Starting phenix.real_space_refine on Tue Jun 17 23:22:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8won_37693/06_2025/8won_37693.cif Found real_map, /net/cci-nas-00/data/ceres_data/8won_37693/06_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_37693/06_2025/8won_37693.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8won_37693/06_2025/8won_37693.map" model { file = "/net/cci-nas-00/data/ceres_data/8won_37693/06_2025/8won_37693.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8won_37693/06_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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 6.26, 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: 4.77 Conformation dependent library (CDL) restraints added in 2.5 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: 3.18 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: 7.46 Time building geometry restraints manager: 5.69 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: 2.270 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: 0.030 Extract box with map and model: 0.930 Check model and map are aligned: 0.160 Set scattering table: 0.170 Process input model: 41.500 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.070 ------------------------------------------------------------------------------- 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 : 2.097 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: 1.5740 time to fit residues: 668.6937 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 : 2.102 ------------------------------------------------------------------------------- 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: 0.3515 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3415 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 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 : 2.588 Fit side-chains revert: symmetry clash REVERT: A 139 ARG cc_start: 0.8794 (tpt170) cc_final: 0.8010 (ttp-110) REVERT: A 236 GLU cc_start: 0.7867 (mt-10) cc_final: 0.7608 (pm20) REVERT: C 134 GLU cc_start: 0.7586 (OUTLIER) cc_final: 0.7348 (mp0) REVERT: D 97 ARG cc_start: 0.7025 (tpt170) cc_final: 0.6777 (tpt170) REVERT: D 107 LEU cc_start: 0.7609 (OUTLIER) cc_final: 0.7163 (tm) REVERT: D 211 THR cc_start: 0.7879 (p) cc_final: 0.7672 (p) REVERT: D 250 GLU cc_start: 0.7834 (tp30) cc_final: 0.7455 (mp0) REVERT: D 251 ARG cc_start: 0.7724 (ptp-110) cc_final: 0.7408 (ptm160) REVERT: E 33 LYS cc_start: 0.8489 (OUTLIER) cc_final: 0.8254 (ttmt) REVERT: E 61 ARG cc_start: 0.7593 (tpp80) cc_final: 0.6713 (tpp80) REVERT: E 139 ARG cc_start: 0.7910 (tpt-90) cc_final: 0.7499 (ttp80) REVERT: F 97 ARG cc_start: 0.6869 (tpt-90) cc_final: 0.6188 (ptm160) REVERT: F 134 GLU cc_start: 0.7566 (OUTLIER) cc_final: 0.7328 (mp0) REVERT: F 180 LYS cc_start: 0.8336 (OUTLIER) cc_final: 0.7863 (mtpp) REVERT: G 107 LEU cc_start: 0.7603 (OUTLIER) cc_final: 0.7173 (tm) REVERT: G 211 THR cc_start: 0.7873 (p) cc_final: 0.7667 (p) REVERT: G 250 GLU cc_start: 0.7884 (tp30) cc_final: 0.7449 (mp0) REVERT: G 251 ARG cc_start: 0.7737 (ptp-110) cc_final: 0.7406 (ptm160) REVERT: H 33 LYS cc_start: 0.8494 (OUTLIER) cc_final: 0.7966 (ttmt) REVERT: H 139 ARG cc_start: 0.7883 (tpt-90) cc_final: 0.7502 (ttp80) REVERT: I 139 ARG cc_start: 0.8797 (tpt-90) cc_final: 0.7970 (ttp-110) REVERT: I 236 GLU cc_start: 0.7907 (mt-10) cc_final: 0.7615 (pm20) outliers start: 49 outliers final: 10 residues processed: 321 average time/residue: 1.7822 time to fit residues: 641.6273 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 : 2.344 ------------------------------------------------------------------------------- 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: 0.8980 chunk 207 optimal weight: 0.9990 chunk 156 optimal weight: 10.0000 chunk 240 optimal weight: 10.0000 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: 2.7788 ------------------------------------------------------------------------------- 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 = 0.169455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.141810 restraints weight = 22922.343| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 1.61 r_work: 0.3460 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3358 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.2545 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= 0.213 Angle : 0.646 6.829 29080 Z= 0.338 Chirality : 0.052 0.162 3450 Planarity : 0.007 0.050 3740 Dihedral : 5.256 20.999 2890 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 3.76 % Allowed : 18.73 % 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: -0.01 (0.16), residues: 2610 helix: 0.85 (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 0.012 0.002 TRP G 182 HIS 0.006 0.001 HIS B 111 PHE 0.019 0.002 PHE C 188 TYR 0.014 0.002 TYR G 315 ARG 0.006 0.001 ARG F 61 Details of bonding type rmsd hydrogen bonds : bond 0.06365 ( 910) hydrogen bonds : angle 5.21262 ( 2790) covalent geometry : bond 0.00526 (21220) covalent geometry : angle 0.64627 (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 366 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 280 time to evaluate : 2.223 Fit side-chains REVERT: A 114 VAL cc_start: 0.3572 (OUTLIER) cc_final: 0.3368 (t) REVERT: A 139 ARG cc_start: 0.8796 (tpt170) cc_final: 0.8043 (ttp-110) REVERT: A 236 GLU cc_start: 0.7854 (mt-10) cc_final: 0.7579 (pm20) REVERT: A 249 GLU cc_start: 0.7919 (tt0) cc_final: 0.7629 (pm20) REVERT: B 33 LYS cc_start: 0.7078 (OUTLIER) cc_final: 0.6449 (mttm) REVERT: C 97 ARG cc_start: 0.7082 (tpt-90) cc_final: 0.6263 (ptm160) REVERT: C 134 GLU cc_start: 0.7559 (OUTLIER) cc_final: 0.7057 (mp0) REVERT: C 273 ARG cc_start: 0.6885 (ttp-110) cc_final: 0.6035 (ttp-170) REVERT: D 61 ARG cc_start: 0.7259 (ttm110) cc_final: 0.6667 (tmm-80) REVERT: D 107 LEU cc_start: 0.7668 (OUTLIER) cc_final: 0.7073 (tm) REVERT: D 110 VAL cc_start: 0.6071 (OUTLIER) cc_final: 0.5843 (t) REVERT: E 33 LYS cc_start: 0.8482 (OUTLIER) cc_final: 0.7964 (ttmt) REVERT: E 59 ILE cc_start: 0.8328 (OUTLIER) cc_final: 0.8120 (mt) REVERT: E 61 ARG cc_start: 0.7557 (tpp80) cc_final: 0.7316 (tpp80) REVERT: E 139 ARG cc_start: 0.8127 (tpt-90) cc_final: 0.7638 (ttp80) REVERT: F 61 ARG cc_start: 0.7964 (mtp85) cc_final: 0.7328 (ttm-80) REVERT: F 97 ARG cc_start: 0.7029 (tpt-90) cc_final: 0.6273 (ptm160) REVERT: F 134 GLU cc_start: 0.7559 (OUTLIER) cc_final: 0.7059 (mp0) REVERT: F 273 ARG cc_start: 0.6915 (ttp-110) cc_final: 0.6067 (ttp-170) REVERT: G 61 ARG cc_start: 0.7274 (ttm110) cc_final: 0.6669 (tmm-80) REVERT: G 107 LEU cc_start: 0.7671 (OUTLIER) cc_final: 0.7083 (tm) REVERT: H 33 LYS cc_start: 0.8508 (OUTLIER) cc_final: 0.7950 (ttmt) REVERT: H 59 ILE cc_start: 0.8407 (OUTLIER) cc_final: 0.8200 (mt) REVERT: H 139 ARG cc_start: 0.8112 (tpt-90) cc_final: 0.7640 (ttp80) REVERT: I 139 ARG cc_start: 0.8860 (tpt-90) cc_final: 0.8057 (ttp-110) REVERT: I 236 GLU cc_start: 0.7817 (mt-10) cc_final: 0.7557 (pm20) REVERT: I 249 GLU cc_start: 0.7959 (tt0) cc_final: 0.7630 (pm20) REVERT: J 33 LYS cc_start: 0.7054 (OUTLIER) cc_final: 0.6476 (mttm) outliers start: 86 outliers final: 28 residues processed: 336 average time/residue: 1.4830 time to fit residues: 559.2949 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 : 2.242 ------------------------------------------------------------------------------- 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 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 59 ILE 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: 3.9990 chunk 211 optimal weight: 0.5980 chunk 6 optimal weight: 7.9990 chunk 217 optimal weight: 0.7980 chunk 110 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 210 optimal weight: 0.7980 chunk 259 optimal weight: 1.9990 chunk 73 optimal weight: 8.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 = 0.3918 r_free = 0.3918 target = 0.172966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.145512 restraints weight = 23216.120| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 1.60 r_work: 0.3521 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3420 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.2812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 21220 Z= 0.121 Angle : 0.532 5.009 29080 Z= 0.280 Chirality : 0.046 0.152 3450 Planarity : 0.006 0.051 3740 Dihedral : 4.789 19.307 2890 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 3.10 % Allowed : 19.52 % Favored : 77.38 % 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: 1.32 (0.19), residues: 670 sheet: 1.06 (0.19), residues: 730 loop : -1.16 (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 0.009 0.001 TYR F 150 ARG 0.008 0.000 ARG B 251 Details of bonding type rmsd hydrogen bonds : bond 0.04534 ( 910) hydrogen bonds : angle 4.78808 ( 2790) covalent geometry : bond 0.00286 (21220) covalent geometry : angle 0.53201 (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 353 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 282 time to evaluate : 2.199 Fit side-chains REVERT: A 236 GLU cc_start: 0.7844 (mt-10) cc_final: 0.7513 (pm20) REVERT: A 249 GLU cc_start: 0.7788 (tt0) cc_final: 0.7472 (pm20) REVERT: B 33 LYS cc_start: 0.7000 (OUTLIER) cc_final: 0.6485 (mttm) REVERT: C 61 ARG cc_start: 0.7861 (mtp85) cc_final: 0.7240 (ttm-80) REVERT: C 273 ARG cc_start: 0.6823 (ttp-110) cc_final: 0.5984 (ttp-170) REVERT: C 277 ILE cc_start: 0.1886 (OUTLIER) cc_final: 0.1625 (mm) REVERT: C 310 ASP cc_start: 0.6889 (p0) cc_final: 0.6324 (t0) REVERT: D 61 ARG cc_start: 0.7252 (ttm110) cc_final: 0.6668 (tmm-80) REVERT: D 107 LEU cc_start: 0.7596 (OUTLIER) cc_final: 0.6909 (tm) REVERT: D 110 VAL cc_start: 0.6134 (OUTLIER) cc_final: 0.5914 (t) REVERT: D 132 THR cc_start: 0.7837 (OUTLIER) cc_final: 0.7568 (p) REVERT: D 239 THR cc_start: 0.7593 (OUTLIER) cc_final: 0.7143 (m) REVERT: E 33 LYS cc_start: 0.8456 (OUTLIER) cc_final: 0.7969 (ttmt) REVERT: E 139 ARG cc_start: 0.7919 (tpt-90) cc_final: 0.7441 (ttp80) REVERT: F 61 ARG cc_start: 0.7882 (mtp85) cc_final: 0.7267 (ttm-80) REVERT: F 97 ARG cc_start: 0.6913 (tpt-90) cc_final: 0.6135 (ptm160) REVERT: F 180 LYS cc_start: 0.8203 (OUTLIER) cc_final: 0.7802 (mtpp) REVERT: F 273 ARG cc_start: 0.6847 (ttp-110) cc_final: 0.6000 (ttp-170) REVERT: F 277 ILE cc_start: 0.1883 (OUTLIER) cc_final: 0.1624 (mm) REVERT: F 310 ASP cc_start: 0.6901 (p0) cc_final: 0.6330 (t0) REVERT: G 61 ARG cc_start: 0.7247 (ttm110) cc_final: 0.6654 (tmm-80) REVERT: G 107 LEU cc_start: 0.7576 (OUTLIER) cc_final: 0.6878 (tm) REVERT: G 132 THR cc_start: 0.7835 (OUTLIER) cc_final: 0.7586 (p) REVERT: G 239 THR cc_start: 0.7602 (OUTLIER) cc_final: 0.7152 (m) REVERT: H 33 LYS cc_start: 0.8449 (OUTLIER) cc_final: 0.7890 (ttmt) REVERT: H 61 ARG cc_start: 0.7620 (tpp80) cc_final: 0.7337 (tpp80) REVERT: H 139 ARG cc_start: 0.7915 (tpt-90) cc_final: 0.7445 (ttp80) REVERT: I 139 ARG cc_start: 0.8779 (tpt-90) cc_final: 0.7974 (ttp-110) REVERT: I 236 GLU cc_start: 0.7881 (mt-10) cc_final: 0.7514 (pm20) REVERT: I 249 GLU cc_start: 0.7822 (tt0) cc_final: 0.7467 (pm20) outliers start: 71 outliers final: 21 residues processed: 333 average time/residue: 1.3162 time to fit residues: 497.5232 Evaluate side-chains 282 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 248 time to evaluate : 2.144 ------------------------------------------------------------------------------- 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: 0.0470 chunk 145 optimal weight: 5.9990 chunk 178 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 19 optimal weight: 3.9990 chunk 74 optimal weight: 8.9990 chunk 99 optimal weight: 2.9990 chunk 208 optimal weight: 6.9990 chunk 14 optimal weight: 6.9990 chunk 195 optimal weight: 2.9990 overall best weight: 2.6086 ------------------------------------------------------------------------------- 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 = 0.3872 r_free = 0.3872 target = 0.168549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.140424 restraints weight = 23290.610| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 1.59 r_work: 0.3449 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3343 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.2936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 21220 Z= 0.198 Angle : 0.625 6.770 29080 Z= 0.326 Chirality : 0.051 0.193 3450 Planarity : 0.006 0.051 3740 Dihedral : 5.089 20.833 2890 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 3.28 % Allowed : 19.69 % Favored : 77.03 % 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: -0.04 (0.16), residues: 2610 helix: 1.04 (0.19), residues: 670 sheet: 0.93 (0.18), residues: 730 loop : -1.27 (0.18), residues: 1210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 182 HIS 0.006 0.001 HIS B 111 PHE 0.020 0.002 PHE F 188 TYR 0.015 0.002 TYR C 150 ARG 0.005 0.000 ARG B 251 Details of bonding type rmsd hydrogen bonds : bond 0.05975 ( 910) hydrogen bonds : angle 5.11739 ( 2790) covalent geometry : bond 0.00486 (21220) covalent geometry : angle 0.62512 (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 309 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 234 time to evaluate : 2.419 Fit side-chains REVERT: A 139 ARG cc_start: 0.8832 (tpt170) cc_final: 0.7968 (ttp-110) REVERT: A 236 GLU cc_start: 0.7856 (mt-10) cc_final: 0.7443 (pm20) REVERT: A 249 GLU cc_start: 0.7847 (tt0) cc_final: 0.7477 (pm20) REVERT: B 33 LYS cc_start: 0.6982 (OUTLIER) cc_final: 0.6326 (mttm) REVERT: B 134 GLU cc_start: 0.8535 (OUTLIER) cc_final: 0.7951 (mp0) REVERT: C 97 ARG cc_start: 0.7038 (tpt-90) cc_final: 0.6088 (ptm160) REVERT: C 134 GLU cc_start: 0.7358 (OUTLIER) cc_final: 0.7156 (mp0) REVERT: C 310 ASP cc_start: 0.6941 (p0) cc_final: 0.6419 (t0) REVERT: D 61 ARG cc_start: 0.7283 (ttm110) cc_final: 0.6694 (tmm-80) REVERT: D 93 GLU cc_start: 0.6688 (pt0) cc_final: 0.5884 (pm20) REVERT: D 107 LEU cc_start: 0.7579 (OUTLIER) cc_final: 0.6886 (tm) REVERT: D 132 THR cc_start: 0.7817 (OUTLIER) cc_final: 0.7554 (p) REVERT: E 33 LYS cc_start: 0.8479 (OUTLIER) cc_final: 0.7956 (ttmt) REVERT: E 139 ARG cc_start: 0.8103 (tpt-90) cc_final: 0.7555 (ttp80) REVERT: F 61 ARG cc_start: 0.7916 (OUTLIER) cc_final: 0.7263 (ttm-80) REVERT: F 97 ARG cc_start: 0.7047 (tpt-90) cc_final: 0.6185 (ptm160) REVERT: F 134 GLU cc_start: 0.7379 (OUTLIER) cc_final: 0.7175 (mp0) REVERT: F 310 ASP cc_start: 0.6902 (p0) cc_final: 0.6409 (t0) REVERT: G 61 ARG cc_start: 0.7305 (ttm110) cc_final: 0.6718 (tmm-80) REVERT: G 93 GLU cc_start: 0.6711 (pt0) cc_final: 0.5911 (pm20) REVERT: G 107 LEU cc_start: 0.7571 (OUTLIER) cc_final: 0.6925 (tm) REVERT: G 132 THR cc_start: 0.7810 (OUTLIER) cc_final: 0.7555 (p) REVERT: H 33 LYS cc_start: 0.8496 (OUTLIER) cc_final: 0.7961 (ttmt) REVERT: H 59 ILE cc_start: 0.8333 (OUTLIER) cc_final: 0.8110 (mt) REVERT: H 61 ARG cc_start: 0.7694 (tpp80) cc_final: 0.7493 (tpp80) REVERT: H 139 ARG cc_start: 0.8104 (tpt-90) cc_final: 0.7561 (ttp80) REVERT: I 139 ARG cc_start: 0.8877 (tpt-90) cc_final: 0.8002 (ttp-110) REVERT: I 236 GLU cc_start: 0.7830 (mt-10) cc_final: 0.7438 (pm20) REVERT: I 249 GLU cc_start: 0.7873 (tt0) cc_final: 0.7475 (pm20) REVERT: J 33 LYS cc_start: 0.6953 (OUTLIER) cc_final: 0.6358 (mttm) REVERT: J 134 GLU cc_start: 0.8523 (OUTLIER) cc_final: 0.7935 (mp0) outliers start: 75 outliers final: 35 residues processed: 286 average time/residue: 1.6156 time to fit residues: 526.1389 Evaluate side-chains 288 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 239 time to evaluate : 2.722 ------------------------------------------------------------------------------- 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 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 177 LEU Chi-restraints excluded: chain B residue 284 SER 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 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 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 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 110 VAL Chi-restraints excluded: chain G residue 114 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 59 ILE Chi-restraints excluded: chain H residue 105 SER 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 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 177 LEU 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: 0.8980 chunk 172 optimal weight: 0.9980 chunk 241 optimal weight: 0.9980 chunk 202 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 chunk 103 optimal weight: 8.9990 chunk 74 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 148 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 chunk 111 optimal weight: 0.8980 overall best weight: 1.3582 ------------------------------------------------------------------------------- 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 = 0.3935 r_free = 0.3935 target = 0.173988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.146212 restraints weight = 23163.572| |-----------------------------------------------------------------------------| r_work (start): 0.3643 rms_B_bonded: 1.63 r_work: 0.3486 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3381 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.3062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 21220 Z= 0.133 Angle : 0.552 6.603 29080 Z= 0.289 Chirality : 0.047 0.184 3450 Planarity : 0.006 0.051 3740 Dihedral : 4.795 19.736 2890 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 3.23 % Allowed : 20.00 % Favored : 76.77 % 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: 0.12 (0.16), residues: 2610 helix: 1.32 (0.19), residues: 670 sheet: 0.90 (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 J 111 PHE 0.016 0.002 PHE F 188 TYR 0.010 0.001 TYR G 150 ARG 0.007 0.000 ARG C 273 Details of bonding type rmsd hydrogen bonds : bond 0.04785 ( 910) hydrogen bonds : angle 4.84056 ( 2790) covalent geometry : bond 0.00316 (21220) covalent geometry : angle 0.55230 (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 328 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 254 time to evaluate : 2.019 Fit side-chains REVERT: A 236 GLU cc_start: 0.8157 (mt-10) cc_final: 0.7709 (pm20) REVERT: A 249 GLU cc_start: 0.7931 (tt0) cc_final: 0.7498 (pm20) REVERT: B 33 LYS cc_start: 0.7028 (OUTLIER) cc_final: 0.6377 (mttm) REVERT: B 134 GLU cc_start: 0.8618 (OUTLIER) cc_final: 0.8144 (mp0) REVERT: C 61 ARG cc_start: 0.7969 (OUTLIER) cc_final: 0.7381 (ttm-80) REVERT: C 97 ARG cc_start: 0.7129 (tpt-90) cc_final: 0.6352 (ptm160) REVERT: C 273 ARG cc_start: 0.6893 (ttp-110) cc_final: 0.6059 (ttp-110) REVERT: C 310 ASP cc_start: 0.6975 (p0) cc_final: 0.6531 (t0) REVERT: D 61 ARG cc_start: 0.7338 (ttm110) cc_final: 0.6753 (tmm-80) REVERT: D 107 LEU cc_start: 0.7559 (OUTLIER) cc_final: 0.6851 (tm) REVERT: D 130 ARG cc_start: 0.8040 (ttp80) cc_final: 0.7835 (tmm160) REVERT: D 132 THR cc_start: 0.7979 (OUTLIER) cc_final: 0.7760 (p) REVERT: D 239 THR cc_start: 0.7788 (OUTLIER) cc_final: 0.7231 (m) REVERT: D 290 TYR cc_start: 0.6896 (m-80) cc_final: 0.5775 (m-80) REVERT: E 33 LYS cc_start: 0.8576 (OUTLIER) cc_final: 0.8001 (ttmt) REVERT: E 139 ARG cc_start: 0.8118 (tpt-90) cc_final: 0.7655 (ttp80) REVERT: F 61 ARG cc_start: 0.8026 (OUTLIER) cc_final: 0.7383 (ttm-80) REVERT: F 97 ARG cc_start: 0.7108 (tpt-90) cc_final: 0.6317 (ptm160) REVERT: F 180 LYS cc_start: 0.8312 (OUTLIER) cc_final: 0.8108 (mtpp) REVERT: F 273 ARG cc_start: 0.6934 (ttp-110) cc_final: 0.6103 (ttp-110) REVERT: F 310 ASP cc_start: 0.6954 (p0) cc_final: 0.6525 (t0) REVERT: G 61 ARG cc_start: 0.7345 (ttm110) cc_final: 0.6760 (tmm-80) REVERT: G 107 LEU cc_start: 0.7647 (OUTLIER) cc_final: 0.7026 (tm) REVERT: G 132 THR cc_start: 0.7969 (OUTLIER) cc_final: 0.7744 (p) REVERT: G 239 THR cc_start: 0.7790 (OUTLIER) cc_final: 0.7239 (m) REVERT: G 290 TYR cc_start: 0.6862 (m-80) cc_final: 0.5625 (m-80) REVERT: H 33 LYS cc_start: 0.8575 (OUTLIER) cc_final: 0.8070 (ttmt) REVERT: H 61 ARG cc_start: 0.7780 (tpp80) cc_final: 0.7525 (tpp80) REVERT: H 139 ARG cc_start: 0.8127 (tpt-90) cc_final: 0.7668 (ttp80) REVERT: I 139 ARG cc_start: 0.8926 (tpt-90) cc_final: 0.8127 (ttp-110) REVERT: I 236 GLU cc_start: 0.8096 (mt-10) cc_final: 0.7691 (pm20) REVERT: I 249 GLU cc_start: 0.7935 (tt0) cc_final: 0.7489 (pm20) REVERT: J 33 LYS cc_start: 0.7071 (OUTLIER) cc_final: 0.6443 (mttm) REVERT: J 134 GLU cc_start: 0.8598 (OUTLIER) cc_final: 0.8112 (mp0) outliers start: 74 outliers final: 34 residues processed: 303 average time/residue: 2.0391 time to fit residues: 698.4538 Evaluate side-chains 288 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 239 time to evaluate : 2.636 ------------------------------------------------------------------------------- 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 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 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 177 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 16 optimal weight: 0.9980 chunk 99 optimal weight: 0.9990 chunk 178 optimal weight: 8.9990 chunk 34 optimal weight: 2.9990 chunk 249 optimal weight: 3.9990 chunk 143 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 152 optimal weight: 3.9990 chunk 189 optimal weight: 5.9990 chunk 109 optimal weight: 8.9990 chunk 188 optimal weight: 10.0000 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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 = 0.3915 r_free = 0.3915 target = 0.172018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.144653 restraints weight = 23151.500| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 1.52 r_work: 0.3498 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3397 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.3100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 21220 Z= 0.166 Angle : 0.594 6.562 29080 Z= 0.309 Chirality : 0.049 0.182 3450 Planarity : 0.006 0.051 3740 Dihedral : 4.919 20.229 2890 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 3.14 % Allowed : 20.00 % Favored : 76.86 % 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: 0.06 (0.16), residues: 2610 helix: 1.22 (0.19), residues: 670 sheet: 0.87 (0.18), residues: 730 loop : -1.19 (0.18), residues: 1210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 182 HIS 0.005 0.001 HIS B 111 PHE 0.019 0.002 PHE C 188 TYR 0.013 0.002 TYR D 150 ARG 0.009 0.000 ARG J 251 Details of bonding type rmsd hydrogen bonds : bond 0.05453 ( 910) hydrogen bonds : angle 4.99614 ( 2790) covalent geometry : bond 0.00405 (21220) covalent geometry : angle 0.59353 (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 323 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 251 time to evaluate : 2.280 Fit side-chains REVERT: A 139 ARG cc_start: 0.8849 (tpt170) cc_final: 0.8039 (ttp-110) REVERT: A 236 GLU cc_start: 0.8054 (mt-10) cc_final: 0.7634 (pm20) REVERT: A 249 GLU cc_start: 0.7873 (tt0) cc_final: 0.7520 (pm20) REVERT: B 33 LYS cc_start: 0.7044 (OUTLIER) cc_final: 0.6423 (mttm) REVERT: B 134 GLU cc_start: 0.8526 (OUTLIER) cc_final: 0.7995 (mp0) REVERT: B 316 GLN cc_start: 0.7527 (OUTLIER) cc_final: 0.6557 (tm-30) REVERT: C 61 ARG cc_start: 0.7969 (OUTLIER) cc_final: 0.7353 (ttm-80) REVERT: C 97 ARG cc_start: 0.7121 (tpt-90) cc_final: 0.6357 (ptm160) REVERT: C 273 ARG cc_start: 0.6922 (ttp-110) cc_final: 0.5954 (mtm180) REVERT: C 310 ASP cc_start: 0.6825 (p0) cc_final: 0.6495 (t0) REVERT: D 61 ARG cc_start: 0.7267 (ttm110) cc_final: 0.6684 (tmm-80) REVERT: D 107 LEU cc_start: 0.7656 (OUTLIER) cc_final: 0.7011 (tm) REVERT: D 132 THR cc_start: 0.7953 (OUTLIER) cc_final: 0.7735 (p) REVERT: D 239 THR cc_start: 0.7831 (OUTLIER) cc_final: 0.7226 (m) REVERT: D 290 TYR cc_start: 0.6895 (m-80) cc_final: 0.6506 (m-80) REVERT: E 33 LYS cc_start: 0.8541 (OUTLIER) cc_final: 0.8023 (ttmt) REVERT: E 139 ARG cc_start: 0.8131 (tpt-90) cc_final: 0.7677 (ttp80) REVERT: F 61 ARG cc_start: 0.7975 (OUTLIER) cc_final: 0.7382 (ttm-80) REVERT: F 97 ARG cc_start: 0.7128 (tpt-90) cc_final: 0.6356 (ptm160) REVERT: F 273 ARG cc_start: 0.6965 (ttp-110) cc_final: 0.5998 (mtm180) REVERT: F 310 ASP cc_start: 0.6807 (p0) cc_final: 0.6505 (t0) REVERT: G 61 ARG cc_start: 0.7286 (ttm110) cc_final: 0.6706 (tmm-80) REVERT: G 107 LEU cc_start: 0.7695 (OUTLIER) cc_final: 0.7066 (tm) REVERT: G 132 THR cc_start: 0.7951 (OUTLIER) cc_final: 0.7725 (p) REVERT: G 239 THR cc_start: 0.7828 (OUTLIER) cc_final: 0.7228 (m) REVERT: G 290 TYR cc_start: 0.6842 (m-80) cc_final: 0.5605 (m-80) REVERT: H 33 LYS cc_start: 0.8561 (OUTLIER) cc_final: 0.8067 (ttmt) REVERT: H 61 ARG cc_start: 0.7765 (tpp80) cc_final: 0.7438 (tpp80) REVERT: H 139 ARG cc_start: 0.8138 (tpt-90) cc_final: 0.7685 (ttp80) REVERT: I 139 ARG cc_start: 0.8862 (tpt-90) cc_final: 0.8082 (ttp-110) REVERT: I 236 GLU cc_start: 0.8025 (mt-10) cc_final: 0.7648 (pm20) REVERT: I 249 GLU cc_start: 0.7867 (tt0) cc_final: 0.7510 (pm20) REVERT: J 33 LYS cc_start: 0.7080 (OUTLIER) cc_final: 0.6473 (mttm) REVERT: J 134 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.7994 (mp0) REVERT: J 316 GLN cc_start: 0.7517 (OUTLIER) cc_final: 0.6548 (tm-30) outliers start: 72 outliers final: 37 residues processed: 299 average time/residue: 2.0691 time to fit residues: 703.1468 Evaluate side-chains 292 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 239 time to evaluate : 4.622 ------------------------------------------------------------------------------- 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 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 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 214 MET 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 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 123 ASP 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 132 THR Chi-restraints excluded: chain G residue 214 MET 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 0 optimal weight: 7.9990 chunk 2 optimal weight: 2.9990 chunk 72 optimal weight: 0.7980 chunk 89 optimal weight: 0.8980 chunk 212 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 237 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 chunk 3 optimal weight: 2.9990 chunk 220 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3958 r_free = 0.3958 target = 0.176066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.148851 restraints weight = 23299.462| |-----------------------------------------------------------------------------| r_work (start): 0.3674 rms_B_bonded: 1.59 r_work: 0.3527 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3424 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.3230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 21220 Z= 0.112 Angle : 0.522 6.661 29080 Z= 0.274 Chirality : 0.046 0.167 3450 Planarity : 0.006 0.050 3740 Dihedral : 4.597 18.938 2890 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 2.14 % Allowed : 21.53 % Favored : 76.33 % 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: 0.36 (0.16), residues: 2610 helix: 1.59 (0.19), residues: 670 sheet: 1.07 (0.18), residues: 710 loop : -1.07 (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 D 111 PHE 0.013 0.001 PHE C 188 TYR 0.017 0.001 TYR E 215 ARG 0.007 0.000 ARG B 251 Details of bonding type rmsd hydrogen bonds : bond 0.04191 ( 910) hydrogen bonds : angle 4.67066 ( 2790) covalent geometry : bond 0.00264 (21220) covalent geometry : angle 0.52228 (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 307 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 258 time to evaluate : 5.389 Fit side-chains revert: symmetry clash REVERT: A 236 GLU cc_start: 0.8163 (mt-10) cc_final: 0.7730 (pm20) REVERT: A 249 GLU cc_start: 0.7821 (tt0) cc_final: 0.7435 (pm20) REVERT: B 134 GLU cc_start: 0.8607 (OUTLIER) cc_final: 0.8130 (mp0) REVERT: C 61 ARG cc_start: 0.7947 (mtp85) cc_final: 0.7352 (ttm-80) REVERT: C 97 ARG cc_start: 0.7077 (tpt-90) cc_final: 0.6279 (ptm160) REVERT: C 273 ARG cc_start: 0.6854 (ttp-110) cc_final: 0.6003 (mtm180) REVERT: C 310 ASP cc_start: 0.6792 (p0) cc_final: 0.6509 (t0) REVERT: D 61 ARG cc_start: 0.7323 (ttm110) cc_final: 0.6742 (tmm-80) REVERT: D 107 LEU cc_start: 0.7579 (OUTLIER) cc_final: 0.6940 (tm) REVERT: D 130 ARG cc_start: 0.8023 (ttp80) cc_final: 0.7748 (tmm160) REVERT: D 290 TYR cc_start: 0.6879 (m-80) cc_final: 0.6049 (m-80) REVERT: E 33 LYS cc_start: 0.8522 (OUTLIER) cc_final: 0.7910 (ttmt) REVERT: E 139 ARG cc_start: 0.8069 (tpt-90) cc_final: 0.7624 (ttp80) REVERT: F 61 ARG cc_start: 0.7964 (OUTLIER) cc_final: 0.7419 (ttm-80) REVERT: F 97 ARG cc_start: 0.7068 (tpt-90) cc_final: 0.6295 (ptm160) REVERT: F 273 ARG cc_start: 0.6844 (ttp-110) cc_final: 0.6014 (mtm180) REVERT: F 310 ASP cc_start: 0.6791 (p0) cc_final: 0.6539 (t0) REVERT: G 61 ARG cc_start: 0.7324 (ttm110) cc_final: 0.6738 (tmm-80) REVERT: G 107 LEU cc_start: 0.7623 (OUTLIER) cc_final: 0.7009 (tm) REVERT: G 290 TYR cc_start: 0.6794 (m-80) cc_final: 0.5575 (m-80) REVERT: H 33 LYS cc_start: 0.8539 (OUTLIER) cc_final: 0.8019 (ttmt) REVERT: H 61 ARG cc_start: 0.7844 (tpp80) cc_final: 0.7589 (tpp80) REVERT: H 139 ARG cc_start: 0.8060 (tpt-90) cc_final: 0.7594 (ttp80) REVERT: I 236 GLU cc_start: 0.8082 (mt-10) cc_final: 0.7705 (pm20) REVERT: I 249 GLU cc_start: 0.7811 (tt0) cc_final: 0.7430 (pm20) REVERT: J 33 LYS cc_start: 0.7007 (OUTLIER) cc_final: 0.6354 (mttm) REVERT: J 61 ARG cc_start: 0.8233 (ttm-80) cc_final: 0.7869 (tpp80) REVERT: J 134 GLU cc_start: 0.8594 (OUTLIER) cc_final: 0.8120 (mp0) outliers start: 49 outliers final: 27 residues processed: 294 average time/residue: 2.2771 time to fit residues: 763.4312 Evaluate side-chains 270 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 235 time to evaluate : 3.721 ------------------------------------------------------------------------------- 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 134 GLU Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 103 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 E residue 33 LYS 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 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 117 LEU Chi-restraints excluded: chain H residue 273 ARG Chi-restraints excluded: chain I residue 177 LEU 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 148 optimal weight: 0.8980 chunk 180 optimal weight: 4.9990 chunk 142 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 152 optimal weight: 0.0670 chunk 205 optimal weight: 8.9990 chunk 117 optimal weight: 2.9990 chunk 162 optimal weight: 0.9980 chunk 188 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 chunk 123 optimal weight: 2.9990 overall best weight: 0.7718 ------------------------------------------------------------------------------- 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 = 0.3965 r_free = 0.3965 target = 0.176718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.149302 restraints weight = 23189.314| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 1.61 r_work: 0.3523 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3419 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.3307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21220 Z= 0.110 Angle : 0.522 6.422 29080 Z= 0.273 Chirality : 0.046 0.191 3450 Planarity : 0.006 0.047 3740 Dihedral : 4.489 18.345 2890 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 1.97 % Allowed : 21.75 % 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: 0.47 (0.16), residues: 2610 helix: 1.72 (0.19), residues: 670 sheet: 1.12 (0.18), residues: 710 loop : -1.01 (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 D 111 PHE 0.013 0.001 PHE C 188 TYR 0.018 0.001 TYR E 215 ARG 0.006 0.000 ARG B 251 Details of bonding type rmsd hydrogen bonds : bond 0.04141 ( 910) hydrogen bonds : angle 4.61098 ( 2790) covalent geometry : bond 0.00257 (21220) covalent geometry : angle 0.52167 (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 300 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 255 time to evaluate : 2.479 Fit side-chains revert: symmetry clash REVERT: A 236 GLU cc_start: 0.8250 (mt-10) cc_final: 0.7749 (pm20) REVERT: A 249 GLU cc_start: 0.7804 (tt0) cc_final: 0.7320 (pm20) REVERT: B 33 LYS cc_start: 0.6899 (OUTLIER) cc_final: 0.6583 (mttp) REVERT: B 134 GLU cc_start: 0.8617 (OUTLIER) cc_final: 0.8400 (tp30) REVERT: C 61 ARG cc_start: 0.8001 (mtp85) cc_final: 0.7397 (ttm-80) REVERT: C 97 ARG cc_start: 0.7057 (tpt-90) cc_final: 0.6270 (ptm160) REVERT: C 128 GLN cc_start: 0.7618 (mt0) cc_final: 0.7086 (mm-40) REVERT: C 273 ARG cc_start: 0.6911 (ttp-110) cc_final: 0.6105 (mtm180) REVERT: C 310 ASP cc_start: 0.6825 (p0) cc_final: 0.6566 (t0) REVERT: D 61 ARG cc_start: 0.7417 (ttm110) cc_final: 0.6833 (tmm-80) REVERT: D 107 LEU cc_start: 0.7585 (OUTLIER) cc_final: 0.7021 (tm) REVERT: D 290 TYR cc_start: 0.6927 (m-80) cc_final: 0.6454 (m-80) REVERT: E 33 LYS cc_start: 0.8498 (OUTLIER) cc_final: 0.7964 (ttmt) REVERT: E 139 ARG cc_start: 0.8086 (tpt-90) cc_final: 0.7613 (ttp80) REVERT: F 61 ARG cc_start: 0.7997 (OUTLIER) cc_final: 0.7456 (ttm-80) REVERT: F 97 ARG cc_start: 0.7092 (tpt-90) cc_final: 0.6256 (ptm160) REVERT: F 128 GLN cc_start: 0.7606 (mt0) cc_final: 0.7071 (mm-40) REVERT: F 273 ARG cc_start: 0.6905 (ttp-110) cc_final: 0.6113 (mtm180) REVERT: F 310 ASP cc_start: 0.6753 (p0) cc_final: 0.6520 (t0) REVERT: G 61 ARG cc_start: 0.7411 (ttm110) cc_final: 0.6824 (tmm-80) REVERT: G 107 LEU cc_start: 0.7594 (OUTLIER) cc_final: 0.6999 (tm) REVERT: G 290 TYR cc_start: 0.6908 (m-80) cc_final: 0.5819 (m-80) REVERT: H 33 LYS cc_start: 0.8538 (OUTLIER) cc_final: 0.7926 (ttmt) REVERT: H 61 ARG cc_start: 0.7879 (tpp80) cc_final: 0.7600 (tpp80) REVERT: H 139 ARG cc_start: 0.8103 (tpt-90) cc_final: 0.7627 (ttp80) REVERT: I 236 GLU cc_start: 0.8194 (mt-10) cc_final: 0.7739 (pm20) REVERT: I 249 GLU cc_start: 0.7752 (tt0) cc_final: 0.7329 (pm20) REVERT: J 33 LYS cc_start: 0.7020 (OUTLIER) cc_final: 0.6699 (mttp) REVERT: J 61 ARG cc_start: 0.8289 (ttm-80) cc_final: 0.7926 (tpp80) REVERT: J 134 GLU cc_start: 0.8597 (OUTLIER) cc_final: 0.8377 (tp30) outliers start: 45 outliers final: 28 residues processed: 286 average time/residue: 1.5188 time to fit residues: 489.5544 Evaluate side-chains 276 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 239 time to evaluate : 2.305 ------------------------------------------------------------------------------- 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 E residue 33 LYS 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 G residue 100 THR Chi-restraints excluded: chain G residue 104 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 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 117 LEU Chi-restraints excluded: chain H residue 273 ARG Chi-restraints excluded: chain I residue 177 LEU 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 175 optimal weight: 4.9990 chunk 75 optimal weight: 9.9990 chunk 93 optimal weight: 3.9990 chunk 116 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 55 optimal weight: 0.5980 chunk 202 optimal weight: 0.9980 chunk 232 optimal weight: 4.9990 chunk 238 optimal weight: 2.9990 chunk 47 optimal weight: 0.0970 chunk 115 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 = 0.3963 r_free = 0.3963 target = 0.176451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.148934 restraints weight = 23122.208| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 1.63 r_work: 0.3535 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3434 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.3350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21220 Z= 0.116 Angle : 0.534 6.349 29080 Z= 0.279 Chirality : 0.046 0.177 3450 Planarity : 0.006 0.047 3740 Dihedral : 4.506 18.298 2890 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 1.70 % Allowed : 22.23 % Favored : 76.07 % 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: 0.50 (0.16), residues: 2610 helix: 1.73 (0.19), residues: 670 sheet: 1.14 (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 D 182 HIS 0.004 0.001 HIS D 111 PHE 0.014 0.001 PHE F 188 TYR 0.018 0.001 TYR H 215 ARG 0.006 0.000 ARG B 251 Details of bonding type rmsd hydrogen bonds : bond 0.04259 ( 910) hydrogen bonds : angle 4.63961 ( 2790) covalent geometry : bond 0.00273 (21220) covalent geometry : angle 0.53398 (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 286 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 247 time to evaluate : 2.450 Fit side-chains revert: symmetry clash REVERT: A 236 GLU cc_start: 0.8161 (mt-10) cc_final: 0.7658 (pm20) REVERT: A 249 GLU cc_start: 0.7725 (tt0) cc_final: 0.7253 (pm20) REVERT: B 33 LYS cc_start: 0.6842 (OUTLIER) cc_final: 0.6538 (mttp) REVERT: B 134 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.8360 (tp30) REVERT: C 61 ARG cc_start: 0.7939 (mtp85) cc_final: 0.7310 (ttm-80) REVERT: C 97 ARG cc_start: 0.6979 (tpt-90) cc_final: 0.6139 (ptm160) REVERT: C 128 GLN cc_start: 0.7494 (mt0) cc_final: 0.6943 (mm-40) REVERT: C 273 ARG cc_start: 0.6794 (ttp-110) cc_final: 0.5997 (mtm180) REVERT: C 310 ASP cc_start: 0.6700 (p0) cc_final: 0.6491 (t0) REVERT: D 61 ARG cc_start: 0.7331 (ttm110) cc_final: 0.6716 (tmm-80) REVERT: D 107 LEU cc_start: 0.7509 (OUTLIER) cc_final: 0.6986 (tm) REVERT: D 290 TYR cc_start: 0.6837 (m-80) cc_final: 0.6402 (m-80) REVERT: E 33 LYS cc_start: 0.8475 (OUTLIER) cc_final: 0.7963 (ttmt) REVERT: E 139 ARG cc_start: 0.8031 (tpt-90) cc_final: 0.7540 (ttp80) REVERT: F 61 ARG cc_start: 0.7916 (OUTLIER) cc_final: 0.7355 (ttm-80) REVERT: F 97 ARG cc_start: 0.7036 (tpt-90) cc_final: 0.6156 (ptm160) REVERT: F 128 GLN cc_start: 0.7493 (mt0) cc_final: 0.6940 (mm-40) REVERT: F 273 ARG cc_start: 0.6793 (ttp-110) cc_final: 0.6010 (mtm180) REVERT: G 61 ARG cc_start: 0.7298 (ttm110) cc_final: 0.6680 (tmm-80) REVERT: G 107 LEU cc_start: 0.7527 (OUTLIER) cc_final: 0.6969 (tm) REVERT: G 290 TYR cc_start: 0.6813 (m-80) cc_final: 0.5638 (m-80) REVERT: H 33 LYS cc_start: 0.8488 (OUTLIER) cc_final: 0.7887 (ttmt) REVERT: H 61 ARG cc_start: 0.7759 (tpp80) cc_final: 0.7246 (tpp80) REVERT: H 139 ARG cc_start: 0.8049 (tpt-90) cc_final: 0.7550 (ttp80) REVERT: I 236 GLU cc_start: 0.8086 (mt-10) cc_final: 0.7643 (pm20) REVERT: I 249 GLU cc_start: 0.7678 (tt0) cc_final: 0.7250 (pm20) REVERT: J 33 LYS cc_start: 0.6887 (OUTLIER) cc_final: 0.6582 (mttp) REVERT: J 61 ARG cc_start: 0.8227 (ttm-80) cc_final: 0.7851 (tpp80) outliers start: 39 outliers final: 27 residues processed: 279 average time/residue: 1.8326 time to fit residues: 578.5672 Evaluate side-chains 276 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 241 time to evaluate : 2.258 ------------------------------------------------------------------------------- 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 305 ASP Chi-restraints excluded: chain C residue 110 VAL 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 161 THR Chi-restraints excluded: chain E residue 33 LYS 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 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 117 LEU Chi-restraints excluded: chain H residue 273 ARG Chi-restraints excluded: chain I residue 177 LEU 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 136 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 135 optimal weight: 2.9990 chunk 215 optimal weight: 0.6980 chunk 137 optimal weight: 2.9990 chunk 130 optimal weight: 5.9990 chunk 258 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 89 optimal weight: 0.9990 chunk 181 optimal weight: 10.0000 chunk 107 optimal weight: 4.9990 chunk 153 optimal weight: 0.8980 chunk 87 optimal weight: 3.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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 = 0.3931 r_free = 0.3931 target = 0.173403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.146024 restraints weight = 23207.072| |-----------------------------------------------------------------------------| r_work (start): 0.3643 rms_B_bonded: 1.51 r_work: 0.3515 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3414 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.3277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 21220 Z= 0.152 Angle : 0.584 6.443 29080 Z= 0.305 Chirality : 0.048 0.184 3450 Planarity : 0.006 0.048 3740 Dihedral : 4.745 19.667 2890 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 1.88 % Allowed : 22.18 % 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: 0.36 (0.16), residues: 2610 helix: 1.57 (0.19), residues: 670 sheet: 1.10 (0.18), residues: 710 loop : -1.08 (0.18), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 182 HIS 0.004 0.001 HIS H 111 PHE 0.018 0.002 PHE C 188 TYR 0.017 0.002 TYR H 215 ARG 0.006 0.000 ARG J 251 Details of bonding type rmsd hydrogen bonds : bond 0.05102 ( 910) hydrogen bonds : angle 4.86175 ( 2790) covalent geometry : bond 0.00368 (21220) covalent geometry : angle 0.58428 (29080) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17429.30 seconds wall clock time: 311 minutes 31.49 seconds (18691.49 seconds total)