 95 ILE cc_start: 0.9481 (pt) cc_final: 0.9214 (mm) REVERT: F 98 GLU cc_start: 0.8552 (pt0) cc_final: 0.8332 (pt0) REVERT: F 106 LEU cc_start: 0.8772 (tp) cc_final: 0.8491 (tp) REVERT: F 108 LEU cc_start: 0.9138 (mt) cc_final: 0.8844 (mt) REVERT: F 139 PHE cc_start: 0.8353 (t80) cc_final: 0.8136 (t80) REVERT: F 159 SER cc_start: 0.8920 (m) cc_final: 0.8562 (p) REVERT: F 187 MET cc_start: 0.6724 (ptt) cc_final: 0.6404 (ptt) REVERT: F 259 SER cc_start: 0.9374 (p) cc_final: 0.8975 (t) REVERT: G 1 MET cc_start: 0.7423 (mtm) cc_final: 0.6831 (mpp) REVERT: G 7 ILE cc_start: 0.9612 (mm) cc_final: 0.9404 (tp) REVERT: G 46 GLU cc_start: 0.8967 (mp0) cc_final: 0.8555 (mp0) REVERT: G 73 TYR cc_start: 0.8480 (m-80) cc_final: 0.8272 (m-80) REVERT: G 98 GLU cc_start: 0.8709 (pt0) cc_final: 0.8352 (pt0) REVERT: G 101 LYS cc_start: 0.8453 (mmtt) cc_final: 0.8154 (mmtt) REVERT: G 107 ILE cc_start: 0.9177 (mt) cc_final: 0.8913 (mm) REVERT: G 108 LEU cc_start: 0.9444 (mt) cc_final: 0.9110 (mt) REVERT: G 124 GLN cc_start: 0.9029 (tm-30) cc_final: 0.8701 (tm-30) REVERT: G 145 ASN cc_start: 0.8079 (m110) cc_final: 0.7805 (m110) REVERT: G 201 ILE cc_start: 0.9544 (mt) cc_final: 0.9246 (tt) REVERT: H 1 MET cc_start: 0.7856 (mtm) cc_final: 0.7639 (ptp) REVERT: H 82 MET cc_start: 0.9383 (ttm) cc_final: 0.9028 (ttm) REVERT: H 88 LEU cc_start: 0.9326 (tp) cc_final: 0.9030 (tp) REVERT: H 106 LEU cc_start: 0.8945 (tp) cc_final: 0.8723 (tp) REVERT: H 126 PHE cc_start: 0.8282 (m-80) cc_final: 0.8011 (m-10) REVERT: H 231 MET cc_start: 0.9225 (tpt) cc_final: 0.8563 (tpp) REVERT: I 1 MET cc_start: 0.5052 (tpp) cc_final: 0.4770 (tpt) REVERT: I 179 LEU cc_start: 0.9229 (tt) cc_final: 0.8779 (mm) outliers start: 2 outliers final: 0 residues processed: 468 average time/residue: 0.3647 time to fit residues: 249.3126 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 : 2.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 158 optimal weight: 5.9990 chunk 141 optimal weight: 3.9990 chunk 142 optimal weight: 0.9990 chunk 162 optimal weight: 9.9990 chunk 215 optimal weight: 10.0000 chunk 160 optimal weight: 0.9980 chunk 181 optimal weight: 9.9990 chunk 223 optimal weight: 20.0000 chunk 10 optimal weight: 0.8980 chunk 28 optimal weight: 10.0000 chunk 87 optimal weight: 5.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 144 HIS C 105 ASN C 144 HIS ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 105 ASN ** D 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 144 HIS ** E 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 105 ASN ** E 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 144 HIS ** G 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 163 ASN ** H 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 144 HIS ** I 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.062144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.049512 restraints weight = 98214.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.051356 restraints weight = 52019.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.052606 restraints weight = 32475.372| |-----------------------------------------------------------------------------| r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.4788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 20367 Z= 0.192 Angle : 0.728 7.431 27486 Z= 0.396 Chirality : 0.048 0.201 2970 Planarity : 0.004 0.039 3447 Dihedral : 12.914 179.201 2997 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 20.47 Ramachandran Plot: Outliers : 2.04 % Allowed : 12.62 % Favored : 85.35 % Rotamer: Outliers : 0.05 % Allowed : 2.96 % Favored : 96.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.74 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.08 (0.16), residues: 2457 helix: 0.01 (0.17), residues: 756 sheet: -2.29 (0.21), residues: 450 loop : -1.89 (0.17), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS B 125 PHE 0.019 0.002 PHE E 158 TYR 0.023 0.002 TYR H 240 ARG 0.019 0.001 ARG G 78 Details of bonding type rmsd hydrogen bonds : bond 0.04294 ( 882) hydrogen bonds : angle 6.69275 ( 2322) covalent geometry : bond 0.00404 (20367) covalent geometry : angle 0.72832 (27486) *********************** 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 408 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 407 time to evaluate : 2.135 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: A 23 GLN cc_start: 0.9185 (tt0) cc_final: 0.8981 (tt0) REVERT: A 73 TYR cc_start: 0.8090 (m-80) cc_final: 0.7847 (m-80) REVERT: A 87 ARG cc_start: 0.9196 (mtt-85) cc_final: 0.8806 (ptp-110) REVERT: A 108 LEU cc_start: 0.9198 (mt) cc_final: 0.8989 (mt) REVERT: A 115 MET cc_start: 0.8473 (mtp) cc_final: 0.8047 (mtt) REVERT: A 211 THR cc_start: 0.8940 (p) cc_final: 0.8423 (p) REVERT: A 215 ILE cc_start: 0.9544 (mm) cc_final: 0.9335 (mm) REVERT: A 227 LYS cc_start: 0.9339 (mmtt) cc_final: 0.9032 (mmtm) REVERT: A 231 MET cc_start: 0.8967 (tpp) cc_final: 0.8583 (tpp) REVERT: B 42 TYR cc_start: 0.7052 (t80) cc_final: 0.6706 (t80) REVERT: B 88 LEU cc_start: 0.9508 (tp) cc_final: 0.9287 (tp) REVERT: B 98 GLU cc_start: 0.8822 (mt-10) cc_final: 0.8464 (pt0) REVERT: B 115 MET cc_start: 0.8908 (ttm) cc_final: 0.8378 (tpp) REVERT: B 126 PHE cc_start: 0.9187 (m-80) cc_final: 0.8945 (m-80) REVERT: B 139 PHE cc_start: 0.7981 (t80) cc_final: 0.7222 (t80) REVERT: B 141 PHE cc_start: 0.9114 (p90) cc_final: 0.7699 (p90) REVERT: C 23 GLN cc_start: 0.8208 (tt0) cc_final: 0.7915 (pp30) REVERT: C 63 ASN cc_start: 0.8893 (m110) cc_final: 0.8506 (t0) REVERT: C 72 MET cc_start: 0.8810 (mtm) cc_final: 0.8536 (mtt) REVERT: C 73 TYR cc_start: 0.8123 (m-80) cc_final: 0.7581 (m-80) REVERT: C 88 LEU cc_start: 0.9732 (tp) cc_final: 0.9531 (tp) REVERT: C 98 GLU cc_start: 0.8737 (pt0) cc_final: 0.8506 (pt0) REVERT: C 115 MET cc_start: 0.8707 (mmm) cc_final: 0.8270 (mmm) REVERT: C 177 LEU cc_start: 0.9049 (tp) cc_final: 0.8765 (tp) REVERT: C 187 MET cc_start: 0.3270 (ptt) cc_final: 0.2803 (ptp) REVERT: C 259 SER cc_start: 0.9232 (p) cc_final: 0.8644 (t) REVERT: D 46 GLU cc_start: 0.8427 (mp0) cc_final: 0.7747 (mp0) REVERT: D 71 GLN cc_start: 0.8746 (mp10) cc_final: 0.8493 (mp10) REVERT: D 87 ARG cc_start: 0.9200 (mtt-85) cc_final: 0.8262 (mtm-85) REVERT: D 98 GLU cc_start: 0.8731 (tp30) cc_final: 0.8295 (tm-30) REVERT: D 118 ASP cc_start: 0.7959 (m-30) cc_final: 0.7624 (m-30) REVERT: D 124 GLN cc_start: 0.9282 (tm-30) cc_final: 0.9000 (tm-30) REVERT: D 240 TYR cc_start: 0.9139 (m-80) cc_final: 0.8686 (m-10) REVERT: E 88 LEU cc_start: 0.9727 (tp) cc_final: 0.9522 (tp) REVERT: E 115 MET cc_start: 0.8131 (tpp) cc_final: 0.7597 (tpp) REVERT: E 148 MET cc_start: 0.8050 (mmm) cc_final: 0.7399 (mmm) REVERT: E 202 MET cc_start: 0.7709 (mmm) cc_final: 0.7253 (mmm) REVERT: E 259 SER cc_start: 0.9244 (p) cc_final: 0.8995 (t) REVERT: F 8 ASP cc_start: 0.8702 (t0) cc_final: 0.8481 (t0) REVERT: F 73 TYR cc_start: 0.8177 (m-80) cc_final: 0.7691 (m-80) REVERT: F 87 ARG cc_start: 0.9244 (mtt-85) cc_final: 0.8654 (mtt90) REVERT: F 95 ILE cc_start: 0.9478 (pt) cc_final: 0.9151 (mm) REVERT: F 98 GLU cc_start: 0.8561 (pt0) cc_final: 0.8141 (pt0) REVERT: F 108 LEU cc_start: 0.9185 (mt) cc_final: 0.8843 (mt) REVERT: F 115 MET cc_start: 0.8753 (tpp) cc_final: 0.8107 (tpp) REVERT: F 118 ASP cc_start: 0.8331 (m-30) cc_final: 0.7973 (m-30) REVERT: F 159 SER cc_start: 0.8944 (m) cc_final: 0.8595 (p) REVERT: F 187 MET cc_start: 0.6776 (ptt) cc_final: 0.6567 (ptt) REVERT: F 259 SER cc_start: 0.9249 (p) cc_final: 0.8934 (t) REVERT: G 46 GLU cc_start: 0.8933 (mp0) cc_final: 0.8436 (mp0) REVERT: G 73 TYR cc_start: 0.8558 (m-80) cc_final: 0.8258 (m-80) REVERT: G 106 LEU cc_start: 0.8795 (tp) cc_final: 0.8590 (tp) REVERT: G 108 LEU cc_start: 0.9548 (mt) cc_final: 0.8525 (mt) REVERT: G 115 MET cc_start: 0.8248 (tpp) cc_final: 0.7118 (tpp) REVERT: G 124 GLN cc_start: 0.9211 (tm-30) cc_final: 0.8824 (tm-30) REVERT: G 148 MET cc_start: 0.7880 (tpt) cc_final: 0.7654 (ttm) REVERT: G 231 MET cc_start: 0.9179 (tpp) cc_final: 0.8752 (tpp) REVERT: H 1 MET cc_start: 0.8036 (mtm) cc_final: 0.7513 (mtp) REVERT: H 47 ARG cc_start: 0.8413 (mpt180) cc_final: 0.8138 (mpt180) REVERT: H 88 LEU cc_start: 0.9350 (tp) cc_final: 0.9064 (tp) REVERT: H 148 MET cc_start: 0.7270 (tpp) cc_final: 0.6970 (mmm) REVERT: H 231 MET cc_start: 0.9335 (tpt) cc_final: 0.8956 (tpp) REVERT: I 45 MET cc_start: 0.0689 (mtm) cc_final: -0.1152 (mtm) REVERT: I 148 MET cc_start: 0.6547 (tpp) cc_final: 0.6283 (tpt) outliers start: 1 outliers final: 0 residues processed: 408 average time/residue: 0.3668 time to fit residues: 219.0240 Evaluate side-chains 292 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 292 time to evaluate : 2.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 44 optimal weight: 20.0000 chunk 231 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 chunk 171 optimal weight: 3.9990 chunk 88 optimal weight: 0.9980 chunk 110 optimal weight: 6.9990 chunk 139 optimal weight: 0.9980 chunk 61 optimal weight: 0.8980 chunk 214 optimal weight: 5.9990 chunk 145 optimal weight: 10.0000 chunk 112 optimal weight: 0.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 163 ASN ** E 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 163 ASN ** F 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 144 HIS ** I 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.063672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.050710 restraints weight = 97429.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.052698 restraints weight = 50370.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.054062 restraints weight = 31000.702| |-----------------------------------------------------------------------------| r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.5307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20367 Z= 0.146 Angle : 0.682 7.428 27486 Z= 0.370 Chirality : 0.046 0.167 2970 Planarity : 0.004 0.040 3447 Dihedral : 12.800 174.161 2997 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 17.47 Ramachandran Plot: Outliers : 1.75 % Allowed : 12.01 % Favored : 86.24 % Rotamer: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.74 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.16), residues: 2457 helix: 0.22 (0.18), residues: 756 sheet: -1.77 (0.22), residues: 486 loop : -1.94 (0.18), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 125 PHE 0.023 0.002 PHE F 270 TYR 0.034 0.002 TYR A 219 ARG 0.005 0.001 ARG G 78 Details of bonding type rmsd hydrogen bonds : bond 0.03982 ( 882) hydrogen bonds : angle 6.40138 ( 2322) covalent geometry : bond 0.00305 (20367) covalent geometry : angle 0.68162 (27486) *********************** 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 404 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 404 time to evaluate : 3.498 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: A 23 GLN cc_start: 0.9178 (tt0) cc_final: 0.8969 (tt0) REVERT: A 73 TYR cc_start: 0.8080 (m-80) cc_final: 0.7823 (m-80) REVERT: A 115 MET cc_start: 0.8493 (mtp) cc_final: 0.8137 (mtt) REVERT: A 211 THR cc_start: 0.8768 (p) cc_final: 0.8513 (p) REVERT: A 227 LYS cc_start: 0.9334 (mmtt) cc_final: 0.9041 (mmtm) REVERT: A 231 MET cc_start: 0.8993 (tpp) cc_final: 0.8658 (tpp) REVERT: B 73 TYR cc_start: 0.7662 (m-80) cc_final: 0.7005 (m-80) REVERT: B 88 LEU cc_start: 0.9476 (tp) cc_final: 0.9267 (tp) REVERT: B 98 GLU cc_start: 0.8845 (mt-10) cc_final: 0.8507 (pt0) REVERT: B 115 MET cc_start: 0.9003 (ttm) cc_final: 0.8473 (tpp) REVERT: B 139 PHE cc_start: 0.7761 (t80) cc_final: 0.7207 (t80) REVERT: B 141 PHE cc_start: 0.9104 (p90) cc_final: 0.7782 (p90) REVERT: B 187 MET cc_start: 0.2989 (ptp) cc_final: 0.2742 (mpp) REVERT: C 23 GLN cc_start: 0.8213 (tt0) cc_final: 0.7922 (pp30) REVERT: C 63 ASN cc_start: 0.8960 (m110) cc_final: 0.8394 (t0) REVERT: C 72 MET cc_start: 0.8883 (mtm) cc_final: 0.8679 (mtt) REVERT: C 98 GLU cc_start: 0.8747 (pt0) cc_final: 0.8475 (pt0) REVERT: C 177 LEU cc_start: 0.9213 (tp) cc_final: 0.8948 (tp) REVERT: C 187 MET cc_start: 0.3585 (ptt) cc_final: 0.3148 (ptp) REVERT: C 259 SER cc_start: 0.9279 (p) cc_final: 0.8854 (t) REVERT: D 46 GLU cc_start: 0.8423 (mp0) cc_final: 0.7675 (mp0) REVERT: D 74 PHE cc_start: 0.7848 (t80) cc_final: 0.7571 (t80) REVERT: D 98 GLU cc_start: 0.8684 (tp30) cc_final: 0.8269 (tm-30) REVERT: D 124 GLN cc_start: 0.9230 (tm-30) cc_final: 0.8979 (tm-30) REVERT: D 145 ASN cc_start: 0.8404 (m-40) cc_final: 0.8135 (t0) REVERT: D 240 TYR cc_start: 0.9094 (m-80) cc_final: 0.8652 (m-10) REVERT: E 88 LEU cc_start: 0.9734 (tp) cc_final: 0.9511 (tp) REVERT: E 115 MET cc_start: 0.8238 (tpp) cc_final: 0.7543 (tpp) REVERT: E 148 MET cc_start: 0.8161 (mmm) cc_final: 0.7387 (mmm) REVERT: E 163 ASN cc_start: 0.6722 (m110) cc_final: 0.5536 (m110) REVERT: F 36 TYR cc_start: 0.7757 (m-80) cc_final: 0.7516 (m-80) REVERT: F 73 TYR cc_start: 0.8102 (m-80) cc_final: 0.7442 (m-80) REVERT: F 87 ARG cc_start: 0.9104 (mtt-85) cc_final: 0.8850 (mtt-85) REVERT: F 106 LEU cc_start: 0.8688 (tp) cc_final: 0.8478 (tp) REVERT: F 108 LEU cc_start: 0.9213 (mt) cc_final: 0.8909 (mt) REVERT: F 115 MET cc_start: 0.8934 (tpp) cc_final: 0.8330 (tpp) REVERT: F 118 ASP cc_start: 0.8256 (m-30) cc_final: 0.7927 (m-30) REVERT: F 159 SER cc_start: 0.8902 (m) cc_final: 0.8595 (p) REVERT: F 203 ASP cc_start: 0.8696 (m-30) cc_final: 0.8483 (m-30) REVERT: F 251 ASP cc_start: 0.8947 (m-30) cc_final: 0.8641 (p0) REVERT: G 57 VAL cc_start: 0.8904 (m) cc_final: 0.8157 (p) REVERT: G 62 LYS cc_start: 0.9106 (mttt) cc_final: 0.8844 (mmmm) REVERT: G 73 TYR cc_start: 0.8548 (m-80) cc_final: 0.8156 (m-80) REVERT: G 124 GLN cc_start: 0.9197 (tm-30) cc_final: 0.8808 (tm-30) REVERT: G 227 LYS cc_start: 0.9480 (mttm) cc_final: 0.9198 (mtpp) REVERT: G 231 MET cc_start: 0.9296 (tpp) cc_final: 0.8657 (tpp) REVERT: H 83 GLU cc_start: 0.8888 (mp0) cc_final: 0.8247 (mp0) REVERT: H 108 LEU cc_start: 0.9117 (mt) cc_final: 0.8551 (mt) REVERT: H 163 ASN cc_start: 0.7518 (m-40) cc_final: 0.7317 (m-40) REVERT: I 45 MET cc_start: 0.1211 (mtm) cc_final: -0.1041 (mtm) REVERT: I 148 MET cc_start: 0.5897 (tpp) cc_final: 0.5538 (tpt) outliers start: 0 outliers final: 0 residues processed: 404 average time/residue: 0.4587 time to fit residues: 276.7782 Evaluate side-chains 286 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 286 time to evaluate : 3.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 58 optimal weight: 0.0770 chunk 66 optimal weight: 5.9990 chunk 93 optimal weight: 7.9990 chunk 9 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 213 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 144 optimal weight: 3.9990 chunk 19 optimal weight: 0.0980 chunk 227 optimal weight: 2.9990 overall best weight: 1.4344 ------------------------------------------------------------------------------- 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 11 ASN ** 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** ** F 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 144 HIS ** I 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.064111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.051400 restraints weight = 97235.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.053304 restraints weight = 51835.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.054601 restraints weight = 32506.686| |-----------------------------------------------------------------------------| r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.5735 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= 0.144 Angle : 0.661 7.271 27486 Z= 0.359 Chirality : 0.046 0.163 2970 Planarity : 0.004 0.039 3447 Dihedral : 12.640 173.749 2997 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 17.22 Ramachandran Plot: Outliers : 1.51 % Allowed : 12.01 % Favored : 86.49 % Rotamer: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.74 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.17), residues: 2457 helix: 0.28 (0.18), residues: 783 sheet: -1.87 (0.22), residues: 504 loop : -1.87 (0.18), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS C 125 PHE 0.025 0.002 PHE H 270 TYR 0.022 0.002 TYR G 56 ARG 0.010 0.001 ARG E 87 Details of bonding type rmsd hydrogen bonds : bond 0.03783 ( 882) hydrogen bonds : angle 6.22403 ( 2322) covalent geometry : bond 0.00306 (20367) covalent geometry : angle 0.66050 (27486) *********************** 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 388 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 388 time to evaluate : 2.598 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: A 73 TYR cc_start: 0.8081 (m-80) cc_final: 0.7817 (m-80) REVERT: A 227 LYS cc_start: 0.9321 (mmtt) cc_final: 0.9032 (mmtm) REVERT: A 231 MET cc_start: 0.8995 (tpp) cc_final: 0.8664 (tpp) REVERT: B 73 TYR cc_start: 0.7582 (m-80) cc_final: 0.6842 (m-80) REVERT: B 88 LEU cc_start: 0.9458 (tp) cc_final: 0.9234 (tp) REVERT: B 98 GLU cc_start: 0.8869 (mt-10) cc_final: 0.8605 (pt0) REVERT: B 126 PHE cc_start: 0.9129 (m-80) cc_final: 0.8916 (m-80) REVERT: B 187 MET cc_start: 0.3025 (ptp) cc_final: 0.2790 (mpp) REVERT: C 1 MET cc_start: 0.8329 (ptm) cc_final: 0.7732 (ptm) REVERT: C 23 GLN cc_start: 0.7956 (tt0) cc_final: 0.7751 (pp30) REVERT: C 63 ASN cc_start: 0.8903 (m110) cc_final: 0.8447 (m-40) REVERT: C 72 MET cc_start: 0.8831 (mtm) cc_final: 0.8328 (mpp) REVERT: C 73 TYR cc_start: 0.8019 (m-80) cc_final: 0.7280 (m-80) REVERT: C 115 MET cc_start: 0.8646 (mmm) cc_final: 0.8424 (mmm) REVERT: C 177 LEU cc_start: 0.9147 (tp) cc_final: 0.8891 (tp) REVERT: C 187 MET cc_start: 0.3476 (ptt) cc_final: 0.3060 (ptp) REVERT: C 259 SER cc_start: 0.9296 (p) cc_final: 0.8856 (t) REVERT: D 46 GLU cc_start: 0.8383 (mp0) cc_final: 0.7922 (mp0) REVERT: D 98 GLU cc_start: 0.8638 (tp30) cc_final: 0.8301 (tm-30) REVERT: D 102 LYS cc_start: 0.8076 (tmtt) cc_final: 0.7572 (tptp) REVERT: D 124 GLN cc_start: 0.9238 (tm-30) cc_final: 0.9004 (tm-30) REVERT: D 148 MET cc_start: 0.7681 (tpt) cc_final: 0.7424 (mmm) REVERT: D 240 TYR cc_start: 0.9091 (m-80) cc_final: 0.8621 (m-10) REVERT: E 1 MET cc_start: 0.8712 (mtp) cc_final: 0.8364 (ttm) REVERT: E 115 MET cc_start: 0.8303 (tpp) cc_final: 0.7693 (tpp) REVERT: E 148 MET cc_start: 0.8215 (mmm) cc_final: 0.7485 (mmm) REVERT: E 163 ASN cc_start: 0.6688 (m110) cc_final: 0.6452 (m110) REVERT: E 202 MET cc_start: 0.7244 (mmm) cc_final: 0.6980 (mmm) REVERT: F 36 TYR cc_start: 0.7729 (m-80) cc_final: 0.7497 (m-80) REVERT: F 46 GLU cc_start: 0.8355 (mp0) cc_final: 0.7943 (mp0) REVERT: F 73 TYR cc_start: 0.8187 (m-80) cc_final: 0.7833 (m-80) REVERT: F 87 ARG cc_start: 0.8999 (mtt-85) cc_final: 0.8794 (ptp-110) REVERT: F 106 LEU cc_start: 0.8649 (tp) cc_final: 0.8322 (tp) REVERT: F 108 LEU cc_start: 0.9192 (mt) cc_final: 0.8859 (mt) REVERT: F 115 MET cc_start: 0.8939 (tpp) cc_final: 0.8255 (tpp) REVERT: F 118 ASP cc_start: 0.8184 (m-30) cc_final: 0.7879 (m-30) REVERT: F 159 SER cc_start: 0.8895 (m) cc_final: 0.8607 (p) REVERT: G 46 GLU cc_start: 0.8698 (mp0) cc_final: 0.8363 (mp0) REVERT: G 57 VAL cc_start: 0.8621 (m) cc_final: 0.8239 (p) REVERT: G 62 LYS cc_start: 0.9048 (mttt) cc_final: 0.8782 (mmmm) REVERT: G 73 TYR cc_start: 0.8608 (m-80) cc_final: 0.8229 (m-80) REVERT: G 108 LEU cc_start: 0.9432 (mt) cc_final: 0.9033 (mt) REVERT: G 115 MET cc_start: 0.7974 (mmp) cc_final: 0.7382 (mmp) REVERT: G 124 GLN cc_start: 0.9194 (tm-30) cc_final: 0.8810 (tm-30) REVERT: G 148 MET cc_start: 0.8208 (tpt) cc_final: 0.7850 (ttm) REVERT: G 231 MET cc_start: 0.9314 (tpp) cc_final: 0.8680 (tpp) REVERT: H 47 ARG cc_start: 0.8443 (mpt180) cc_final: 0.7960 (mpt180) REVERT: H 88 LEU cc_start: 0.9419 (tp) cc_final: 0.9190 (tp) REVERT: H 126 PHE cc_start: 0.8183 (m-80) cc_final: 0.7954 (m-10) REVERT: H 231 MET cc_start: 0.9308 (tpt) cc_final: 0.9039 (tpt) REVERT: I 1 MET cc_start: 0.3485 (tpt) cc_final: 0.2003 (tmm) REVERT: I 115 MET cc_start: 0.8250 (mmm) cc_final: 0.7988 (mmm) outliers start: 0 outliers final: 0 residues processed: 388 average time/residue: 0.4409 time to fit residues: 256.0566 Evaluate side-chains 283 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 283 time to evaluate : 2.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 118 optimal weight: 0.7980 chunk 227 optimal weight: 0.9980 chunk 71 optimal weight: 10.0000 chunk 119 optimal weight: 0.9990 chunk 24 optimal weight: 0.0970 chunk 161 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 214 optimal weight: 10.0000 chunk 164 optimal weight: 0.3980 chunk 100 optimal weight: 9.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 HIS ** 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 11 ASN ** 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** ** F 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.065552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.052758 restraints weight = 95201.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.054779 restraints weight = 50247.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.056137 restraints weight = 31122.495| |-----------------------------------------------------------------------------| r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.6093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20367 Z= 0.124 Angle : 0.656 10.182 27486 Z= 0.352 Chirality : 0.046 0.172 2970 Planarity : 0.004 0.038 3447 Dihedral : 12.463 171.646 2997 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 15.90 Ramachandran Plot: Outliers : 1.47 % Allowed : 11.03 % Favored : 87.51 % Rotamer: Outliers : 0.05 % Allowed : 1.81 % Favored : 98.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.74 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.17), residues: 2457 helix: 0.26 (0.18), residues: 783 sheet: -1.79 (0.20), residues: 594 loop : -1.93 (0.19), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS I 34 PHE 0.025 0.001 PHE F 270 TYR 0.021 0.002 TYR G 56 ARG 0.008 0.001 ARG G 78 Details of bonding type rmsd hydrogen bonds : bond 0.03564 ( 882) hydrogen bonds : angle 6.06713 ( 2322) covalent geometry : bond 0.00258 (20367) covalent geometry : angle 0.65587 (27486) *********************** 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 406 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 405 time to evaluate : 2.070 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 23 GLN cc_start: 0.9136 (tt0) cc_final: 0.8935 (tt0) REVERT: A 73 TYR cc_start: 0.8156 (m-80) cc_final: 0.7894 (m-80) REVERT: A 202 MET cc_start: 0.6820 (tpp) cc_final: 0.6553 (tpp) REVERT: A 211 THR cc_start: 0.8768 (p) cc_final: 0.8443 (p) REVERT: A 215 ILE cc_start: 0.9455 (mm) cc_final: 0.9091 (tp) REVERT: A 227 LYS cc_start: 0.9293 (mmtt) cc_final: 0.8952 (mmtm) REVERT: A 231 MET cc_start: 0.9023 (tpp) cc_final: 0.8649 (tpp) REVERT: B 1 MET cc_start: 0.8056 (ttt) cc_final: 0.7339 (tmm) REVERT: B 98 GLU cc_start: 0.8890 (mt-10) cc_final: 0.8639 (pt0) REVERT: B 115 MET cc_start: 0.8774 (tpp) cc_final: 0.8521 (tpp) REVERT: B 126 PHE cc_start: 0.9072 (m-80) cc_final: 0.8834 (m-80) REVERT: B 187 MET cc_start: 0.3020 (ptp) cc_final: 0.2789 (mpp) REVERT: C 23 GLN cc_start: 0.7945 (tt0) cc_final: 0.7714 (pp30) REVERT: C 63 ASN cc_start: 0.8903 (m110) cc_final: 0.8384 (m-40) REVERT: C 71 GLN cc_start: 0.8564 (mp10) cc_final: 0.8262 (mp10) REVERT: C 72 MET cc_start: 0.8773 (mtm) cc_final: 0.8386 (mpp) REVERT: C 73 TYR cc_start: 0.8062 (m-80) cc_final: 0.7347 (m-80) REVERT: C 88 LEU cc_start: 0.9757 (tp) cc_final: 0.9540 (tp) REVERT: C 115 MET cc_start: 0.8761 (mmm) cc_final: 0.8508 (mmm) REVERT: C 177 LEU cc_start: 0.9123 (tp) cc_final: 0.8915 (tp) REVERT: C 187 MET cc_start: 0.3304 (ptt) cc_final: 0.2938 (ptp) REVERT: C 202 MET cc_start: 0.7678 (mmm) cc_final: 0.7100 (mmm) REVERT: C 259 SER cc_start: 0.9185 (p) cc_final: 0.8804 (t) REVERT: D 46 GLU cc_start: 0.8407 (mp0) cc_final: 0.7912 (mp0) REVERT: D 98 GLU cc_start: 0.8565 (tp30) cc_final: 0.8229 (tt0) REVERT: D 124 GLN cc_start: 0.9209 (tm-30) cc_final: 0.8920 (tm-30) REVERT: D 240 TYR cc_start: 0.9093 (m-80) cc_final: 0.8660 (m-10) REVERT: E 1 MET cc_start: 0.8770 (mtp) cc_final: 0.8390 (ttm) REVERT: E 88 LEU cc_start: 0.9769 (tp) cc_final: 0.9550 (tp) REVERT: E 115 MET cc_start: 0.8328 (tpp) cc_final: 0.7779 (tpp) REVERT: E 148 MET cc_start: 0.8199 (mmm) cc_final: 0.7452 (mmm) REVERT: E 163 ASN cc_start: 0.6740 (m110) cc_final: 0.6081 (m110) REVERT: F 73 TYR cc_start: 0.8250 (m-80) cc_final: 0.7744 (m-80) REVERT: F 115 MET cc_start: 0.9018 (tpp) cc_final: 0.8343 (tpp) REVERT: F 118 ASP cc_start: 0.8298 (m-30) cc_final: 0.7969 (m-30) REVERT: G 57 VAL cc_start: 0.8572 (m) cc_final: 0.8143 (p) REVERT: G 62 LYS cc_start: 0.9029 (mttt) cc_final: 0.8792 (mmmt) REVERT: G 73 TYR cc_start: 0.8497 (m-80) cc_final: 0.8032 (m-80) REVERT: G 108 LEU cc_start: 0.9376 (mt) cc_final: 0.8979 (mt) REVERT: G 115 MET cc_start: 0.8057 (mmp) cc_final: 0.7733 (mmp) REVERT: G 124 GLN cc_start: 0.9188 (tm-30) cc_final: 0.8790 (tm-30) REVERT: G 231 MET cc_start: 0.9345 (tpp) cc_final: 0.8707 (tpp) REVERT: H 1 MET cc_start: 0.7703 (mtp) cc_final: 0.7495 (ttm) REVERT: H 47 ARG cc_start: 0.8513 (mpt180) cc_final: 0.8149 (mpt180) REVERT: H 85 GLN cc_start: 0.8606 (mt0) cc_final: 0.8260 (mp10) REVERT: H 88 LEU cc_start: 0.9393 (tp) cc_final: 0.9191 (tp) REVERT: H 115 MET cc_start: 0.8806 (tpp) cc_final: 0.7989 (mmt) REVERT: H 231 MET cc_start: 0.9331 (tpt) cc_final: 0.9059 (tpt) REVERT: I 1 MET cc_start: 0.3427 (tpt) cc_final: 0.1818 (tmm) REVERT: I 115 MET cc_start: 0.8389 (mmm) cc_final: 0.8048 (mmm) REVERT: I 131 GLU cc_start: 0.8097 (pm20) cc_final: 0.7767 (tm-30) REVERT: I 187 MET cc_start: 0.7085 (mpp) cc_final: 0.6339 (mpp) outliers start: 1 outliers final: 1 residues processed: 406 average time/residue: 0.3334 time to fit residues: 202.6007 Evaluate side-chains 300 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 299 time to evaluate : 2.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 8 optimal weight: 0.8980 chunk 30 optimal weight: 9.9990 chunk 45 optimal weight: 10.0000 chunk 183 optimal weight: 6.9990 chunk 240 optimal weight: 20.0000 chunk 92 optimal weight: 0.0370 chunk 196 optimal weight: 0.9990 chunk 78 optimal weight: 10.0000 chunk 234 optimal weight: 6.9990 chunk 169 optimal weight: 0.7980 chunk 110 optimal weight: 0.0040 overall best weight: 0.5472 ------------------------------------------------------------------------------- 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 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 HIS ** 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 11 ASN ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 125 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** ** G 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.066228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.053495 restraints weight = 94949.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.055528 restraints weight = 50102.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.056898 restraints weight = 30952.300| |-----------------------------------------------------------------------------| r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.6441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 20367 Z= 0.122 Angle : 0.654 9.204 27486 Z= 0.353 Chirality : 0.046 0.176 2970 Planarity : 0.003 0.034 3447 Dihedral : 12.301 168.401 2997 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 16.33 Ramachandran Plot: Outliers : 1.30 % Allowed : 11.07 % Favored : 87.63 % Rotamer: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.74 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.17), residues: 2457 helix: 0.26 (0.18), residues: 783 sheet: -1.62 (0.22), residues: 504 loop : -1.99 (0.18), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS I 125 PHE 0.038 0.001 PHE H 270 TYR 0.035 0.002 TYR G 90 ARG 0.007 0.001 ARG G 78 Details of bonding type rmsd hydrogen bonds : bond 0.03467 ( 882) hydrogen bonds : angle 5.99056 ( 2322) covalent geometry : bond 0.00251 (20367) covalent geometry : angle 0.65358 (27486) *********************** 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 392 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 392 time to evaluate : 2.310 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: A 1 MET cc_start: 0.7706 (ttp) cc_final: 0.7100 (tmm) REVERT: A 23 GLN cc_start: 0.9125 (tt0) cc_final: 0.8915 (tt0) REVERT: A 73 TYR cc_start: 0.8177 (m-80) cc_final: 0.7930 (m-80) REVERT: A 202 MET cc_start: 0.6612 (tpp) cc_final: 0.6338 (tpp) REVERT: A 211 THR cc_start: 0.8920 (p) cc_final: 0.8669 (p) REVERT: A 215 ILE cc_start: 0.9426 (mm) cc_final: 0.9182 (tp) REVERT: A 227 LYS cc_start: 0.9276 (mmtt) cc_final: 0.8928 (mmtm) REVERT: A 231 MET cc_start: 0.9051 (tpp) cc_final: 0.8729 (tpp) REVERT: B 1 MET cc_start: 0.7822 (ttt) cc_final: 0.6463 (tmm) REVERT: B 63 ASN cc_start: 0.8638 (m110) cc_final: 0.8322 (t0) REVERT: B 98 GLU cc_start: 0.8909 (mt-10) cc_final: 0.8666 (pt0) REVERT: B 115 MET cc_start: 0.8858 (tpp) cc_final: 0.8340 (tpp) REVERT: B 126 PHE cc_start: 0.9028 (m-80) cc_final: 0.8814 (m-80) REVERT: B 187 MET cc_start: 0.2973 (ptp) cc_final: 0.2718 (mpp) REVERT: C 1 MET cc_start: 0.7727 (ptm) cc_final: 0.7489 (ppp) REVERT: C 63 ASN cc_start: 0.8895 (m110) cc_final: 0.8458 (m-40) REVERT: C 71 GLN cc_start: 0.8525 (mp10) cc_final: 0.8185 (mp10) REVERT: C 73 TYR cc_start: 0.8026 (m-80) cc_final: 0.7405 (m-80) REVERT: C 187 MET cc_start: 0.3214 (ptt) cc_final: 0.2871 (ptp) REVERT: C 259 SER cc_start: 0.9136 (p) cc_final: 0.8768 (t) REVERT: D 46 GLU cc_start: 0.8453 (mp0) cc_final: 0.7901 (mp0) REVERT: D 124 GLN cc_start: 0.9259 (tm-30) cc_final: 0.8922 (tm-30) REVERT: E 1 MET cc_start: 0.8818 (mtp) cc_final: 0.8354 (ttm) REVERT: E 115 MET cc_start: 0.8374 (tpp) cc_final: 0.7828 (tpp) REVERT: E 148 MET cc_start: 0.8127 (mmm) cc_final: 0.7312 (mmm) REVERT: F 23 GLN cc_start: 0.9014 (mp10) cc_final: 0.8800 (tt0) REVERT: F 73 TYR cc_start: 0.8239 (m-80) cc_final: 0.7653 (m-80) REVERT: F 115 MET cc_start: 0.9053 (tpp) cc_final: 0.8415 (tpp) REVERT: F 118 ASP cc_start: 0.8169 (m-30) cc_final: 0.7926 (m-30) REVERT: F 203 ASP cc_start: 0.8664 (m-30) cc_final: 0.8454 (m-30) REVERT: G 62 LYS cc_start: 0.9050 (mttt) cc_final: 0.8802 (mmmt) REVERT: G 73 TYR cc_start: 0.8667 (m-80) cc_final: 0.8259 (m-80) REVERT: G 124 GLN cc_start: 0.9164 (tm-30) cc_final: 0.8748 (tm-30) REVERT: G 231 MET cc_start: 0.9309 (tpp) cc_final: 0.8724 (tpp) REVERT: H 120 LYS cc_start: 0.9474 (mmpt) cc_final: 0.9267 (mmmt) REVERT: H 231 MET cc_start: 0.9312 (tpt) cc_final: 0.9072 (tpp) REVERT: I 1 MET cc_start: 0.3514 (tpt) cc_final: 0.1320 (tmm) REVERT: I 131 GLU cc_start: 0.7965 (pm20) cc_final: 0.7685 (tm-30) REVERT: I 231 MET cc_start: 0.9343 (mmm) cc_final: 0.9067 (mmm) outliers start: 0 outliers final: 0 residues processed: 392 average time/residue: 0.3428 time to fit residues: 200.2377 Evaluate side-chains 293 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 293 time to evaluate : 2.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 97 optimal weight: 9.9990 chunk 242 optimal weight: 8.9990 chunk 19 optimal weight: 9.9990 chunk 72 optimal weight: 7.9990 chunk 167 optimal weight: 3.9990 chunk 172 optimal weight: 1.9990 chunk 128 optimal weight: 5.9990 chunk 78 optimal weight: 9.9990 chunk 83 optimal weight: 0.0060 chunk 77 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 overall best weight: 2.8004 ------------------------------------------------------------------------------- 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 105 ASN ** A 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 11 ASN ** 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 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 163 ASN ** F 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 163 ASN ** H 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.062847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.050423 restraints weight = 98309.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.052257 restraints weight = 52796.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.053511 restraints weight = 33133.312| |-----------------------------------------------------------------------------| r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.6530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 20367 Z= 0.196 Angle : 0.711 8.518 27486 Z= 0.383 Chirality : 0.048 0.198 2970 Planarity : 0.004 0.056 3447 Dihedral : 12.247 175.200 2997 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 19.58 Ramachandran Plot: Outliers : 1.18 % Allowed : 12.01 % Favored : 86.81 % Rotamer: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.74 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.17), residues: 2457 helix: 0.68 (0.19), residues: 711 sheet: -2.00 (0.21), residues: 540 loop : -1.96 (0.17), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS B 125 PHE 0.031 0.002 PHE E 270 TYR 0.035 0.002 TYR G 90 ARG 0.014 0.001 ARG G 78 Details of bonding type rmsd hydrogen bonds : bond 0.03663 ( 882) hydrogen bonds : angle 6.10253 ( 2322) covalent geometry : bond 0.00418 (20367) covalent geometry : angle 0.71076 (27486) *********************** 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 346 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 346 time to evaluate : 2.200 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: A 73 TYR cc_start: 0.8190 (m-80) cc_final: 0.7844 (m-80) REVERT: A 101 LYS cc_start: 0.7090 (mmtt) cc_final: 0.6683 (mmmt) REVERT: A 187 MET cc_start: 0.7068 (mtm) cc_final: 0.6691 (ptp) REVERT: A 211 THR cc_start: 0.8947 (p) cc_final: 0.8557 (p) REVERT: A 227 LYS cc_start: 0.9287 (mmtt) cc_final: 0.8980 (mmtm) REVERT: A 231 MET cc_start: 0.9057 (tpp) cc_final: 0.8721 (tpp) REVERT: B 1 MET cc_start: 0.8043 (ttt) cc_final: 0.6705 (tmm) REVERT: B 73 TYR cc_start: 0.7349 (m-80) cc_final: 0.6645 (m-80) REVERT: B 98 GLU cc_start: 0.8894 (mt-10) cc_final: 0.8626 (pt0) REVERT: C 1 MET cc_start: 0.7897 (ptm) cc_final: 0.7367 (ppp) REVERT: C 15 LYS cc_start: 0.9236 (ptpt) cc_final: 0.9008 (ptmt) REVERT: C 23 GLN cc_start: 0.8228 (tt0) cc_final: 0.7854 (pp30) REVERT: C 63 ASN cc_start: 0.9054 (m110) cc_final: 0.8587 (m-40) REVERT: C 71 GLN cc_start: 0.8734 (mp10) cc_final: 0.8321 (mp10) REVERT: C 72 MET cc_start: 0.8782 (mtm) cc_final: 0.8411 (mpp) REVERT: C 73 TYR cc_start: 0.8035 (m-80) cc_final: 0.7280 (m-80) REVERT: C 115 MET cc_start: 0.8380 (mmm) cc_final: 0.8145 (mmm) REVERT: C 187 MET cc_start: 0.3223 (ptt) cc_final: 0.2841 (ptp) REVERT: C 202 MET cc_start: 0.7414 (mmm) cc_final: 0.7205 (mmm) REVERT: C 259 SER cc_start: 0.9171 (p) cc_final: 0.8886 (t) REVERT: D 46 GLU cc_start: 0.8543 (mp0) cc_final: 0.8120 (mp0) REVERT: D 102 LYS cc_start: 0.8224 (tmtt) cc_final: 0.7523 (ttpt) REVERT: D 124 GLN cc_start: 0.9250 (tm-30) cc_final: 0.8932 (tm-30) REVERT: D 148 MET cc_start: 0.7667 (tpt) cc_final: 0.6695 (tpt) REVERT: D 151 GLU cc_start: 0.8269 (mt-10) cc_final: 0.7830 (mt-10) REVERT: D 191 THR cc_start: 0.8646 (m) cc_final: 0.8419 (p) REVERT: D 240 TYR cc_start: 0.9190 (m-80) cc_final: 0.8793 (m-10) REVERT: E 1 MET cc_start: 0.8847 (mtp) cc_final: 0.8528 (ttm) REVERT: E 46 GLU cc_start: 0.7601 (mp0) cc_final: 0.7344 (mp0) REVERT: E 115 MET cc_start: 0.8340 (tpp) cc_final: 0.7606 (tpp) REVERT: E 148 MET cc_start: 0.8125 (mmm) cc_final: 0.7508 (mmm) REVERT: F 73 TYR cc_start: 0.8402 (m-80) cc_final: 0.8039 (m-80) REVERT: F 106 LEU cc_start: 0.8802 (tp) cc_final: 0.8549 (tp) REVERT: F 115 MET cc_start: 0.8993 (tpp) cc_final: 0.8366 (tpp) REVERT: F 216 ASP cc_start: 0.8609 (t0) cc_final: 0.8356 (t0) REVERT: G 39 LEU cc_start: 0.8360 (tp) cc_final: 0.8147 (tt) REVERT: G 62 LYS cc_start: 0.9199 (mttt) cc_final: 0.8879 (mmmm) REVERT: G 73 TYR cc_start: 0.8736 (m-80) cc_final: 0.8289 (m-80) REVERT: G 101 LYS cc_start: 0.8131 (mmtt) cc_final: 0.7926 (mmtt) REVERT: G 124 GLN cc_start: 0.9219 (tm-30) cc_final: 0.8782 (tm-30) REVERT: G 231 MET cc_start: 0.9239 (tpp) cc_final: 0.8648 (tpp) REVERT: H 47 ARG cc_start: 0.8541 (mpt180) cc_final: 0.8317 (mpt180) REVERT: H 115 MET cc_start: 0.8703 (tpp) cc_final: 0.7942 (mmm) REVERT: H 231 MET cc_start: 0.9336 (tpt) cc_final: 0.9067 (tpt) REVERT: H 262 LEU cc_start: 0.9468 (mt) cc_final: 0.9180 (mt) REVERT: I 1 MET cc_start: 0.3380 (tpt) cc_final: 0.1232 (tmm) REVERT: I 148 MET cc_start: 0.6713 (tpt) cc_final: 0.5994 (tpt) REVERT: I 231 MET cc_start: 0.9409 (mmm) cc_final: 0.9158 (mmm) outliers start: 0 outliers final: 0 residues processed: 346 average time/residue: 0.3650 time to fit residues: 188.2859 Evaluate side-chains 268 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 268 time to evaluate : 2.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 105 optimal weight: 8.9990 chunk 203 optimal weight: 9.9990 chunk 37 optimal weight: 10.0000 chunk 19 optimal weight: 1.9990 chunk 230 optimal weight: 9.9990 chunk 172 optimal weight: 4.9990 chunk 119 optimal weight: 5.9990 chunk 102 optimal weight: 0.0770 chunk 125 optimal weight: 9.9990 chunk 201 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 overall best weight: 2.2144 ------------------------------------------------------------------------------- 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 63 ASN ** 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 124 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** F 163 ASN ** H 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.063168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.050764 restraints weight = 96545.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.052651 restraints weight = 51748.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.053934 restraints weight = 32250.403| |-----------------------------------------------------------------------------| r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.6728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 20367 Z= 0.166 Angle : 0.690 9.235 27486 Z= 0.372 Chirality : 0.047 0.177 2970 Planarity : 0.004 0.076 3447 Dihedral : 12.230 164.638 2997 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 18.44 Ramachandran Plot: Outliers : 1.06 % Allowed : 11.97 % Favored : 86.98 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.74 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.16), residues: 2457 helix: 0.51 (0.19), residues: 720 sheet: -1.90 (0.21), residues: 531 loop : -1.91 (0.17), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.001 HIS E 125 PHE 0.019 0.002 PHE A 274 TYR 0.033 0.002 TYR H 56 ARG 0.012 0.001 ARG G 68 Details of bonding type rmsd hydrogen bonds : bond 0.03644 ( 882) hydrogen bonds : angle 6.03287 ( 2322) covalent geometry : bond 0.00361 (20367) covalent geometry : angle 0.69002 (27486) *********************** 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 343 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 343 time to evaluate : 4.069 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 1 MET cc_start: 0.7399 (ttm) cc_final: 0.6793 (tmm) REVERT: A 73 TYR cc_start: 0.8090 (m-80) cc_final: 0.7718 (m-80) REVERT: A 101 LYS cc_start: 0.7061 (mmtt) cc_final: 0.6683 (mmmt) REVERT: A 187 MET cc_start: 0.6993 (mtm) cc_final: 0.6583 (ptp) REVERT: A 202 MET cc_start: 0.6797 (tpp) cc_final: 0.6494 (tpp) REVERT: A 227 LYS cc_start: 0.9260 (mmtt) cc_final: 0.8963 (mmtm) REVERT: A 231 MET cc_start: 0.9050 (tpp) cc_final: 0.8716 (tpp) REVERT: B 1 MET cc_start: 0.8463 (ttt) cc_final: 0.7222 (tmm) REVERT: B 98 GLU cc_start: 0.8885 (mt-10) cc_final: 0.8623 (pt0) REVERT: C 23 GLN cc_start: 0.8305 (tt0) cc_final: 0.7904 (pp30) REVERT: C 63 ASN cc_start: 0.9046 (m-40) cc_final: 0.8589 (m-40) REVERT: C 71 GLN cc_start: 0.8728 (mp10) cc_final: 0.8329 (mp10) REVERT: C 72 MET cc_start: 0.8720 (mtm) cc_final: 0.8415 (mpp) REVERT: C 73 TYR cc_start: 0.8005 (m-80) cc_final: 0.7178 (m-80) REVERT: C 88 LEU cc_start: 0.9723 (tp) cc_final: 0.9482 (tp) REVERT: C 187 MET cc_start: 0.3074 (ptt) cc_final: 0.2661 (ptp) REVERT: C 202 MET cc_start: 0.7403 (mmm) cc_final: 0.7194 (mmm) REVERT: C 259 SER cc_start: 0.9169 (p) cc_final: 0.8888 (t) REVERT: D 46 GLU cc_start: 0.8510 (mp0) cc_final: 0.8055 (mp0) REVERT: D 108 LEU cc_start: 0.9458 (mm) cc_final: 0.9149 (mm) REVERT: D 124 GLN cc_start: 0.9278 (tm-30) cc_final: 0.8983 (tm-30) REVERT: D 148 MET cc_start: 0.7672 (tpt) cc_final: 0.6683 (tpt) REVERT: D 151 GLU cc_start: 0.8237 (mt-10) cc_final: 0.7693 (mt-10) REVERT: E 83 GLU cc_start: 0.9037 (mp0) cc_final: 0.8401 (mp0) REVERT: E 115 MET cc_start: 0.8339 (tpp) cc_final: 0.7798 (tpp) REVERT: E 148 MET cc_start: 0.8110 (mmm) cc_final: 0.7475 (mmm) REVERT: F 73 TYR cc_start: 0.8371 (m-80) cc_final: 0.8097 (m-80) REVERT: F 101 LYS cc_start: 0.7403 (mmtt) cc_final: 0.6698 (mttt) REVERT: F 106 LEU cc_start: 0.8809 (tp) cc_final: 0.8560 (tp) REVERT: F 115 MET cc_start: 0.9050 (tpp) cc_final: 0.8372 (tpp) REVERT: G 39 LEU cc_start: 0.8445 (tp) cc_final: 0.8214 (tt) REVERT: G 62 LYS cc_start: 0.9198 (mttt) cc_final: 0.8889 (mmmm) REVERT: G 73 TYR cc_start: 0.8667 (m-80) cc_final: 0.8099 (m-80) REVERT: G 101 LYS cc_start: 0.8092 (mmtt) cc_final: 0.7881 (mmtt) REVERT: G 124 GLN cc_start: 0.9223 (tm-30) cc_final: 0.8782 (tm-30) REVERT: G 202 MET cc_start: 0.7899 (mmt) cc_final: 0.7625 (mmt) REVERT: G 231 MET cc_start: 0.9298 (tpp) cc_final: 0.8729 (tpp) REVERT: H 45 MET cc_start: 0.7467 (tpp) cc_final: 0.7195 (tpp) REVERT: H 115 MET cc_start: 0.8774 (tpp) cc_final: 0.8030 (mmm) REVERT: H 231 MET cc_start: 0.9320 (tpt) cc_final: 0.9008 (tpt) REVERT: I 1 MET cc_start: 0.3350 (tpt) cc_final: 0.1178 (tmm) REVERT: I 148 MET cc_start: 0.6721 (tpt) cc_final: 0.6206 (tpt) REVERT: I 231 MET cc_start: 0.9400 (mmm) cc_final: 0.9145 (mmm) outliers start: 0 outliers final: 0 residues processed: 343 average time/residue: 0.4102 time to fit residues: 210.9776 Evaluate side-chains 271 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 271 time to evaluate : 2.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 58 optimal weight: 0.0370 chunk 225 optimal weight: 10.0000 chunk 5 optimal weight: 6.9990 chunk 195 optimal weight: 10.0000 chunk 91 optimal weight: 6.9990 chunk 156 optimal weight: 8.9990 chunk 214 optimal weight: 4.9990 chunk 88 optimal weight: 4.9990 chunk 213 optimal weight: 9.9990 chunk 203 optimal weight: 6.9990 chunk 97 optimal weight: 9.9990 overall best weight: 4.8066 ------------------------------------------------------------------------------- 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** D 11 ASN ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 23 GLN F 163 ASN ** H 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 105 ASN ** 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 = 0.3348 r_free = 0.3348 target = 0.060218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.047829 restraints weight = 101092.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.049605 restraints weight = 54708.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.050828 restraints weight = 34639.914| |-----------------------------------------------------------------------------| r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.6850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 20367 Z= 0.289 Angle : 0.816 11.561 27486 Z= 0.435 Chirality : 0.051 0.206 2970 Planarity : 0.005 0.065 3447 Dihedral : 12.437 173.974 2997 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 23.82 Ramachandran Plot: Outliers : 1.14 % Allowed : 13.19 % Favored : 85.67 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.74 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.15 (0.16), residues: 2457 helix: 0.22 (0.19), residues: 684 sheet: -1.96 (0.19), residues: 630 loop : -2.10 (0.17), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS F 81 PHE 0.045 0.002 PHE E 270 TYR 0.042 0.003 TYR H 219 ARG 0.011 0.001 ARG G 78 Details of bonding type rmsd hydrogen bonds : bond 0.04101 ( 882) hydrogen bonds : angle 6.39683 ( 2322) covalent geometry : bond 0.00615 (20367) covalent geometry : angle 0.81573 (27486) ********************** 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 327 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 327 time to evaluate : 2.177 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 1 MET cc_start: 0.7488 (ttm) cc_final: 0.6919 (tmm) REVERT: A 72 MET cc_start: 0.8439 (mtp) cc_final: 0.8238 (mtp) REVERT: A 73 TYR cc_start: 0.8076 (m-80) cc_final: 0.7623 (m-80) REVERT: A 101 LYS cc_start: 0.7348 (mmtt) cc_final: 0.6989 (mmmt) REVERT: A 106 LEU cc_start: 0.8813 (tp) cc_final: 0.8611 (tp) REVERT: A 108 LEU cc_start: 0.9358 (mt) cc_final: 0.9118 (mt) REVERT: A 227 LYS cc_start: 0.9229 (mmtt) cc_final: 0.8934 (mmtm) REVERT: A 231 MET cc_start: 0.9062 (tpp) cc_final: 0.8681 (tpp) REVERT: C 23 GLN cc_start: 0.8566 (tt0) cc_final: 0.8289 (pp30) REVERT: C 39 LEU cc_start: 0.8390 (tp) cc_final: 0.8190 (tp) REVERT: C 63 ASN cc_start: 0.9072 (m-40) cc_final: 0.8559 (m-40) REVERT: C 73 TYR cc_start: 0.8037 (m-80) cc_final: 0.7334 (m-80) REVERT: C 88 LEU cc_start: 0.9749 (tp) cc_final: 0.9530 (tp) REVERT: C 98 GLU cc_start: 0.8871 (pt0) cc_final: 0.8552 (pt0) REVERT: D 46 GLU cc_start: 0.8688 (mp0) cc_final: 0.8207 (mp0) REVERT: D 78 ARG cc_start: 0.6906 (tpp80) cc_final: 0.6594 (ttp80) REVERT: D 101 LYS cc_start: 0.7896 (mmtt) cc_final: 0.7472 (mmtt) REVERT: D 124 GLN cc_start: 0.9234 (tm-30) cc_final: 0.8995 (tm-30) REVERT: D 240 TYR cc_start: 0.9268 (m-80) cc_final: 0.8939 (m-10) REVERT: E 83 GLU cc_start: 0.9036 (mp0) cc_final: 0.8378 (mp0) REVERT: E 115 MET cc_start: 0.8284 (tpp) cc_final: 0.7559 (tpp) REVERT: E 148 MET cc_start: 0.8071 (mmm) cc_final: 0.7439 (mmm) REVERT: F 106 LEU cc_start: 0.8939 (tp) cc_final: 0.8669 (tp) REVERT: F 115 MET cc_start: 0.8984 (tpp) cc_final: 0.8347 (tpp) REVERT: F 118 ASP cc_start: 0.8171 (m-30) cc_final: 0.7801 (m-30) REVERT: F 268 ARG cc_start: 0.8647 (mmp80) cc_final: 0.8254 (mmp80) REVERT: G 73 TYR cc_start: 0.8866 (m-80) cc_final: 0.8295 (m-80) REVERT: G 115 MET cc_start: 0.8037 (mmp) cc_final: 0.7382 (mmm) REVERT: G 124 GLN cc_start: 0.9323 (tm-30) cc_final: 0.8884 (tm-30) REVERT: H 45 MET cc_start: 0.7869 (tpp) cc_final: 0.7415 (tpp) REVERT: H 231 MET cc_start: 0.9297 (tpt) cc_final: 0.8878 (tpt) REVERT: I 1 MET cc_start: 0.3459 (tpt) cc_final: 0.1557 (tmm) REVERT: I 148 MET cc_start: 0.6670 (tpt) cc_final: 0.6119 (tpt) REVERT: I 202 MET cc_start: 0.7622 (mmt) cc_final: 0.7293 (mmt) REVERT: I 231 MET cc_start: 0.9446 (mmm) cc_final: 0.9234 (mmm) outliers start: 0 outliers final: 0 residues processed: 327 average time/residue: 0.3499 time to fit residues: 170.4833 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 : 2.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 237 optimal weight: 5.9990 chunk 199 optimal weight: 2.9990 chunk 114 optimal weight: 0.9990 chunk 174 optimal weight: 0.9980 chunk 153 optimal weight: 0.7980 chunk 232 optimal weight: 9.9990 chunk 43 optimal weight: 30.0000 chunk 152 optimal weight: 0.7980 chunk 18 optimal weight: 7.9990 chunk 149 optimal weight: 9.9990 chunk 67 optimal weight: 4.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 34 HIS ** 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** F 23 GLN ** F 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 163 ASN G 11 ASN G 23 GLN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.063455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.050950 restraints weight = 97588.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.052844 restraints weight = 52529.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.054115 restraints weight = 32885.894| |-----------------------------------------------------------------------------| r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.7068 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= 0.148 Angle : 0.705 9.992 27486 Z= 0.379 Chirality : 0.048 0.174 2970 Planarity : 0.004 0.033 3447 Dihedral : 12.348 165.061 2997 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 18.97 Ramachandran Plot: Outliers : 1.02 % Allowed : 11.72 % Favored : 87.26 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.74 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (0.16), residues: 2457 helix: 0.36 (0.19), residues: 684 sheet: -1.75 (0.19), residues: 630 loop : -1.99 (0.17), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS I 125 PHE 0.037 0.002 PHE E 270 TYR 0.043 0.002 TYR F 56 ARG 0.008 0.001 ARG G 78 Details of bonding type rmsd hydrogen bonds : bond 0.03760 ( 882) hydrogen bonds : angle 6.15497 ( 2322) covalent geometry : bond 0.00321 (20367) covalent geometry : angle 0.70469 (27486) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7038.70 seconds wall clock time: 127 minutes 26.20 seconds (7646.20 seconds total)