Starting phenix.real_space_refine on Tue May 20 21:27:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8won_37693/05_2025/8won_37693.cif Found real_map, /net/cci-nas-00/data/ceres_data/8won_37693/05_2025/8won_37693.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8won_37693/05_2025/8won_37693.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8won_37693/05_2025/8won_37693.map" model { file = "/net/cci-nas-00/data/ceres_data/8won_37693/05_2025/8won_37693.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8won_37693/05_2025/8won_37693.cif" } resolution = 2.69 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.168 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 20 5.16 5 C 13280 2.51 5 N 3510 2.21 5 O 3910 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 20720 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2072 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 20, 'TRANS': 244} Chain breaks: 1 Restraints were copied for chains: C, B, E, D, G, F, I, H, J Time building chain proxies: 6.29, per 1000 atoms: 0.30 Number of scatterers: 20720 At special positions: 0 Unit cell: (115.648, 123.968, 139.776, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 20 16.00 O 3910 8.00 N 3510 7.00 C 13280 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: 4.91 Conformation dependent library (CDL) restraints added in 2.6 seconds 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4960 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 40 sheets defined 27.5% alpha, 35.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.69 Creating SS restraints... Processing helix chain 'A' and resid 45 through 50 Processing helix chain 'A' and resid 120 through 147 Processing helix chain 'A' and resid 151 through 156 removed outlier: 3.543A pdb=" N ALA A 156 " --> pdb=" O LEU A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 159 No H-bonds generated for 'chain 'A' and resid 157 through 159' Processing helix chain 'A' and resid 170 through 181 Processing helix chain 'A' and resid 191 through 205 Processing helix chain 'A' and resid 297 through 299 No H-bonds generated for 'chain 'A' and resid 297 through 299' Processing helix chain 'B' and resid 45 through 50 Processing helix chain 'B' and resid 120 through 147 Processing helix chain 'B' and resid 151 through 156 removed outlier: 3.543A pdb=" N ALA B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 159 No H-bonds generated for 'chain 'B' and resid 157 through 159' Processing helix chain 'B' and resid 170 through 181 Processing helix chain 'B' and resid 191 through 205 Processing helix chain 'B' and resid 297 through 299 No H-bonds generated for 'chain 'B' and resid 297 through 299' Processing helix chain 'C' and resid 45 through 50 Processing helix chain 'C' and resid 120 through 147 Processing helix chain 'C' and resid 151 through 156 removed outlier: 3.544A pdb=" N ALA C 156 " --> pdb=" O LEU C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 159 No H-bonds generated for 'chain 'C' and resid 157 through 159' Processing helix chain 'C' and resid 170 through 181 Processing helix chain 'C' and resid 191 through 205 Processing helix chain 'C' and resid 297 through 299 No H-bonds generated for 'chain 'C' and resid 297 through 299' Processing helix chain 'D' and resid 45 through 50 Processing helix chain 'D' and resid 120 through 147 Processing helix chain 'D' and resid 151 through 156 removed outlier: 3.542A pdb=" N ALA D 156 " --> pdb=" O LEU D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 159 No H-bonds generated for 'chain 'D' and resid 157 through 159' Processing helix chain 'D' and resid 170 through 181 Processing helix chain 'D' and resid 191 through 205 Processing helix chain 'D' and resid 297 through 299 No H-bonds generated for 'chain 'D' and resid 297 through 299' Processing helix chain 'E' and resid 45 through 50 Processing helix chain 'E' and resid 120 through 147 Processing helix chain 'E' and resid 151 through 156 removed outlier: 3.542A pdb=" N ALA E 156 " --> pdb=" O LEU E 152 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 159 No H-bonds generated for 'chain 'E' and resid 157 through 159' Processing helix chain 'E' and resid 170 through 181 Processing helix chain 'E' and resid 191 through 205 Processing helix chain 'E' and resid 297 through 299 No H-bonds generated for 'chain 'E' and resid 297 through 299' Processing helix chain 'F' and resid 45 through 50 Processing helix chain 'F' and resid 120 through 147 Processing helix chain 'F' and resid 151 through 156 removed outlier: 3.543A pdb=" N ALA F 156 " --> pdb=" O LEU F 152 " (cutoff:3.500A) Processing helix chain 'F' and resid 157 through 159 No H-bonds generated for 'chain 'F' and resid 157 through 159' Processing helix chain 'F' and resid 170 through 181 Processing helix chain 'F' and resid 191 through 205 Processing helix chain 'F' and resid 297 through 299 No H-bonds generated for 'chain 'F' and resid 297 through 299' Processing helix chain 'G' and resid 45 through 50 Processing helix chain 'G' and resid 120 through 147 Processing helix chain 'G' and resid 151 through 156 removed outlier: 3.543A pdb=" N ALA G 156 " --> pdb=" O LEU G 152 " (cutoff:3.500A) Processing helix chain 'G' and resid 157 through 159 No H-bonds generated for 'chain 'G' and resid 157 through 159' Processing helix chain 'G' and resid 170 through 181 Processing helix chain 'G' and resid 191 through 205 Processing helix chain 'G' and resid 297 through 299 No H-bonds generated for 'chain 'G' and resid 297 through 299' Processing helix chain 'H' and resid 45 through 50 Processing helix chain 'H' and resid 120 through 147 Processing helix chain 'H' and resid 151 through 156 removed outlier: 3.543A pdb=" N ALA H 156 " --> pdb=" O LEU H 152 " (cutoff:3.500A) Processing helix chain 'H' and resid 157 through 159 No H-bonds generated for 'chain 'H' and resid 157 through 159' Processing helix chain 'H' and resid 170 through 181 Processing helix chain 'H' and resid 191 through 205 Processing helix chain 'H' and resid 297 through 299 No H-bonds generated for 'chain 'H' and resid 297 through 299' Processing helix chain 'I' and resid 45 through 50 Processing helix chain 'I' and resid 120 through 147 Processing helix chain 'I' and resid 151 through 156 removed outlier: 3.542A pdb=" N ALA I 156 " --> pdb=" O LEU I 152 " (cutoff:3.500A) Processing helix chain 'I' and resid 157 through 159 No H-bonds generated for 'chain 'I' and resid 157 through 159' Processing helix chain 'I' and resid 170 through 181 Processing helix chain 'I' and resid 191 through 205 Processing helix chain 'I' and resid 297 through 299 No H-bonds generated for 'chain 'I' and resid 297 through 299' Processing helix chain 'J' and resid 45 through 50 Processing helix chain 'J' and resid 120 through 147 Processing helix chain 'J' and resid 151 through 156 removed outlier: 3.542A pdb=" N ALA J 156 " --> pdb=" O LEU J 152 " (cutoff:3.500A) Processing helix chain 'J' and resid 157 through 159 No H-bonds generated for 'chain 'J' and resid 157 through 159' Processing helix chain 'J' and resid 170 through 181 Processing helix chain 'J' and resid 191 through 205 Processing helix chain 'J' and resid 297 through 299 No H-bonds generated for 'chain 'J' and resid 297 through 299' Processing sheet with id=AA1, first strand: chain 'A' and resid 51 through 54 removed outlier: 4.452A pdb=" N SER A 51 " --> pdb=" O VAL A 254 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 51 through 54 removed outlier: 4.452A pdb=" N SER A 51 " --> pdb=" O VAL A 254 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N SER A 284 " --> pdb=" O THR A 275 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 59 through 65 removed outlier: 3.530A pdb=" N ARG A 64 " --> pdb=" O HIS A 95 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 161 through 163 removed outlier: 6.761A pdb=" N ILE A 162 " --> pdb=" O ASP A 305 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N VAL A 307 " --> pdb=" O ILE A 162 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLY A 306 " --> pdb=" O THR A 240 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N THR A 240 " --> pdb=" O GLY A 306 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ILE A 220 " --> pdb=" O ILE A 227 " (cutoff:3.500A) removed outlier: 10.306A pdb=" N GLN A 218 " --> pdb=" O PRO A 229 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 51 through 54 removed outlier: 4.452A pdb=" N SER B 51 " --> pdb=" O VAL B 254 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 51 through 54 removed outlier: 4.452A pdb=" N SER B 51 " --> pdb=" O VAL B 254 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N SER B 284 " --> pdb=" O THR B 275 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 59 through 65 removed outlier: 3.529A pdb=" N ARG B 64 " --> pdb=" O HIS B 95 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 161 through 163 removed outlier: 6.761A pdb=" N ILE B 162 " --> pdb=" O ASP B 305 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N VAL B 307 " --> pdb=" O ILE B 162 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLY B 306 " --> pdb=" O THR B 240 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N THR B 240 " --> pdb=" O GLY B 306 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ILE B 220 " --> pdb=" O ILE B 227 " (cutoff:3.500A) removed outlier: 10.306A pdb=" N GLN B 218 " --> pdb=" O PRO B 229 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 51 through 54 removed outlier: 4.452A pdb=" N SER C 51 " --> pdb=" O VAL C 254 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 51 through 54 removed outlier: 4.452A pdb=" N SER C 51 " --> pdb=" O VAL C 254 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N SER C 284 " --> pdb=" O THR C 275 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 59 through 65 removed outlier: 3.529A pdb=" N ARG C 64 " --> pdb=" O HIS C 95 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 161 through 163 removed outlier: 6.761A pdb=" N ILE C 162 " --> pdb=" O ASP C 305 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N VAL C 307 " --> pdb=" O ILE C 162 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLY C 306 " --> pdb=" O THR C 240 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N THR C 240 " --> pdb=" O GLY C 306 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ILE C 220 " --> pdb=" O ILE C 227 " (cutoff:3.500A) removed outlier: 10.306A pdb=" N GLN C 218 " --> pdb=" O PRO C 229 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 51 through 54 removed outlier: 4.451A pdb=" N SER D 51 " --> pdb=" O VAL D 254 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 51 through 54 removed outlier: 4.451A pdb=" N SER D 51 " --> pdb=" O VAL D 254 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N SER D 284 " --> pdb=" O THR D 275 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 59 through 65 removed outlier: 3.530A pdb=" N ARG D 64 " --> pdb=" O HIS D 95 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 161 through 163 removed outlier: 6.761A pdb=" N ILE D 162 " --> pdb=" O ASP D 305 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N VAL D 307 " --> pdb=" O ILE D 162 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLY D 306 " --> pdb=" O THR D 240 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N THR D 240 " --> pdb=" O GLY D 306 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ILE D 220 " --> pdb=" O ILE D 227 " (cutoff:3.500A) removed outlier: 10.306A pdb=" N GLN D 218 " --> pdb=" O PRO D 229 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 51 through 54 removed outlier: 4.452A pdb=" N SER E 51 " --> pdb=" O VAL E 254 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 51 through 54 removed outlier: 4.452A pdb=" N SER E 51 " --> pdb=" O VAL E 254 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N SER E 284 " --> pdb=" O THR E 275 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 59 through 65 removed outlier: 3.529A pdb=" N ARG E 64 " --> pdb=" O HIS E 95 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 161 through 163 removed outlier: 6.760A pdb=" N ILE E 162 " --> pdb=" O ASP E 305 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N VAL E 307 " --> pdb=" O ILE E 162 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLY E 306 " --> pdb=" O THR E 240 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N THR E 240 " --> pdb=" O GLY E 306 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ILE E 220 " --> pdb=" O ILE E 227 " (cutoff:3.500A) removed outlier: 10.306A pdb=" N GLN E 218 " --> pdb=" O PRO E 229 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 51 through 54 removed outlier: 4.452A pdb=" N SER F 51 " --> pdb=" O VAL F 254 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 51 through 54 removed outlier: 4.452A pdb=" N SER F 51 " --> pdb=" O VAL F 254 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N SER F 284 " --> pdb=" O THR F 275 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 59 through 65 removed outlier: 3.529A pdb=" N ARG F 64 " --> pdb=" O HIS F 95 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 161 through 163 removed outlier: 6.761A pdb=" N ILE F 162 " --> pdb=" O ASP F 305 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N VAL F 307 " --> pdb=" O ILE F 162 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLY F 306 " --> pdb=" O THR F 240 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N THR F 240 " --> pdb=" O GLY F 306 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ILE F 220 " --> pdb=" O ILE F 227 " (cutoff:3.500A) removed outlier: 10.306A pdb=" N GLN F 218 " --> pdb=" O PRO F 229 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 51 through 54 removed outlier: 4.452A pdb=" N SER G 51 " --> pdb=" O VAL G 254 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 51 through 54 removed outlier: 4.452A pdb=" N SER G 51 " --> pdb=" O VAL G 254 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N SER G 284 " --> pdb=" O THR G 275 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 59 through 65 removed outlier: 3.529A pdb=" N ARG G 64 " --> pdb=" O HIS G 95 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 161 through 163 removed outlier: 6.762A pdb=" N ILE G 162 " --> pdb=" O ASP G 305 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N VAL G 307 " --> pdb=" O ILE G 162 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLY G 306 " --> pdb=" O THR G 240 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N THR G 240 " --> pdb=" O GLY G 306 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ILE G 220 " --> pdb=" O ILE G 227 " (cutoff:3.500A) removed outlier: 10.306A pdb=" N GLN G 218 " --> pdb=" O PRO G 229 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 51 through 54 removed outlier: 4.452A pdb=" N SER H 51 " --> pdb=" O VAL H 254 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 51 through 54 removed outlier: 4.452A pdb=" N SER H 51 " --> pdb=" O VAL H 254 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N SER H 284 " --> pdb=" O THR H 275 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 59 through 65 removed outlier: 3.529A pdb=" N ARG H 64 " --> pdb=" O HIS H 95 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 161 through 163 removed outlier: 6.761A pdb=" N ILE H 162 " --> pdb=" O ASP H 305 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N VAL H 307 " --> pdb=" O ILE H 162 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLY H 306 " --> pdb=" O THR H 240 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N THR H 240 " --> pdb=" O GLY H 306 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ILE H 220 " --> pdb=" O ILE H 227 " (cutoff:3.500A) removed outlier: 10.306A pdb=" N GLN H 218 " --> pdb=" O PRO H 229 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 51 through 54 removed outlier: 4.451A pdb=" N SER I 51 " --> pdb=" O VAL I 254 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 51 through 54 removed outlier: 4.451A pdb=" N SER I 51 " --> pdb=" O VAL I 254 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N SER I 284 " --> pdb=" O THR I 275 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 59 through 65 removed outlier: 3.530A pdb=" N ARG I 64 " --> pdb=" O HIS I 95 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 161 through 163 removed outlier: 6.761A pdb=" N ILE I 162 " --> pdb=" O ASP I 305 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N VAL I 307 " --> pdb=" O ILE I 162 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLY I 306 " --> pdb=" O THR I 240 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N THR I 240 " --> pdb=" O GLY I 306 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ILE I 220 " --> pdb=" O ILE I 227 " (cutoff:3.500A) removed outlier: 10.306A pdb=" N GLN I 218 " --> pdb=" O PRO I 229 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 51 through 54 removed outlier: 4.452A pdb=" N SER J 51 " --> pdb=" O VAL J 254 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 51 through 54 removed outlier: 4.452A pdb=" N SER J 51 " --> pdb=" O VAL J 254 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N SER J 284 " --> pdb=" O THR J 275 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 59 through 65 removed outlier: 3.529A pdb=" N ARG J 64 " --> pdb=" O HIS J 95 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 161 through 163 removed outlier: 6.760A pdb=" N ILE J 162 " --> pdb=" O ASP J 305 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N VAL J 307 " --> pdb=" O ILE J 162 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLY J 306 " --> pdb=" O THR J 240 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N THR J 240 " --> pdb=" O GLY J 306 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ILE J 220 " --> pdb=" O ILE J 227 " (cutoff:3.500A) removed outlier: 10.306A pdb=" N GLN J 218 " --> pdb=" O PRO J 229 " (cutoff:3.500A) 980 hydrogen bonds defined for protein. 2790 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: 7.32 Time building geometry restraints manager: 5.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 3400 1.29 - 1.42: 5299 1.42 - 1.55: 12461 1.55 - 1.67: 30 1.67 - 1.80: 30 Bond restraints: 21220 Sorted by residual: bond pdb=" CA ASN H 67 " pdb=" C ASN H 67 " ideal model delta sigma weight residual 1.522 1.441 0.081 1.08e-02 8.57e+03 5.62e+01 bond pdb=" CA ASN C 67 " pdb=" C ASN C 67 " ideal model delta sigma weight residual 1.522 1.441 0.081 1.08e-02 8.57e+03 5.61e+01 bond pdb=" CA ASN D 67 " pdb=" C ASN D 67 " ideal model delta sigma weight residual 1.522 1.441 0.081 1.08e-02 8.57e+03 5.61e+01 bond pdb=" CA ASN A 67 " pdb=" C ASN A 67 " ideal model delta sigma weight residual 1.522 1.441 0.081 1.08e-02 8.57e+03 5.59e+01 bond pdb=" CA ASN I 67 " pdb=" C ASN I 67 " ideal model delta sigma weight residual 1.522 1.441 0.081 1.08e-02 8.57e+03 5.59e+01 ... (remaining 21215 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.13: 28295 2.13 - 4.26: 645 4.26 - 6.38: 89 6.38 - 8.51: 41 8.51 - 10.64: 10 Bond angle restraints: 29080 Sorted by residual: angle pdb=" N VAL B 66 " pdb=" CA VAL B 66 " pdb=" C VAL B 66 " ideal model delta sigma weight residual 110.72 119.03 -8.31 1.01e+00 9.80e-01 6.77e+01 angle pdb=" N VAL G 66 " pdb=" CA VAL G 66 " pdb=" C VAL G 66 " ideal model delta sigma weight residual 110.72 119.02 -8.30 1.01e+00 9.80e-01 6.76e+01 angle pdb=" N VAL J 66 " pdb=" CA VAL J 66 " pdb=" C VAL J 66 " ideal model delta sigma weight residual 110.72 119.00 -8.28 1.01e+00 9.80e-01 6.73e+01 angle pdb=" N VAL A 66 " pdb=" CA VAL A 66 " pdb=" C VAL A 66 " ideal model delta sigma weight residual 110.72 119.00 -8.28 1.01e+00 9.80e-01 6.72e+01 angle pdb=" N VAL C 66 " pdb=" CA VAL C 66 " pdb=" C VAL C 66 " ideal model delta sigma weight residual 110.72 118.99 -8.27 1.01e+00 9.80e-01 6.71e+01 ... (remaining 29075 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.27: 10940 17.27 - 34.53: 1340 34.53 - 51.80: 270 51.80 - 69.06: 80 69.06 - 86.33: 20 Dihedral angle restraints: 12650 sinusoidal: 4950 harmonic: 7700 Sorted by residual: dihedral pdb=" CA VAL D 145 " pdb=" C VAL D 145 " pdb=" N ASN D 146 " pdb=" CA ASN D 146 " ideal model delta harmonic sigma weight residual -180.00 -158.75 -21.25 0 5.00e+00 4.00e-02 1.81e+01 dihedral pdb=" CA VAL I 145 " pdb=" C VAL I 145 " pdb=" N ASN I 146 " pdb=" CA ASN I 146 " ideal model delta harmonic sigma weight residual -180.00 -158.75 -21.25 0 5.00e+00 4.00e-02 1.81e+01 dihedral pdb=" CA VAL H 145 " pdb=" C VAL H 145 " pdb=" N ASN H 146 " pdb=" CA ASN H 146 " ideal model delta harmonic sigma weight residual -180.00 -158.76 -21.24 0 5.00e+00 4.00e-02 1.80e+01 ... (remaining 12647 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 2783 0.065 - 0.129: 578 0.129 - 0.194: 49 0.194 - 0.258: 20 0.258 - 0.323: 20 Chirality restraints: 3450 Sorted by residual: chirality pdb=" CA PRO H 68 " pdb=" N PRO H 68 " pdb=" C PRO H 68 " pdb=" CB PRO H 68 " both_signs ideal model delta sigma weight residual False 2.72 2.40 0.32 2.00e-01 2.50e+01 2.60e+00 chirality pdb=" CA PRO C 68 " pdb=" N PRO C 68 " pdb=" C PRO C 68 " pdb=" CB PRO C 68 " both_signs ideal model delta sigma weight residual False 2.72 2.40 0.32 2.00e-01 2.50e+01 2.58e+00 chirality pdb=" CA PRO G 68 " pdb=" N PRO G 68 " pdb=" C PRO G 68 " pdb=" CB PRO G 68 " both_signs ideal model delta sigma weight residual False 2.72 2.40 0.32 2.00e-01 2.50e+01 2.58e+00 ... (remaining 3447 not shown) Planarity restraints: 3740 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN I 67 " 0.052 5.00e-02 4.00e+02 7.77e-02 9.67e+00 pdb=" N PRO I 68 " -0.134 5.00e-02 4.00e+02 pdb=" CA PRO I 68 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO I 68 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN G 67 " 0.052 5.00e-02 4.00e+02 7.76e-02 9.63e+00 pdb=" N PRO G 68 " -0.134 5.00e-02 4.00e+02 pdb=" CA PRO G 68 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO G 68 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN C 67 " 0.052 5.00e-02 4.00e+02 7.76e-02 9.63e+00 pdb=" N PRO C 68 " -0.134 5.00e-02 4.00e+02 pdb=" CA PRO C 68 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO C 68 " 0.046 5.00e-02 4.00e+02 ... (remaining 3737 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2347 2.75 - 3.29: 18481 3.29 - 3.82: 34433 3.82 - 4.36: 43035 4.36 - 4.90: 72542 Nonbonded interactions: 170838 Sorted by model distance: nonbonded pdb=" OE1 GLU J 143 " pdb=" ND2 ASN J 147 " model vdw 2.212 3.120 nonbonded pdb=" OE1 GLU I 143 " pdb=" ND2 ASN I 147 " model vdw 2.212 3.120 nonbonded pdb=" OE1 GLU D 143 " pdb=" ND2 ASN D 147 " model vdw 2.212 3.120 nonbonded pdb=" OE1 GLU E 143 " pdb=" ND2 ASN E 147 " model vdw 2.213 3.120 nonbonded pdb=" OE1 GLU A 143 " pdb=" ND2 ASN A 147 " model vdw 2.213 3.120 ... (remaining 170833 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: 0.18 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' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.820 Check model and map are aligned: 0.140 Set scattering table: 0.180 Process input model: 40.590 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:12.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 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 : 0.007 0.081 21220 Z= 0.444 Angle : 0.787 10.638 29080 Z= 0.439 Chirality : 0.059 0.323 3450 Planarity : 0.008 0.078 3740 Dihedral : 16.527 86.329 7690 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 0.44 % Allowed : 16.20 % Favored : 83.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.16), residues: 2610 helix: 0.53 (0.19), residues: 670 sheet: 1.44 (0.19), residues: 730 loop : -1.39 (0.17), residues: 1210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP I 52 HIS 0.003 0.001 HIS H 111 PHE 0.015 0.002 PHE E 188 TYR 0.012 0.003 TYR I 315 ARG 0.004 0.001 ARG G 64 Details of bonding type rmsd hydrogen bonds : bond 0.17514 ( 910) hydrogen bonds : angle 6.37392 ( 2790) covalent geometry : bond 0.00717 (21220) covalent geometry : angle 0.78718 (29080) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 378 time to evaluate : 2.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 249 GLU cc_start: 0.7913 (tt0) cc_final: 0.7671 (pm20) REVERT: E 271 SER cc_start: 0.8482 (t) cc_final: 0.8261 (t) REVERT: H 271 SER cc_start: 0.8486 (t) cc_final: 0.8265 (t) REVERT: I 139 ARG cc_start: 0.8205 (tpt-90) cc_final: 0.7975 (tmt-80) REVERT: I 249 GLU cc_start: 0.7894 (tt0) cc_final: 0.7667 (pm20) outliers start: 10 outliers final: 4 residues processed: 382 average time/residue: 1.5812 time to fit residues: 669.0843 Evaluate side-chains 254 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 250 time to evaluate : 2.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain I residue 100 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 219 optimal weight: 0.0270 chunk 197 optimal weight: 9.9990 chunk 109 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 chunk 132 optimal weight: 8.9990 chunk 105 optimal weight: 2.9990 chunk 203 optimal weight: 8.9990 chunk 78 optimal weight: 0.8980 chunk 123 optimal weight: 9.9990 chunk 151 optimal weight: 8.9990 chunk 236 optimal weight: 0.9990 overall best weight: 1.5844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 ASN B 122 HIS C 128 GLN C 191 HIS C 218 GLN D 252 GLN D 316 GLN E 313 HIS F 128 GLN F 191 HIS F 218 GLN G 252 GLN G 316 GLN H 313 HIS I 63 ASN J 122 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.172991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.145141 restraints weight = 22927.370| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 1.60 r_work: 0.3516 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3423 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 21220 Z= 0.153 Angle : 0.584 6.395 29080 Z= 0.309 Chirality : 0.048 0.156 3450 Planarity : 0.006 0.046 3740 Dihedral : 5.096 21.387 2894 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 2.14 % Allowed : 19.39 % Favored : 78.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.16), residues: 2610 helix: 1.09 (0.19), residues: 670 sheet: 1.58 (0.19), residues: 710 loop : -1.21 (0.17), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 52 HIS 0.006 0.001 HIS J 111 PHE 0.013 0.002 PHE F 188 TYR 0.012 0.002 TYR J 290 ARG 0.004 0.001 ARG F 61 Details of bonding type rmsd hydrogen bonds : bond 0.05367 ( 910) hydrogen bonds : angle 4.98637 ( 2790) covalent geometry : bond 0.00361 (21220) covalent geometry : angle 0.58356 (29080) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 297 time to evaluate : 2.292 Fit side-chains revert: symmetry clash REVERT: A 139 ARG cc_start: 0.8774 (tpt170) cc_final: 0.8009 (ttp-110) REVERT: A 236 GLU cc_start: 0.7868 (mt-10) cc_final: 0.7616 (pm20) REVERT: C 134 GLU cc_start: 0.7587 (OUTLIER) cc_final: 0.7349 (mp0) REVERT: D 97 ARG cc_start: 0.7048 (tpt170) cc_final: 0.6802 (tpt170) REVERT: D 107 LEU cc_start: 0.7596 (OUTLIER) cc_final: 0.7148 (tm) REVERT: D 211 THR cc_start: 0.7882 (p) cc_final: 0.7672 (p) REVERT: D 250 GLU cc_start: 0.7826 (tp30) cc_final: 0.7472 (mp0) REVERT: D 251 ARG cc_start: 0.7724 (ptp-110) cc_final: 0.7413 (ptm160) REVERT: E 33 LYS cc_start: 0.8501 (OUTLIER) cc_final: 0.8273 (ttmt) REVERT: E 61 ARG cc_start: 0.7607 (tpp80) cc_final: 0.6745 (tpp80) REVERT: E 139 ARG cc_start: 0.7919 (tpt-90) cc_final: 0.7512 (ttp80) REVERT: F 97 ARG cc_start: 0.6889 (tpt-90) cc_final: 0.6222 (ptm160) REVERT: F 134 GLU cc_start: 0.7562 (OUTLIER) cc_final: 0.7322 (mp0) REVERT: F 180 LYS cc_start: 0.8338 (OUTLIER) cc_final: 0.7865 (mtpp) REVERT: G 107 LEU cc_start: 0.7593 (OUTLIER) cc_final: 0.7164 (tm) REVERT: G 211 THR cc_start: 0.7877 (p) cc_final: 0.7668 (p) REVERT: G 250 GLU cc_start: 0.7861 (tp30) cc_final: 0.7470 (mp0) REVERT: G 251 ARG cc_start: 0.7737 (ptp-110) cc_final: 0.7413 (ptm160) REVERT: H 33 LYS cc_start: 0.8504 (OUTLIER) cc_final: 0.7988 (ttmt) REVERT: H 139 ARG cc_start: 0.7901 (tpt-90) cc_final: 0.7512 (ttp80) REVERT: I 139 ARG cc_start: 0.8795 (tpt-90) cc_final: 0.7969 (ttp-110) REVERT: I 236 GLU cc_start: 0.7909 (mt-10) cc_final: 0.7627 (pm20) outliers start: 49 outliers final: 10 residues processed: 321 average time/residue: 1.6072 time to fit residues: 575.3480 Evaluate side-chains 276 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 259 time to evaluate : 2.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain C residue 134 GLU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 214 MET Chi-restraints excluded: chain E residue 33 LYS Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain F residue 134 GLU Chi-restraints excluded: chain F residue 180 LYS Chi-restraints excluded: chain F residue 240 THR Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain G residue 214 MET Chi-restraints excluded: chain H residue 33 LYS Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain I residue 177 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 134 optimal weight: 10.0000 chunk 65 optimal weight: 4.9990 chunk 233 optimal weight: 3.9990 chunk 128 optimal weight: 0.9990 chunk 207 optimal weight: 0.9980 chunk 156 optimal weight: 10.0000 chunk 240 optimal weight: 9.9990 chunk 234 optimal weight: 5.9990 chunk 102 optimal weight: 7.9990 chunk 23 optimal weight: 7.9990 chunk 194 optimal weight: 2.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 63 ASN C 122 HIS C 160 GLN D 252 GLN E 48 HIS F 63 ASN F 122 HIS F 160 GLN G 252 GLN H 48 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.169454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.141856 restraints weight = 22919.420| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 1.61 r_work: 0.3461 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3357 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 21220 Z= 0.211 Angle : 0.646 6.793 29080 Z= 0.338 Chirality : 0.052 0.162 3450 Planarity : 0.007 0.050 3740 Dihedral : 5.266 21.027 2890 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 3.80 % Allowed : 18.69 % Favored : 77.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.16), residues: 2610 helix: 0.84 (0.19), residues: 670 sheet: 1.27 (0.19), residues: 710 loop : -1.33 (0.17), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 182 HIS 0.006 0.001 HIS J 111 PHE 0.019 0.002 PHE F 188 TYR 0.014 0.002 TYR D 315 ARG 0.007 0.001 ARG E 61 Details of bonding type rmsd hydrogen bonds : bond 0.06374 ( 910) hydrogen bonds : angle 5.21836 ( 2790) covalent geometry : bond 0.00520 (21220) covalent geometry : angle 0.64608 (29080) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 281 time to evaluate : 2.209 Fit side-chains REVERT: A 114 VAL cc_start: 0.3580 (OUTLIER) cc_final: 0.3370 (t) REVERT: A 139 ARG cc_start: 0.8791 (tpt170) cc_final: 0.8039 (ttp-110) REVERT: A 236 GLU cc_start: 0.7849 (mt-10) cc_final: 0.7569 (pm20) REVERT: A 249 GLU cc_start: 0.7948 (tt0) cc_final: 0.7637 (pm20) REVERT: B 33 LYS cc_start: 0.7074 (OUTLIER) cc_final: 0.6450 (mttm) REVERT: C 97 ARG cc_start: 0.7088 (tpt-90) cc_final: 0.6260 (ptm160) REVERT: C 134 GLU cc_start: 0.7546 (OUTLIER) cc_final: 0.7094 (mp0) REVERT: C 273 ARG cc_start: 0.6886 (ttp-110) cc_final: 0.6063 (ttp-170) REVERT: D 61 ARG cc_start: 0.7262 (ttm110) cc_final: 0.6673 (tmm-80) REVERT: D 107 LEU cc_start: 0.7663 (OUTLIER) cc_final: 0.7074 (tm) REVERT: D 110 VAL cc_start: 0.6110 (OUTLIER) cc_final: 0.5882 (t) REVERT: D 138 GLU cc_start: 0.7220 (tp30) cc_final: 0.6998 (tp30) REVERT: E 33 LYS cc_start: 0.8484 (OUTLIER) cc_final: 0.7967 (ttmt) REVERT: E 61 ARG cc_start: 0.7564 (tpp80) cc_final: 0.7325 (tpp80) REVERT: E 139 ARG cc_start: 0.8136 (tpt-90) cc_final: 0.7642 (ttp80) REVERT: F 61 ARG cc_start: 0.7966 (mtp85) cc_final: 0.7326 (ttm-80) REVERT: F 97 ARG cc_start: 0.7041 (tpt-90) cc_final: 0.6277 (ptm160) REVERT: F 134 GLU cc_start: 0.7553 (OUTLIER) cc_final: 0.7102 (mp0) REVERT: F 273 ARG cc_start: 0.6915 (ttp-110) cc_final: 0.6093 (ttp-170) REVERT: G 61 ARG cc_start: 0.7272 (ttm110) cc_final: 0.6669 (tmm-80) REVERT: G 107 LEU cc_start: 0.7663 (OUTLIER) cc_final: 0.7074 (tm) REVERT: G 138 GLU cc_start: 0.7203 (tp30) cc_final: 0.6977 (tp30) REVERT: H 33 LYS cc_start: 0.8508 (OUTLIER) cc_final: 0.7945 (ttmt) REVERT: H 59 ILE cc_start: 0.8392 (OUTLIER) cc_final: 0.8188 (mt) REVERT: H 139 ARG cc_start: 0.8133 (tpt-90) cc_final: 0.7647 (ttp80) REVERT: I 139 ARG cc_start: 0.8854 (tpt-90) cc_final: 0.8050 (ttp-110) REVERT: I 236 GLU cc_start: 0.7811 (mt-10) cc_final: 0.7551 (pm20) REVERT: I 249 GLU cc_start: 0.7964 (tt0) cc_final: 0.7632 (pm20) REVERT: J 33 LYS cc_start: 0.7049 (OUTLIER) cc_final: 0.6480 (mttm) outliers start: 87 outliers final: 29 residues processed: 335 average time/residue: 1.4431 time to fit residues: 540.6575 Evaluate side-chains 285 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 245 time to evaluate : 2.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain B residue 33 LYS Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain C residue 134 GLU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 103 SER Chi-restraints excluded: chain D residue 105 SER Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 214 MET Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain E residue 33 LYS Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain E residue 162 ILE Chi-restraints excluded: chain F residue 134 GLU Chi-restraints excluded: chain F residue 180 LYS Chi-restraints excluded: chain F residue 240 THR Chi-restraints excluded: chain G residue 100 THR Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain G residue 136 ILE Chi-restraints excluded: chain G residue 214 MET Chi-restraints excluded: chain H residue 33 LYS Chi-restraints excluded: chain H residue 59 ILE Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain H residue 162 ILE Chi-restraints excluded: chain I residue 177 LEU Chi-restraints excluded: chain I residue 263 VAL Chi-restraints excluded: chain J residue 33 LYS Chi-restraints excluded: chain J residue 136 ILE Chi-restraints excluded: chain J residue 177 LEU Chi-restraints excluded: chain J residue 284 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 94 optimal weight: 3.9990 chunk 226 optimal weight: 4.9990 chunk 48 optimal weight: 4.9990 chunk 211 optimal weight: 0.9980 chunk 6 optimal weight: 7.9990 chunk 217 optimal weight: 1.9990 chunk 110 optimal weight: 7.9990 chunk 61 optimal weight: 2.9990 chunk 210 optimal weight: 0.9990 chunk 259 optimal weight: 0.9990 chunk 73 optimal weight: 0.1980 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 HIS D 122 HIS E 48 HIS G 122 HIS H 48 HIS I 122 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.172981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.145352 restraints weight = 23204.860| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 1.56 r_work: 0.3526 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3426 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.2827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 21220 Z= 0.121 Angle : 0.532 4.998 29080 Z= 0.280 Chirality : 0.046 0.152 3450 Planarity : 0.006 0.051 3740 Dihedral : 4.783 19.260 2890 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 3.06 % Allowed : 19.69 % Favored : 77.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.16), residues: 2610 helix: 1.33 (0.19), residues: 670 sheet: 1.06 (0.19), residues: 730 loop : -1.17 (0.18), residues: 1210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 52 HIS 0.005 0.001 HIS B 111 PHE 0.014 0.001 PHE F 188 TYR 0.010 0.001 TYR G 150 ARG 0.009 0.000 ARG B 251 Details of bonding type rmsd hydrogen bonds : bond 0.04513 ( 910) hydrogen bonds : angle 4.78537 ( 2790) covalent geometry : bond 0.00288 (21220) covalent geometry : angle 0.53169 (29080) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 281 time to evaluate : 2.267 Fit side-chains REVERT: A 236 GLU cc_start: 0.7837 (mt-10) cc_final: 0.7511 (pm20) REVERT: A 249 GLU cc_start: 0.7784 (tt0) cc_final: 0.7477 (pm20) REVERT: B 33 LYS cc_start: 0.7000 (OUTLIER) cc_final: 0.6480 (mttm) REVERT: C 61 ARG cc_start: 0.7868 (mtp85) cc_final: 0.7245 (ttm-80) REVERT: C 273 ARG cc_start: 0.6819 (ttp-110) cc_final: 0.5979 (ttp-170) REVERT: C 277 ILE cc_start: 0.1883 (OUTLIER) cc_final: 0.1621 (mm) REVERT: C 310 ASP cc_start: 0.6869 (p0) cc_final: 0.6345 (t0) REVERT: D 61 ARG cc_start: 0.7247 (ttm110) cc_final: 0.6665 (tmm-80) REVERT: D 107 LEU cc_start: 0.7589 (OUTLIER) cc_final: 0.6902 (tm) REVERT: D 110 VAL cc_start: 0.6179 (OUTLIER) cc_final: 0.5955 (t) REVERT: D 132 THR cc_start: 0.7821 (OUTLIER) cc_final: 0.7558 (p) REVERT: D 239 THR cc_start: 0.7602 (OUTLIER) cc_final: 0.7145 (m) REVERT: E 33 LYS cc_start: 0.8443 (OUTLIER) cc_final: 0.7969 (ttmt) REVERT: E 139 ARG cc_start: 0.7899 (tpt-90) cc_final: 0.7431 (ttp80) REVERT: F 61 ARG cc_start: 0.7899 (mtp85) cc_final: 0.7283 (ttm-80) REVERT: F 97 ARG cc_start: 0.6896 (tpt-90) cc_final: 0.6132 (ptm160) REVERT: F 180 LYS cc_start: 0.8195 (OUTLIER) cc_final: 0.7841 (mtpp) REVERT: F 273 ARG cc_start: 0.6836 (ttp-110) cc_final: 0.5994 (ttp-170) REVERT: F 277 ILE cc_start: 0.1883 (OUTLIER) cc_final: 0.1626 (mm) REVERT: F 310 ASP cc_start: 0.6882 (p0) cc_final: 0.6330 (t0) REVERT: G 61 ARG cc_start: 0.7245 (ttm110) cc_final: 0.6653 (tmm-80) REVERT: G 107 LEU cc_start: 0.7567 (OUTLIER) cc_final: 0.6871 (tm) REVERT: G 132 THR cc_start: 0.7822 (OUTLIER) cc_final: 0.7573 (p) REVERT: G 239 THR cc_start: 0.7625 (OUTLIER) cc_final: 0.7159 (m) REVERT: H 33 LYS cc_start: 0.8440 (OUTLIER) cc_final: 0.7882 (ttmt) REVERT: H 61 ARG cc_start: 0.7595 (tpp80) cc_final: 0.7327 (tpp80) REVERT: H 139 ARG cc_start: 0.7898 (tpt-90) cc_final: 0.7431 (ttp80) REVERT: I 139 ARG cc_start: 0.8767 (tpt-90) cc_final: 0.7965 (ttp-110) REVERT: I 236 GLU cc_start: 0.7864 (mt-10) cc_final: 0.7517 (pm20) REVERT: I 249 GLU cc_start: 0.7808 (tt0) cc_final: 0.7476 (pm20) outliers start: 70 outliers final: 21 residues processed: 331 average time/residue: 1.3334 time to fit residues: 497.1980 Evaluate side-chains 276 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 242 time to evaluate : 2.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain B residue 33 LYS Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain D residue 103 SER Chi-restraints excluded: chain D residue 105 SER Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain E residue 33 LYS Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 273 ARG Chi-restraints excluded: chain F residue 180 LYS Chi-restraints excluded: chain F residue 240 THR Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain G residue 239 THR Chi-restraints excluded: chain H residue 33 LYS Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 273 ARG Chi-restraints excluded: chain I residue 277 ILE Chi-restraints excluded: chain J residue 136 ILE Chi-restraints excluded: chain J residue 284 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 209 optimal weight: 0.8980 chunk 145 optimal weight: 5.9990 chunk 178 optimal weight: 0.1980 chunk 67 optimal weight: 0.9990 chunk 0 optimal weight: 8.9990 chunk 19 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 chunk 99 optimal weight: 30.0000 chunk 208 optimal weight: 5.9990 chunk 14 optimal weight: 6.9990 chunk 195 optimal weight: 1.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 128 GLN F 128 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.170908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.143353 restraints weight = 23216.748| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 1.59 r_work: 0.3483 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3380 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.2945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 21220 Z= 0.146 Angle : 0.566 6.786 29080 Z= 0.296 Chirality : 0.048 0.181 3450 Planarity : 0.006 0.050 3740 Dihedral : 4.827 19.793 2890 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 2.88 % Allowed : 20.22 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.16), residues: 2610 helix: 1.29 (0.19), residues: 670 sheet: 0.98 (0.18), residues: 730 loop : -1.20 (0.18), residues: 1210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 52 HIS 0.005 0.001 HIS B 111 PHE 0.017 0.002 PHE F 188 TYR 0.011 0.001 TYR F 150 ARG 0.004 0.000 ARG J 251 Details of bonding type rmsd hydrogen bonds : bond 0.05143 ( 910) hydrogen bonds : angle 4.89923 ( 2790) covalent geometry : bond 0.00351 (21220) covalent geometry : angle 0.56610 (29080) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 247 time to evaluate : 2.412 Fit side-chains REVERT: A 139 ARG cc_start: 0.8808 (tpt170) cc_final: 0.7988 (ttp-110) REVERT: A 236 GLU cc_start: 0.7902 (mt-10) cc_final: 0.7575 (pm20) REVERT: A 249 GLU cc_start: 0.7803 (tt0) cc_final: 0.7501 (pm20) REVERT: B 33 LYS cc_start: 0.7031 (OUTLIER) cc_final: 0.6381 (mttm) REVERT: B 134 GLU cc_start: 0.8518 (OUTLIER) cc_final: 0.7997 (mp0) REVERT: C 61 ARG cc_start: 0.7934 (OUTLIER) cc_final: 0.7324 (ttm-80) REVERT: C 97 ARG cc_start: 0.7009 (tpt-90) cc_final: 0.6098 (ptm160) REVERT: C 310 ASP cc_start: 0.6886 (p0) cc_final: 0.6447 (t0) REVERT: D 61 ARG cc_start: 0.7330 (ttm110) cc_final: 0.6760 (tmm-80) REVERT: D 107 LEU cc_start: 0.7556 (OUTLIER) cc_final: 0.6859 (tm) REVERT: D 132 THR cc_start: 0.7813 (OUTLIER) cc_final: 0.7595 (p) REVERT: D 239 THR cc_start: 0.7748 (OUTLIER) cc_final: 0.7196 (m) REVERT: E 33 LYS cc_start: 0.8497 (OUTLIER) cc_final: 0.7987 (ttmt) REVERT: E 139 ARG cc_start: 0.8042 (tpt-90) cc_final: 0.7556 (ttp80) REVERT: F 61 ARG cc_start: 0.7968 (OUTLIER) cc_final: 0.7343 (ttm-80) REVERT: F 97 ARG cc_start: 0.7002 (tpt-90) cc_final: 0.6242 (ptm160) REVERT: F 180 LYS cc_start: 0.8294 (OUTLIER) cc_final: 0.8072 (mtpp) REVERT: F 310 ASP cc_start: 0.6901 (p0) cc_final: 0.6452 (t0) REVERT: G 61 ARG cc_start: 0.7355 (ttm110) cc_final: 0.6785 (tmm-80) REVERT: G 107 LEU cc_start: 0.7591 (OUTLIER) cc_final: 0.6910 (tm) REVERT: G 239 THR cc_start: 0.7741 (OUTLIER) cc_final: 0.7196 (m) REVERT: H 33 LYS cc_start: 0.8498 (OUTLIER) cc_final: 0.7942 (ttmt) REVERT: H 61 ARG cc_start: 0.7719 (tpp80) cc_final: 0.7464 (tpp80) REVERT: H 139 ARG cc_start: 0.8050 (tpt-90) cc_final: 0.7567 (ttp80) REVERT: I 139 ARG cc_start: 0.8862 (tpt-90) cc_final: 0.8055 (ttp-110) REVERT: I 236 GLU cc_start: 0.7904 (mt-10) cc_final: 0.7573 (pm20) REVERT: I 249 GLU cc_start: 0.7826 (tt0) cc_final: 0.7511 (pm20) REVERT: J 33 LYS cc_start: 0.7006 (OUTLIER) cc_final: 0.6397 (mttm) REVERT: J 134 GLU cc_start: 0.8523 (OUTLIER) cc_final: 0.8005 (mp0) outliers start: 66 outliers final: 29 residues processed: 292 average time/residue: 1.4731 time to fit residues: 483.8198 Evaluate side-chains 270 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 227 time to evaluate : 2.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain B residue 33 LYS Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain C residue 61 ARG Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 103 SER Chi-restraints excluded: chain D residue 105 SER Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain E residue 33 LYS Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 273 ARG Chi-restraints excluded: chain F residue 61 ARG Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain F residue 180 LYS Chi-restraints excluded: chain F residue 240 THR Chi-restraints excluded: chain G residue 100 THR Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain G residue 239 THR Chi-restraints excluded: chain H residue 33 LYS Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 273 ARG Chi-restraints excluded: chain I residue 177 LEU Chi-restraints excluded: chain I residue 277 ILE Chi-restraints excluded: chain J residue 33 LYS Chi-restraints excluded: chain J residue 134 GLU Chi-restraints excluded: chain J residue 136 ILE Chi-restraints excluded: chain J residue 284 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 258 optimal weight: 1.9990 chunk 172 optimal weight: 0.9980 chunk 241 optimal weight: 2.9990 chunk 202 optimal weight: 6.9990 chunk 31 optimal weight: 0.9990 chunk 103 optimal weight: 9.9990 chunk 74 optimal weight: 4.9990 chunk 38 optimal weight: 0.9980 chunk 148 optimal weight: 6.9990 chunk 28 optimal weight: 5.9990 chunk 111 optimal weight: 3.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.170907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.143281 restraints weight = 23168.135| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 1.61 r_work: 0.3490 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3388 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.3041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 21220 Z= 0.145 Angle : 0.565 6.477 29080 Z= 0.295 Chirality : 0.048 0.182 3450 Planarity : 0.006 0.051 3740 Dihedral : 4.790 19.765 2890 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 3.32 % Allowed : 20.26 % Favored : 76.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.16), residues: 2610 helix: 1.32 (0.19), residues: 670 sheet: 0.93 (0.18), residues: 730 loop : -1.19 (0.18), residues: 1210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP I 52 HIS 0.005 0.001 HIS B 111 PHE 0.017 0.002 PHE C 188 TYR 0.015 0.002 TYR H 215 ARG 0.008 0.000 ARG J 251 Details of bonding type rmsd hydrogen bonds : bond 0.05010 ( 910) hydrogen bonds : angle 4.86787 ( 2790) covalent geometry : bond 0.00347 (21220) covalent geometry : angle 0.56493 (29080) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 249 time to evaluate : 2.460 Fit side-chains REVERT: A 139 ARG cc_start: 0.8810 (tpt170) cc_final: 0.7974 (ttp-110) REVERT: A 236 GLU cc_start: 0.7880 (mt-10) cc_final: 0.7488 (pm20) REVERT: A 249 GLU cc_start: 0.7791 (tt0) cc_final: 0.7441 (pm20) REVERT: B 33 LYS cc_start: 0.6950 (OUTLIER) cc_final: 0.6313 (mttm) REVERT: B 134 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.7930 (mp0) REVERT: B 316 GLN cc_start: 0.7418 (OUTLIER) cc_final: 0.6366 (tm-30) REVERT: C 61 ARG cc_start: 0.7871 (OUTLIER) cc_final: 0.7259 (ttm-80) REVERT: C 97 ARG cc_start: 0.7035 (tpt-90) cc_final: 0.6046 (ptm160) REVERT: C 134 GLU cc_start: 0.7423 (OUTLIER) cc_final: 0.7174 (mp0) REVERT: C 273 ARG cc_start: 0.6740 (ttp-110) cc_final: 0.5868 (ttp-110) REVERT: C 310 ASP cc_start: 0.6828 (p0) cc_final: 0.6430 (t0) REVERT: D 61 ARG cc_start: 0.7300 (ttm110) cc_final: 0.6706 (tmm-80) REVERT: D 107 LEU cc_start: 0.7547 (OUTLIER) cc_final: 0.6864 (tm) REVERT: D 132 THR cc_start: 0.7725 (OUTLIER) cc_final: 0.7489 (p) REVERT: D 239 THR cc_start: 0.7734 (OUTLIER) cc_final: 0.7198 (m) REVERT: E 33 LYS cc_start: 0.8457 (OUTLIER) cc_final: 0.7850 (ttmt) REVERT: E 139 ARG cc_start: 0.7974 (tpt-90) cc_final: 0.7473 (ttp80) REVERT: E 299 ASP cc_start: 0.6787 (p0) cc_final: 0.6387 (p0) REVERT: F 61 ARG cc_start: 0.7890 (OUTLIER) cc_final: 0.7296 (ttm-80) REVERT: F 97 ARG cc_start: 0.7009 (tpt-90) cc_final: 0.6143 (ptm160) REVERT: F 273 ARG cc_start: 0.6772 (ttp-110) cc_final: 0.5907 (ttp-110) REVERT: F 310 ASP cc_start: 0.6839 (p0) cc_final: 0.6435 (t0) REVERT: G 61 ARG cc_start: 0.7301 (ttm110) cc_final: 0.6706 (tmm-80) REVERT: G 107 LEU cc_start: 0.7577 (OUTLIER) cc_final: 0.6963 (tm) REVERT: G 239 THR cc_start: 0.7723 (OUTLIER) cc_final: 0.7197 (m) REVERT: H 33 LYS cc_start: 0.8462 (OUTLIER) cc_final: 0.7928 (ttmt) REVERT: H 59 ILE cc_start: 0.8316 (OUTLIER) cc_final: 0.8088 (mt) REVERT: H 61 ARG cc_start: 0.7659 (tpp80) cc_final: 0.7319 (tpp80) REVERT: H 139 ARG cc_start: 0.7975 (tpt-90) cc_final: 0.7467 (ttp80) REVERT: I 139 ARG cc_start: 0.8831 (tpt-90) cc_final: 0.7995 (ttp-110) REVERT: I 236 GLU cc_start: 0.7856 (mt-10) cc_final: 0.7467 (pm20) REVERT: I 249 GLU cc_start: 0.7798 (tt0) cc_final: 0.7445 (pm20) REVERT: J 33 LYS cc_start: 0.6945 (OUTLIER) cc_final: 0.6313 (mttm) REVERT: J 134 GLU cc_start: 0.8506 (OUTLIER) cc_final: 0.7922 (mp0) REVERT: J 316 GLN cc_start: 0.7402 (OUTLIER) cc_final: 0.6352 (tm-30) outliers start: 76 outliers final: 39 residues processed: 302 average time/residue: 1.3590 time to fit residues: 462.6534 Evaluate side-chains 305 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 249 time to evaluate : 2.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain B residue 33 LYS Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 316 GLN Chi-restraints excluded: chain C residue 61 ARG Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 134 GLU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 103 SER Chi-restraints excluded: chain D residue 105 SER Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain E residue 33 LYS Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 159 GLU Chi-restraints excluded: chain E residue 273 ARG Chi-restraints excluded: chain F residue 61 ARG Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain F residue 180 LYS Chi-restraints excluded: chain F residue 240 THR Chi-restraints excluded: chain G residue 100 THR Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 239 THR Chi-restraints excluded: chain H residue 33 LYS Chi-restraints excluded: chain H residue 59 ILE Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 159 GLU Chi-restraints excluded: chain H residue 273 ARG Chi-restraints excluded: chain I residue 177 LEU Chi-restraints excluded: chain I residue 263 VAL Chi-restraints excluded: chain I residue 271 SER Chi-restraints excluded: chain I residue 277 ILE Chi-restraints excluded: chain J residue 33 LYS Chi-restraints excluded: chain J residue 134 GLU Chi-restraints excluded: chain J residue 136 ILE Chi-restraints excluded: chain J residue 284 SER Chi-restraints excluded: chain J residue 316 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 16 optimal weight: 0.9980 chunk 99 optimal weight: 2.9990 chunk 178 optimal weight: 10.0000 chunk 34 optimal weight: 1.9990 chunk 249 optimal weight: 0.7980 chunk 143 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 152 optimal weight: 3.9990 chunk 189 optimal weight: 3.9990 chunk 109 optimal weight: 8.9990 chunk 188 optimal weight: 5.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.173667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.145713 restraints weight = 23134.539| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 1.66 r_work: 0.3494 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3389 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.3114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 21220 Z= 0.143 Angle : 0.564 6.378 29080 Z= 0.295 Chirality : 0.048 0.170 3450 Planarity : 0.006 0.050 3740 Dihedral : 4.757 19.694 2890 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 3.10 % Allowed : 20.39 % Favored : 76.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.16), residues: 2610 helix: 1.39 (0.19), residues: 670 sheet: 0.93 (0.18), residues: 730 loop : -1.16 (0.18), residues: 1210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 182 HIS 0.005 0.001 HIS B 111 PHE 0.017 0.002 PHE F 188 TYR 0.016 0.002 TYR E 215 ARG 0.007 0.000 ARG B 251 Details of bonding type rmsd hydrogen bonds : bond 0.04985 ( 910) hydrogen bonds : angle 4.85927 ( 2790) covalent geometry : bond 0.00344 (21220) covalent geometry : angle 0.56442 (29080) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 270 time to evaluate : 2.800 Fit side-chains REVERT: A 139 ARG cc_start: 0.8888 (tpt170) cc_final: 0.7997 (ttp-110) REVERT: A 236 GLU cc_start: 0.8074 (mt-10) cc_final: 0.7597 (pm20) REVERT: A 249 GLU cc_start: 0.7882 (tt0) cc_final: 0.7436 (pm20) REVERT: B 33 LYS cc_start: 0.6936 (OUTLIER) cc_final: 0.6291 (mttm) REVERT: B 134 GLU cc_start: 0.8595 (OUTLIER) cc_final: 0.8067 (mp0) REVERT: C 61 ARG cc_start: 0.7904 (OUTLIER) cc_final: 0.7304 (ttm-80) REVERT: C 97 ARG cc_start: 0.7124 (tpt-90) cc_final: 0.6234 (ptm160) REVERT: C 273 ARG cc_start: 0.6804 (ttp-110) cc_final: 0.5894 (mtm180) REVERT: C 310 ASP cc_start: 0.6773 (p0) cc_final: 0.6429 (t0) REVERT: D 61 ARG cc_start: 0.7247 (ttm110) cc_final: 0.6625 (tmm-80) REVERT: D 107 LEU cc_start: 0.7562 (OUTLIER) cc_final: 0.6909 (tm) REVERT: D 132 THR cc_start: 0.7835 (OUTLIER) cc_final: 0.7582 (p) REVERT: D 239 THR cc_start: 0.7803 (OUTLIER) cc_final: 0.7238 (m) REVERT: D 290 TYR cc_start: 0.6884 (m-80) cc_final: 0.6361 (m-80) REVERT: E 33 LYS cc_start: 0.8494 (OUTLIER) cc_final: 0.7917 (ttmt) REVERT: E 139 ARG cc_start: 0.8062 (tpt-90) cc_final: 0.7551 (ttp80) REVERT: E 299 ASP cc_start: 0.6812 (p0) cc_final: 0.6456 (p0) REVERT: F 61 ARG cc_start: 0.7916 (OUTLIER) cc_final: 0.7315 (ttm-80) REVERT: F 97 ARG cc_start: 0.7084 (tpt-90) cc_final: 0.6204 (ptm160) REVERT: F 273 ARG cc_start: 0.6839 (ttp-110) cc_final: 0.5935 (mtm180) REVERT: F 310 ASP cc_start: 0.6749 (p0) cc_final: 0.6423 (t0) REVERT: G 61 ARG cc_start: 0.7266 (ttm110) cc_final: 0.6646 (tmm-80) REVERT: G 107 LEU cc_start: 0.7575 (OUTLIER) cc_final: 0.6973 (tm) REVERT: G 239 THR cc_start: 0.7781 (OUTLIER) cc_final: 0.7240 (m) REVERT: G 290 TYR cc_start: 0.6829 (m-80) cc_final: 0.5561 (m-80) REVERT: H 33 LYS cc_start: 0.8516 (OUTLIER) cc_final: 0.7960 (ttmt) REVERT: H 59 ILE cc_start: 0.8390 (OUTLIER) cc_final: 0.8175 (mt) REVERT: H 61 ARG cc_start: 0.7743 (tpp80) cc_final: 0.7394 (tpp80) REVERT: H 139 ARG cc_start: 0.8075 (tpt-90) cc_final: 0.7551 (ttp80) REVERT: I 139 ARG cc_start: 0.8877 (tpt-90) cc_final: 0.8056 (ttp-110) REVERT: I 236 GLU cc_start: 0.8037 (mt-10) cc_final: 0.7576 (pm20) REVERT: I 249 GLU cc_start: 0.7883 (tt0) cc_final: 0.7440 (pm20) REVERT: J 33 LYS cc_start: 0.7004 (OUTLIER) cc_final: 0.6376 (mttm) REVERT: J 134 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.8037 (mp0) outliers start: 71 outliers final: 38 residues processed: 317 average time/residue: 1.4879 time to fit residues: 529.7421 Evaluate side-chains 300 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 248 time to evaluate : 2.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain B residue 33 LYS Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain C residue 61 ARG Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 103 SER Chi-restraints excluded: chain D residue 105 SER Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain E residue 33 LYS Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 159 GLU Chi-restraints excluded: chain E residue 273 ARG Chi-restraints excluded: chain F residue 61 ARG Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain F residue 180 LYS Chi-restraints excluded: chain F residue 240 THR Chi-restraints excluded: chain G residue 100 THR Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 239 THR Chi-restraints excluded: chain H residue 33 LYS Chi-restraints excluded: chain H residue 59 ILE Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 159 GLU Chi-restraints excluded: chain H residue 273 ARG Chi-restraints excluded: chain I residue 177 LEU Chi-restraints excluded: chain I residue 263 VAL Chi-restraints excluded: chain I residue 271 SER Chi-restraints excluded: chain I residue 277 ILE Chi-restraints excluded: chain J residue 33 LYS Chi-restraints excluded: chain J residue 134 GLU Chi-restraints excluded: chain J residue 136 ILE Chi-restraints excluded: chain J residue 284 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 0 optimal weight: 8.9990 chunk 2 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 212 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 237 optimal weight: 4.9990 chunk 44 optimal weight: 0.0670 chunk 3 optimal weight: 0.9980 chunk 220 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 overall best weight: 0.9720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 111 HIS J 111 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.175659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.147967 restraints weight = 23270.950| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 1.64 r_work: 0.3524 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3421 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.3229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21220 Z= 0.117 Angle : 0.530 6.625 29080 Z= 0.278 Chirality : 0.046 0.164 3450 Planarity : 0.006 0.050 3740 Dihedral : 4.581 18.894 2890 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 2.27 % Allowed : 21.44 % Favored : 76.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.16), residues: 2610 helix: 1.60 (0.19), residues: 670 sheet: 1.13 (0.18), residues: 710 loop : -1.10 (0.18), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 182 HIS 0.004 0.001 HIS H 111 PHE 0.014 0.001 PHE C 188 TYR 0.018 0.001 TYR E 215 ARG 0.007 0.000 ARG B 251 Details of bonding type rmsd hydrogen bonds : bond 0.04361 ( 910) hydrogen bonds : angle 4.69273 ( 2790) covalent geometry : bond 0.00276 (21220) covalent geometry : angle 0.53041 (29080) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 261 time to evaluate : 2.544 Fit side-chains revert: symmetry clash REVERT: A 236 GLU cc_start: 0.8094 (mt-10) cc_final: 0.7614 (pm20) REVERT: A 249 GLU cc_start: 0.7823 (tt0) cc_final: 0.7373 (pm20) REVERT: B 134 GLU cc_start: 0.8591 (OUTLIER) cc_final: 0.8065 (mp0) REVERT: C 61 ARG cc_start: 0.7911 (mtp85) cc_final: 0.7291 (ttm-80) REVERT: C 97 ARG cc_start: 0.7035 (tpt-90) cc_final: 0.6181 (ptm160) REVERT: C 273 ARG cc_start: 0.6784 (ttp-110) cc_final: 0.5895 (mtm180) REVERT: C 310 ASP cc_start: 0.6779 (p0) cc_final: 0.6487 (t0) REVERT: D 61 ARG cc_start: 0.7250 (ttm110) cc_final: 0.6630 (tmm-80) REVERT: D 107 LEU cc_start: 0.7538 (OUTLIER) cc_final: 0.6899 (tm) REVERT: D 132 THR cc_start: 0.7852 (OUTLIER) cc_final: 0.7643 (p) REVERT: D 290 TYR cc_start: 0.6839 (m-80) cc_final: 0.6243 (m-80) REVERT: E 33 LYS cc_start: 0.8470 (OUTLIER) cc_final: 0.7924 (ttmt) REVERT: E 139 ARG cc_start: 0.8007 (tpt-90) cc_final: 0.7506 (ttp80) REVERT: E 299 ASP cc_start: 0.6712 (p0) cc_final: 0.6361 (p0) REVERT: F 61 ARG cc_start: 0.7908 (OUTLIER) cc_final: 0.7338 (ttm-80) REVERT: F 97 ARG cc_start: 0.7037 (tpt-90) cc_final: 0.6163 (ptm160) REVERT: F 237 ASP cc_start: 0.7416 (t0) cc_final: 0.7049 (t0) REVERT: F 273 ARG cc_start: 0.6826 (ttp-110) cc_final: 0.5953 (mtm180) REVERT: F 310 ASP cc_start: 0.6713 (p0) cc_final: 0.6459 (t0) REVERT: G 61 ARG cc_start: 0.7242 (ttm110) cc_final: 0.6612 (tmm-80) REVERT: G 107 LEU cc_start: 0.7558 (OUTLIER) cc_final: 0.6938 (tm) REVERT: G 285 TYR cc_start: 0.7958 (m-80) cc_final: 0.7687 (m-80) REVERT: G 290 TYR cc_start: 0.6772 (m-80) cc_final: 0.5478 (m-80) REVERT: H 33 LYS cc_start: 0.8490 (OUTLIER) cc_final: 0.7945 (ttmt) REVERT: H 59 ILE cc_start: 0.8364 (OUTLIER) cc_final: 0.8158 (mt) REVERT: H 61 ARG cc_start: 0.7764 (tpp80) cc_final: 0.7482 (tpp80) REVERT: H 139 ARG cc_start: 0.8021 (tpt-90) cc_final: 0.7521 (ttp80) REVERT: I 236 GLU cc_start: 0.8036 (mt-10) cc_final: 0.7591 (pm20) REVERT: I 249 GLU cc_start: 0.7801 (tt0) cc_final: 0.7371 (pm20) REVERT: J 33 LYS cc_start: 0.6906 (OUTLIER) cc_final: 0.6419 (mttm) REVERT: J 61 ARG cc_start: 0.8202 (ttm-80) cc_final: 0.7821 (tpp80) REVERT: J 134 GLU cc_start: 0.8573 (OUTLIER) cc_final: 0.8047 (mp0) outliers start: 52 outliers final: 30 residues processed: 297 average time/residue: 1.4717 time to fit residues: 496.9345 Evaluate side-chains 289 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 249 time to evaluate : 2.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 103 SER Chi-restraints excluded: chain D residue 104 ILE Chi-restraints excluded: chain D residue 105 SER Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain E residue 33 LYS Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 273 ARG Chi-restraints excluded: chain F residue 61 ARG Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain G residue 100 THR Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 161 THR Chi-restraints excluded: chain H residue 33 LYS Chi-restraints excluded: chain H residue 59 ILE Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 159 GLU Chi-restraints excluded: chain H residue 273 ARG Chi-restraints excluded: chain I residue 177 LEU Chi-restraints excluded: chain I residue 277 ILE Chi-restraints excluded: chain J residue 33 LYS Chi-restraints excluded: chain J residue 134 GLU Chi-restraints excluded: chain J residue 136 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 148 optimal weight: 0.2980 chunk 180 optimal weight: 0.0980 chunk 142 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 152 optimal weight: 0.9990 chunk 205 optimal weight: 4.9990 chunk 117 optimal weight: 3.9990 chunk 162 optimal weight: 8.9990 chunk 188 optimal weight: 7.9990 chunk 34 optimal weight: 1.9990 chunk 123 optimal weight: 0.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.176526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.148557 restraints weight = 23182.138| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 1.62 r_work: 0.3543 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3443 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.3284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 21220 Z= 0.114 Angle : 0.529 6.808 29080 Z= 0.277 Chirality : 0.046 0.159 3450 Planarity : 0.006 0.048 3740 Dihedral : 4.501 18.452 2890 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 2.14 % Allowed : 21.83 % Favored : 76.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.16), residues: 2610 helix: 1.68 (0.19), residues: 670 sheet: 1.15 (0.18), residues: 710 loop : -1.04 (0.18), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 182 HIS 0.004 0.001 HIS H 111 PHE 0.014 0.001 PHE F 188 TYR 0.017 0.001 TYR H 215 ARG 0.006 0.000 ARG B 251 Details of bonding type rmsd hydrogen bonds : bond 0.04250 ( 910) hydrogen bonds : angle 4.64169 ( 2790) covalent geometry : bond 0.00268 (21220) covalent geometry : angle 0.52907 (29080) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 264 time to evaluate : 2.197 Fit side-chains revert: symmetry clash REVERT: A 236 GLU cc_start: 0.8169 (mt-10) cc_final: 0.7719 (pm20) REVERT: A 249 GLU cc_start: 0.7754 (tt0) cc_final: 0.7344 (pm20) REVERT: B 33 LYS cc_start: 0.6930 (OUTLIER) cc_final: 0.6626 (mttp) REVERT: B 134 GLU cc_start: 0.8556 (OUTLIER) cc_final: 0.8336 (tp30) REVERT: C 61 ARG cc_start: 0.7979 (mtp85) cc_final: 0.7366 (ttm-80) REVERT: C 97 ARG cc_start: 0.7022 (tpt-90) cc_final: 0.6262 (ptm160) REVERT: C 128 GLN cc_start: 0.7570 (mt0) cc_final: 0.7035 (mm-40) REVERT: C 273 ARG cc_start: 0.6841 (ttp-110) cc_final: 0.6096 (mtm180) REVERT: C 310 ASP cc_start: 0.6773 (p0) cc_final: 0.6567 (t0) REVERT: D 61 ARG cc_start: 0.7361 (ttm110) cc_final: 0.6759 (tmm-80) REVERT: D 107 LEU cc_start: 0.7609 (OUTLIER) cc_final: 0.7002 (tm) REVERT: D 290 TYR cc_start: 0.6874 (m-80) cc_final: 0.6466 (m-80) REVERT: E 33 LYS cc_start: 0.8489 (OUTLIER) cc_final: 0.7984 (ttmt) REVERT: E 139 ARG cc_start: 0.8056 (tpt-90) cc_final: 0.7637 (ttp80) REVERT: E 299 ASP cc_start: 0.6681 (p0) cc_final: 0.6366 (p0) REVERT: F 61 ARG cc_start: 0.7964 (OUTLIER) cc_final: 0.7417 (ttm-80) REVERT: F 97 ARG cc_start: 0.7058 (tpt-90) cc_final: 0.6235 (ptm160) REVERT: F 128 GLN cc_start: 0.7585 (mt0) cc_final: 0.7051 (mm-40) REVERT: F 273 ARG cc_start: 0.6863 (ttp-110) cc_final: 0.6130 (mtm180) REVERT: G 61 ARG cc_start: 0.7360 (ttm110) cc_final: 0.6763 (tmm-80) REVERT: G 107 LEU cc_start: 0.7590 (OUTLIER) cc_final: 0.6999 (tm) REVERT: G 290 TYR cc_start: 0.6850 (m-80) cc_final: 0.5760 (m-80) REVERT: H 33 LYS cc_start: 0.8513 (OUTLIER) cc_final: 0.7951 (ttmt) REVERT: H 61 ARG cc_start: 0.7828 (tpp80) cc_final: 0.7538 (tpp80) REVERT: H 139 ARG cc_start: 0.8058 (tpt-90) cc_final: 0.7636 (ttp80) REVERT: I 236 GLU cc_start: 0.8073 (mt-10) cc_final: 0.7677 (pm20) REVERT: I 249 GLU cc_start: 0.7734 (tt0) cc_final: 0.7369 (pm20) REVERT: J 33 LYS cc_start: 0.6968 (OUTLIER) cc_final: 0.6468 (mttm) REVERT: J 61 ARG cc_start: 0.8210 (ttm-80) cc_final: 0.7854 (tpp80) REVERT: J 134 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.8060 (mp0) outliers start: 49 outliers final: 31 residues processed: 299 average time/residue: 1.3714 time to fit residues: 462.1703 Evaluate side-chains 285 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 245 time to evaluate : 2.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain B residue 33 LYS Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 103 SER Chi-restraints excluded: chain D residue 105 SER Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain E residue 33 LYS Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 273 ARG Chi-restraints excluded: chain F residue 61 ARG Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 161 THR Chi-restraints excluded: chain H residue 33 LYS Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 159 GLU Chi-restraints excluded: chain H residue 273 ARG Chi-restraints excluded: chain I residue 177 LEU Chi-restraints excluded: chain I residue 277 ILE Chi-restraints excluded: chain J residue 33 LYS Chi-restraints excluded: chain J residue 134 GLU Chi-restraints excluded: chain J residue 136 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 175 optimal weight: 5.9990 chunk 75 optimal weight: 10.0000 chunk 93 optimal weight: 0.9990 chunk 116 optimal weight: 4.9990 chunk 65 optimal weight: 4.9990 chunk 55 optimal weight: 0.9980 chunk 202 optimal weight: 0.0970 chunk 232 optimal weight: 0.6980 chunk 238 optimal weight: 0.9980 chunk 47 optimal weight: 0.0970 chunk 115 optimal weight: 2.9990 overall best weight: 0.5776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 146 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.178771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.151656 restraints weight = 23098.308| |-----------------------------------------------------------------------------| r_work (start): 0.3707 rms_B_bonded: 1.58 r_work: 0.3557 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3455 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.3427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 21220 Z= 0.103 Angle : 0.511 6.682 29080 Z= 0.267 Chirality : 0.045 0.189 3450 Planarity : 0.005 0.048 3740 Dihedral : 4.354 17.642 2890 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 1.75 % Allowed : 22.31 % Favored : 75.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.16), residues: 2610 helix: 1.87 (0.19), residues: 670 sheet: 1.20 (0.18), residues: 710 loop : -0.95 (0.18), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 182 HIS 0.004 0.001 HIS H 111 PHE 0.011 0.001 PHE C 188 TYR 0.016 0.001 TYR H 215 ARG 0.006 0.000 ARG J 251 Details of bonding type rmsd hydrogen bonds : bond 0.03806 ( 910) hydrogen bonds : angle 4.50681 ( 2790) covalent geometry : bond 0.00240 (21220) covalent geometry : angle 0.51110 (29080) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 273 time to evaluate : 2.325 Fit side-chains revert: symmetry clash REVERT: A 236 GLU cc_start: 0.8217 (mt-10) cc_final: 0.7783 (pm20) REVERT: A 249 GLU cc_start: 0.7671 (tt0) cc_final: 0.7266 (pm20) REVERT: B 134 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.8369 (tp30) REVERT: C 61 ARG cc_start: 0.7978 (mtp85) cc_final: 0.7375 (ttm-80) REVERT: C 97 ARG cc_start: 0.6991 (tpt-90) cc_final: 0.6191 (ptm160) REVERT: C 128 GLN cc_start: 0.7502 (mt0) cc_final: 0.7009 (mm-40) REVERT: C 236 GLU cc_start: 0.7560 (mt-10) cc_final: 0.7311 (mt-10) REVERT: C 273 ARG cc_start: 0.6862 (ttp-110) cc_final: 0.6086 (mtm180) REVERT: D 61 ARG cc_start: 0.7331 (ttm110) cc_final: 0.6709 (tmm-80) REVERT: D 107 LEU cc_start: 0.7536 (OUTLIER) cc_final: 0.7012 (tm) REVERT: D 290 TYR cc_start: 0.6851 (m-80) cc_final: 0.6279 (m-80) REVERT: E 33 LYS cc_start: 0.8476 (OUTLIER) cc_final: 0.7943 (ttmt) REVERT: E 139 ARG cc_start: 0.8037 (tpt-90) cc_final: 0.7610 (ttp80) REVERT: E 299 ASP cc_start: 0.6705 (p0) cc_final: 0.6387 (p0) REVERT: F 61 ARG cc_start: 0.7982 (mtp85) cc_final: 0.7447 (ttm-80) REVERT: F 97 ARG cc_start: 0.7045 (tpt-90) cc_final: 0.6183 (ptm160) REVERT: F 128 GLN cc_start: 0.7500 (mt0) cc_final: 0.7002 (mm-40) REVERT: F 236 GLU cc_start: 0.7551 (mt-10) cc_final: 0.7312 (mt-10) REVERT: F 273 ARG cc_start: 0.6871 (ttp-110) cc_final: 0.6101 (mtm180) REVERT: G 61 ARG cc_start: 0.7317 (ttm110) cc_final: 0.6701 (tmm-80) REVERT: G 107 LEU cc_start: 0.7548 (OUTLIER) cc_final: 0.7027 (tm) REVERT: G 290 TYR cc_start: 0.6848 (m-80) cc_final: 0.5707 (m-80) REVERT: H 33 LYS cc_start: 0.8505 (OUTLIER) cc_final: 0.7933 (ttmt) REVERT: H 61 ARG cc_start: 0.7844 (tpp80) cc_final: 0.7472 (tpp80) REVERT: H 139 ARG cc_start: 0.8059 (tpt-90) cc_final: 0.7607 (ttp80) REVERT: I 236 GLU cc_start: 0.8132 (mt-10) cc_final: 0.7728 (pm20) REVERT: I 249 GLU cc_start: 0.7646 (tt0) cc_final: 0.7294 (pm20) REVERT: J 33 LYS cc_start: 0.6875 (OUTLIER) cc_final: 0.6428 (mttm) REVERT: J 61 ARG cc_start: 0.8256 (ttm-80) cc_final: 0.7893 (tpp80) REVERT: J 134 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.8358 (tp30) outliers start: 40 outliers final: 25 residues processed: 305 average time/residue: 1.4239 time to fit residues: 487.7970 Evaluate side-chains 296 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 264 time to evaluate : 2.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain E residue 33 LYS Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 273 ARG Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 161 THR Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain H residue 33 LYS Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 159 GLU Chi-restraints excluded: chain H residue 273 ARG Chi-restraints excluded: chain I residue 177 LEU Chi-restraints excluded: chain I residue 277 ILE Chi-restraints excluded: chain J residue 33 LYS Chi-restraints excluded: chain J residue 134 GLU Chi-restraints excluded: chain J residue 136 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 135 optimal weight: 6.9990 chunk 215 optimal weight: 2.9990 chunk 137 optimal weight: 0.7980 chunk 130 optimal weight: 0.6980 chunk 258 optimal weight: 0.8980 chunk 25 optimal weight: 8.9990 chunk 89 optimal weight: 0.0370 chunk 181 optimal weight: 10.0000 chunk 107 optimal weight: 9.9990 chunk 153 optimal weight: 6.9990 chunk 87 optimal weight: 3.9990 overall best weight: 1.0860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 146 ASN G 146 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.176071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.148134 restraints weight = 23187.900| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 1.60 r_work: 0.3545 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3445 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.3356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21220 Z= 0.123 Angle : 0.549 6.818 29080 Z= 0.286 Chirality : 0.046 0.185 3450 Planarity : 0.006 0.047 3740 Dihedral : 4.487 18.469 2890 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 1.79 % Allowed : 22.58 % Favored : 75.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.16), residues: 2610 helix: 1.76 (0.19), residues: 670 sheet: 1.19 (0.18), residues: 710 loop : -0.99 (0.18), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 182 HIS 0.004 0.001 HIS H 111 PHE 0.015 0.001 PHE F 188 TYR 0.017 0.001 TYR E 215 ARG 0.006 0.000 ARG J 251 Details of bonding type rmsd hydrogen bonds : bond 0.04414 ( 910) hydrogen bonds : angle 4.65029 ( 2790) covalent geometry : bond 0.00291 (21220) covalent geometry : angle 0.54949 (29080) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15269.77 seconds wall clock time: 263 minutes 38.79 seconds (15818.79 seconds total)