Starting phenix.real_space_refine on Sat Jun 14 03:59:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gnb_34159/06_2025/8gnb_34159.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gnb_34159/06_2025/8gnb_34159.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gnb_34159/06_2025/8gnb_34159.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gnb_34159/06_2025/8gnb_34159.map" model { file = "/net/cci-nas-00/data/ceres_data/8gnb_34159/06_2025/8gnb_34159.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gnb_34159/06_2025/8gnb_34159.cif" } resolution = 3.9 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= 0.002 sd= 0.038 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 140 5.16 5 C 10410 2.51 5 N 2670 2.21 5 O 2550 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 50 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 15770 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1577 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 11, 'TRANS': 189} Chain breaks: 1 Restraints were copied for chains: C, B, E, D, G, F, I, H, J Time building chain proxies: 5.97, per 1000 atoms: 0.38 Number of scatterers: 15770 At special positions: 0 Unit cell: (148.12, 122.36, 100.28, 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 140 16.00 O 2550 8.00 N 2670 7.00 C 10410 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 186 " distance=2.05 Simple disulfide: pdb=" SG CYS D 61 " - pdb=" SG CYS D 180 " distance=2.04 Simple disulfide: pdb=" SG CYS D 65 " - pdb=" SG CYS D 175 " distance=2.03 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: 3.87 Conformation dependent library (CDL) restraints added in 2.2 seconds 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3740 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 10 sheets defined 72.6% alpha, 3.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.28 Creating SS restraints... Processing helix chain 'D' and resid 11 through 16 Processing helix chain 'D' and resid 19 through 32 Processing helix chain 'D' and resid 33 through 45 removed outlier: 3.875A pdb=" N ILE D 37 " --> pdb=" O ARG D 33 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N VAL D 38 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ARG D 42 " --> pdb=" O VAL D 38 " (cutoff:3.500A) Proline residue: D 43 - end of helix Processing helix chain 'D' and resid 46 through 49 removed outlier: 3.946A pdb=" N GLN D 49 " --> pdb=" O GLN D 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 46 through 49' Processing helix chain 'D' and resid 60 through 70 removed outlier: 4.169A pdb=" N VAL D 64 " --> pdb=" O GLY D 60 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 107 removed outlier: 3.542A pdb=" N PHE D 77 " --> pdb=" O SER D 73 " (cutoff:3.500A) Proline residue: D 88 - end of helix removed outlier: 4.064A pdb=" N LEU D 103 " --> pdb=" O ARG D 99 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ALA D 104 " --> pdb=" O GLY D 100 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ALA D 105 " --> pdb=" O ALA D 101 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LEU D 106 " --> pdb=" O THR D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 166 removed outlier: 3.529A pdb=" N ILE D 144 " --> pdb=" O SER D 140 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE D 145 " --> pdb=" O ALA D 141 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA D 155 " --> pdb=" O THR D 151 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ALA D 156 " --> pdb=" O LEU D 152 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N PHE D 157 " --> pdb=" O LEU D 153 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY D 166 " --> pdb=" O TYR D 162 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 225 removed outlier: 4.060A pdb=" N LYS D 194 " --> pdb=" O ARG D 190 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ARG D 221 " --> pdb=" O VAL D 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 11 through 16 Processing helix chain 'A' and resid 19 through 32 Processing helix chain 'A' and resid 33 through 45 removed outlier: 3.876A pdb=" N ILE A 37 " --> pdb=" O ARG A 33 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N VAL A 38 " --> pdb=" O MET A 34 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ARG A 42 " --> pdb=" O VAL A 38 " (cutoff:3.500A) Proline residue: A 43 - end of helix Processing helix chain 'A' and resid 46 through 49 removed outlier: 3.947A pdb=" N GLN A 49 " --> pdb=" O GLN A 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 46 through 49' Processing helix chain 'A' and resid 60 through 70 removed outlier: 4.169A pdb=" N VAL A 64 " --> pdb=" O GLY A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 107 removed outlier: 3.542A pdb=" N PHE A 77 " --> pdb=" O SER A 73 " (cutoff:3.500A) Proline residue: A 88 - end of helix removed outlier: 4.063A pdb=" N LEU A 103 " --> pdb=" O ARG A 99 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ALA A 104 " --> pdb=" O GLY A 100 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ALA A 105 " --> pdb=" O ALA A 101 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LEU A 106 " --> pdb=" O THR A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 166 removed outlier: 3.530A pdb=" N ILE A 144 " --> pdb=" O SER A 140 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE A 145 " --> pdb=" O ALA A 141 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA A 155 " --> pdb=" O THR A 151 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ALA A 156 " --> pdb=" O LEU A 152 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N PHE A 157 " --> pdb=" O LEU A 153 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY A 166 " --> pdb=" O TYR A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 225 removed outlier: 4.060A pdb=" N LYS A 194 " --> pdb=" O ARG A 190 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ARG A 221 " --> pdb=" O VAL A 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 16 Processing helix chain 'B' and resid 19 through 32 Processing helix chain 'B' and resid 33 through 45 removed outlier: 3.875A pdb=" N ILE B 37 " --> pdb=" O ARG B 33 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N VAL B 38 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ARG B 42 " --> pdb=" O VAL B 38 " (cutoff:3.500A) Proline residue: B 43 - end of helix Processing helix chain 'B' and resid 46 through 49 removed outlier: 3.947A pdb=" N GLN B 49 " --> pdb=" O GLN B 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 46 through 49' Processing helix chain 'B' and resid 60 through 70 removed outlier: 4.169A pdb=" N VAL B 64 " --> pdb=" O GLY B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 107 removed outlier: 3.541A pdb=" N PHE B 77 " --> pdb=" O SER B 73 " (cutoff:3.500A) Proline residue: B 88 - end of helix removed outlier: 4.064A pdb=" N LEU B 103 " --> pdb=" O ARG B 99 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ALA B 104 " --> pdb=" O GLY B 100 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ALA B 105 " --> pdb=" O ALA B 101 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LEU B 106 " --> pdb=" O THR B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 166 removed outlier: 3.530A pdb=" N ILE B 144 " --> pdb=" O SER B 140 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE B 145 " --> pdb=" O ALA B 141 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA B 155 " --> pdb=" O THR B 151 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ALA B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N PHE B 157 " --> pdb=" O LEU B 153 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY B 166 " --> pdb=" O TYR B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 225 removed outlier: 4.060A pdb=" N LYS B 194 " --> pdb=" O ARG B 190 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ARG B 221 " --> pdb=" O VAL B 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 11 through 16 Processing helix chain 'C' and resid 19 through 32 Processing helix chain 'C' and resid 33 through 45 removed outlier: 3.876A pdb=" N ILE C 37 " --> pdb=" O ARG C 33 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N VAL C 38 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ARG C 42 " --> pdb=" O VAL C 38 " (cutoff:3.500A) Proline residue: C 43 - end of helix Processing helix chain 'C' and resid 46 through 49 removed outlier: 3.947A pdb=" N GLN C 49 " --> pdb=" O GLN C 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 46 through 49' Processing helix chain 'C' and resid 60 through 70 removed outlier: 4.169A pdb=" N VAL C 64 " --> pdb=" O GLY C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 107 removed outlier: 3.542A pdb=" N PHE C 77 " --> pdb=" O SER C 73 " (cutoff:3.500A) Proline residue: C 88 - end of helix removed outlier: 4.063A pdb=" N LEU C 103 " --> pdb=" O ARG C 99 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ALA C 104 " --> pdb=" O GLY C 100 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ALA C 105 " --> pdb=" O ALA C 101 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LEU C 106 " --> pdb=" O THR C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 166 removed outlier: 3.530A pdb=" N ILE C 144 " --> pdb=" O SER C 140 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE C 145 " --> pdb=" O ALA C 141 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA C 155 " --> pdb=" O THR C 151 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ALA C 156 " --> pdb=" O LEU C 152 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N PHE C 157 " --> pdb=" O LEU C 153 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY C 166 " --> pdb=" O TYR C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 225 removed outlier: 4.060A pdb=" N LYS C 194 " --> pdb=" O ARG C 190 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ARG C 221 " --> pdb=" O VAL C 217 " (cutoff:3.500A) Processing helix chain 'E' and resid 11 through 16 Processing helix chain 'E' and resid 19 through 32 Processing helix chain 'E' and resid 33 through 45 removed outlier: 3.875A pdb=" N ILE E 37 " --> pdb=" O ARG E 33 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N VAL E 38 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ARG E 42 " --> pdb=" O VAL E 38 " (cutoff:3.500A) Proline residue: E 43 - end of helix Processing helix chain 'E' and resid 46 through 49 removed outlier: 3.947A pdb=" N GLN E 49 " --> pdb=" O GLN E 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 46 through 49' Processing helix chain 'E' and resid 60 through 70 removed outlier: 4.170A pdb=" N VAL E 64 " --> pdb=" O GLY E 60 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 107 removed outlier: 3.541A pdb=" N PHE E 77 " --> pdb=" O SER E 73 " (cutoff:3.500A) Proline residue: E 88 - end of helix removed outlier: 4.064A pdb=" N LEU E 103 " --> pdb=" O ARG E 99 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ALA E 104 " --> pdb=" O GLY E 100 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ALA E 105 " --> pdb=" O ALA E 101 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LEU E 106 " --> pdb=" O THR E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 140 through 166 removed outlier: 3.529A pdb=" N ILE E 144 " --> pdb=" O SER E 140 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE E 145 " --> pdb=" O ALA E 141 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA E 155 " --> pdb=" O THR E 151 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ALA E 156 " --> pdb=" O LEU E 152 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N PHE E 157 " --> pdb=" O LEU E 153 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY E 166 " --> pdb=" O TYR E 162 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 225 removed outlier: 4.060A pdb=" N LYS E 194 " --> pdb=" O ARG E 190 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ARG E 221 " --> pdb=" O VAL E 217 " (cutoff:3.500A) Processing helix chain 'F' and resid 11 through 16 Processing helix chain 'F' and resid 19 through 32 Processing helix chain 'F' and resid 33 through 45 removed outlier: 3.875A pdb=" N ILE F 37 " --> pdb=" O ARG F 33 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N VAL F 38 " --> pdb=" O MET F 34 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ARG F 42 " --> pdb=" O VAL F 38 " (cutoff:3.500A) Proline residue: F 43 - end of helix Processing helix chain 'F' and resid 46 through 49 removed outlier: 3.946A pdb=" N GLN F 49 " --> pdb=" O GLN F 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 46 through 49' Processing helix chain 'F' and resid 60 through 70 removed outlier: 4.169A pdb=" N VAL F 64 " --> pdb=" O GLY F 60 " (cutoff:3.500A) Processing helix chain 'F' and resid 73 through 107 removed outlier: 3.542A pdb=" N PHE F 77 " --> pdb=" O SER F 73 " (cutoff:3.500A) Proline residue: F 88 - end of helix removed outlier: 4.064A pdb=" N LEU F 103 " --> pdb=" O ARG F 99 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ALA F 104 " --> pdb=" O GLY F 100 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ALA F 105 " --> pdb=" O ALA F 101 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LEU F 106 " --> pdb=" O THR F 102 " (cutoff:3.500A) Processing helix chain 'F' and resid 140 through 166 removed outlier: 3.529A pdb=" N ILE F 144 " --> pdb=" O SER F 140 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE F 145 " --> pdb=" O ALA F 141 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA F 155 " --> pdb=" O THR F 151 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ALA F 156 " --> pdb=" O LEU F 152 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N PHE F 157 " --> pdb=" O LEU F 153 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY F 166 " --> pdb=" O TYR F 162 " (cutoff:3.500A) Processing helix chain 'F' and resid 190 through 225 removed outlier: 4.060A pdb=" N LYS F 194 " --> pdb=" O ARG F 190 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ARG F 221 " --> pdb=" O VAL F 217 " (cutoff:3.500A) Processing helix chain 'G' and resid 11 through 16 Processing helix chain 'G' and resid 19 through 32 Processing helix chain 'G' and resid 33 through 45 removed outlier: 3.876A pdb=" N ILE G 37 " --> pdb=" O ARG G 33 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N VAL G 38 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ARG G 42 " --> pdb=" O VAL G 38 " (cutoff:3.500A) Proline residue: G 43 - end of helix Processing helix chain 'G' and resid 46 through 49 removed outlier: 3.947A pdb=" N GLN G 49 " --> pdb=" O GLN G 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 46 through 49' Processing helix chain 'G' and resid 60 through 70 removed outlier: 4.169A pdb=" N VAL G 64 " --> pdb=" O GLY G 60 " (cutoff:3.500A) Processing helix chain 'G' and resid 73 through 107 removed outlier: 3.542A pdb=" N PHE G 77 " --> pdb=" O SER G 73 " (cutoff:3.500A) Proline residue: G 88 - end of helix removed outlier: 4.063A pdb=" N LEU G 103 " --> pdb=" O ARG G 99 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ALA G 104 " --> pdb=" O GLY G 100 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ALA G 105 " --> pdb=" O ALA G 101 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LEU G 106 " --> pdb=" O THR G 102 " (cutoff:3.500A) Processing helix chain 'G' and resid 140 through 166 removed outlier: 3.530A pdb=" N ILE G 144 " --> pdb=" O SER G 140 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE G 145 " --> pdb=" O ALA G 141 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA G 155 " --> pdb=" O THR G 151 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ALA G 156 " --> pdb=" O LEU G 152 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N PHE G 157 " --> pdb=" O LEU G 153 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY G 166 " --> pdb=" O TYR G 162 " (cutoff:3.500A) Processing helix chain 'G' and resid 190 through 225 removed outlier: 4.060A pdb=" N LYS G 194 " --> pdb=" O ARG G 190 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ARG G 221 " --> pdb=" O VAL G 217 " (cutoff:3.500A) Processing helix chain 'H' and resid 11 through 16 Processing helix chain 'H' and resid 19 through 32 Processing helix chain 'H' and resid 33 through 45 removed outlier: 3.876A pdb=" N ILE H 37 " --> pdb=" O ARG H 33 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N VAL H 38 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ARG H 42 " --> pdb=" O VAL H 38 " (cutoff:3.500A) Proline residue: H 43 - end of helix Processing helix chain 'H' and resid 46 through 49 removed outlier: 3.947A pdb=" N GLN H 49 " --> pdb=" O GLN H 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 46 through 49' Processing helix chain 'H' and resid 60 through 70 removed outlier: 4.169A pdb=" N VAL H 64 " --> pdb=" O GLY H 60 " (cutoff:3.500A) Processing helix chain 'H' and resid 73 through 107 removed outlier: 3.542A pdb=" N PHE H 77 " --> pdb=" O SER H 73 " (cutoff:3.500A) Proline residue: H 88 - end of helix removed outlier: 4.063A pdb=" N LEU H 103 " --> pdb=" O ARG H 99 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ALA H 104 " --> pdb=" O GLY H 100 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ALA H 105 " --> pdb=" O ALA H 101 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LEU H 106 " --> pdb=" O THR H 102 " (cutoff:3.500A) Processing helix chain 'H' and resid 140 through 166 removed outlier: 3.529A pdb=" N ILE H 144 " --> pdb=" O SER H 140 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE H 145 " --> pdb=" O ALA H 141 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ALA H 155 " --> pdb=" O THR H 151 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ALA H 156 " --> pdb=" O LEU H 152 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N PHE H 157 " --> pdb=" O LEU H 153 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY H 166 " --> pdb=" O TYR H 162 " (cutoff:3.500A) Processing helix chain 'H' and resid 190 through 225 removed outlier: 4.060A pdb=" N LYS H 194 " --> pdb=" O ARG H 190 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ARG H 221 " --> pdb=" O VAL H 217 " (cutoff:3.500A) Processing helix chain 'I' and resid 11 through 16 Processing helix chain 'I' and resid 19 through 32 Processing helix chain 'I' and resid 33 through 45 removed outlier: 3.875A pdb=" N ILE I 37 " --> pdb=" O ARG I 33 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N VAL I 38 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ARG I 42 " --> pdb=" O VAL I 38 " (cutoff:3.500A) Proline residue: I 43 - end of helix Processing helix chain 'I' and resid 46 through 49 removed outlier: 3.948A pdb=" N GLN I 49 " --> pdb=" O GLN I 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 46 through 49' Processing helix chain 'I' and resid 60 through 70 removed outlier: 4.169A pdb=" N VAL I 64 " --> pdb=" O GLY I 60 " (cutoff:3.500A) Processing helix chain 'I' and resid 73 through 107 removed outlier: 3.542A pdb=" N PHE I 77 " --> pdb=" O SER I 73 " (cutoff:3.500A) Proline residue: I 88 - end of helix removed outlier: 4.063A pdb=" N LEU I 103 " --> pdb=" O ARG I 99 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ALA I 104 " --> pdb=" O GLY I 100 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ALA I 105 " --> pdb=" O ALA I 101 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LEU I 106 " --> pdb=" O THR I 102 " (cutoff:3.500A) Processing helix chain 'I' and resid 140 through 166 removed outlier: 3.530A pdb=" N ILE I 144 " --> pdb=" O SER I 140 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE I 145 " --> pdb=" O ALA I 141 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA I 155 " --> pdb=" O THR I 151 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ALA I 156 " --> pdb=" O LEU I 152 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N PHE I 157 " --> pdb=" O LEU I 153 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY I 166 " --> pdb=" O TYR I 162 " (cutoff:3.500A) Processing helix chain 'I' and resid 190 through 225 removed outlier: 4.060A pdb=" N LYS I 194 " --> pdb=" O ARG I 190 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ARG I 221 " --> pdb=" O VAL I 217 " (cutoff:3.500A) Processing helix chain 'J' and resid 11 through 16 Processing helix chain 'J' and resid 19 through 32 Processing helix chain 'J' and resid 33 through 45 removed outlier: 3.875A pdb=" N ILE J 37 " --> pdb=" O ARG J 33 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N VAL J 38 " --> pdb=" O MET J 34 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ARG J 42 " --> pdb=" O VAL J 38 " (cutoff:3.500A) Proline residue: J 43 - end of helix Processing helix chain 'J' and resid 46 through 49 removed outlier: 3.947A pdb=" N GLN J 49 " --> pdb=" O GLN J 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 46 through 49' Processing helix chain 'J' and resid 60 through 70 removed outlier: 4.170A pdb=" N VAL J 64 " --> pdb=" O GLY J 60 " (cutoff:3.500A) Processing helix chain 'J' and resid 73 through 107 removed outlier: 3.541A pdb=" N PHE J 77 " --> pdb=" O SER J 73 " (cutoff:3.500A) Proline residue: J 88 - end of helix removed outlier: 4.064A pdb=" N LEU J 103 " --> pdb=" O ARG J 99 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ALA J 104 " --> pdb=" O GLY J 100 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ALA J 105 " --> pdb=" O ALA J 101 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LEU J 106 " --> pdb=" O THR J 102 " (cutoff:3.500A) Processing helix chain 'J' and resid 140 through 166 removed outlier: 3.529A pdb=" N ILE J 144 " --> pdb=" O SER J 140 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE J 145 " --> pdb=" O ALA J 141 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA J 155 " --> pdb=" O THR J 151 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ALA J 156 " --> pdb=" O LEU J 152 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N PHE J 157 " --> pdb=" O LEU J 153 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY J 166 " --> pdb=" O TYR J 162 " (cutoff:3.500A) Processing helix chain 'J' and resid 190 through 225 removed outlier: 4.060A pdb=" N LYS J 194 " --> pdb=" O ARG J 190 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ARG J 221 " --> pdb=" O VAL J 217 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 172 through 175 Processing sheet with id=AA2, first strand: chain 'A' and resid 172 through 175 Processing sheet with id=AA3, first strand: chain 'B' and resid 172 through 175 Processing sheet with id=AA4, first strand: chain 'C' and resid 172 through 175 Processing sheet with id=AA5, first strand: chain 'E' and resid 172 through 175 Processing sheet with id=AA6, first strand: chain 'F' and resid 172 through 175 Processing sheet with id=AA7, first strand: chain 'G' and resid 172 through 175 Processing sheet with id=AA8, first strand: chain 'H' and resid 172 through 175 Processing sheet with id=AA9, first strand: chain 'I' and resid 172 through 175 Processing sheet with id=AB1, first strand: chain 'J' and resid 172 through 175 950 hydrogen bonds defined for protein. 2820 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.86 Time building geometry restraints manager: 4.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 4880 1.35 - 1.47: 3922 1.47 - 1.59: 7168 1.59 - 1.71: 0 1.71 - 1.83: 190 Bond restraints: 16160 Sorted by residual: bond pdb=" CB GLN I 46 " pdb=" CG GLN I 46 " ideal model delta sigma weight residual 1.520 1.558 -0.038 3.00e-02 1.11e+03 1.62e+00 bond pdb=" CB GLN F 46 " pdb=" CG GLN F 46 " ideal model delta sigma weight residual 1.520 1.558 -0.038 3.00e-02 1.11e+03 1.57e+00 bond pdb=" CB GLN D 46 " pdb=" CG GLN D 46 " ideal model delta sigma weight residual 1.520 1.558 -0.038 3.00e-02 1.11e+03 1.57e+00 bond pdb=" CB GLN H 46 " pdb=" CG GLN H 46 " ideal model delta sigma weight residual 1.520 1.557 -0.037 3.00e-02 1.11e+03 1.56e+00 bond pdb=" CB GLN J 46 " pdb=" CG GLN J 46 " ideal model delta sigma weight residual 1.520 1.557 -0.037 3.00e-02 1.11e+03 1.55e+00 ... (remaining 16155 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.35: 19936 1.35 - 2.71: 1516 2.71 - 4.06: 276 4.06 - 5.41: 190 5.41 - 6.76: 62 Bond angle restraints: 21980 Sorted by residual: angle pdb=" N PRO H 179 " pdb=" CA PRO H 179 " pdb=" C PRO H 179 " ideal model delta sigma weight residual 114.98 108.22 6.76 1.46e+00 4.69e-01 2.15e+01 angle pdb=" N PRO A 179 " pdb=" CA PRO A 179 " pdb=" C PRO A 179 " ideal model delta sigma weight residual 114.98 108.22 6.76 1.46e+00 4.69e-01 2.14e+01 angle pdb=" N PRO G 179 " pdb=" CA PRO G 179 " pdb=" C PRO G 179 " ideal model delta sigma weight residual 114.98 108.22 6.76 1.46e+00 4.69e-01 2.14e+01 angle pdb=" N PRO B 179 " pdb=" CA PRO B 179 " pdb=" C PRO B 179 " ideal model delta sigma weight residual 114.98 108.24 6.74 1.46e+00 4.69e-01 2.13e+01 angle pdb=" N PRO C 179 " pdb=" CA PRO C 179 " pdb=" C PRO C 179 " ideal model delta sigma weight residual 114.98 108.24 6.74 1.46e+00 4.69e-01 2.13e+01 ... (remaining 21975 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.09: 8498 14.09 - 28.19: 719 28.19 - 42.28: 184 42.28 - 56.38: 77 56.38 - 70.47: 31 Dihedral angle restraints: 9509 sinusoidal: 3719 harmonic: 5790 Sorted by residual: dihedral pdb=" CA PRO B 178 " pdb=" C PRO B 178 " pdb=" N PRO B 179 " pdb=" CA PRO B 179 " ideal model delta harmonic sigma weight residual 180.00 135.38 44.62 0 5.00e+00 4.00e-02 7.96e+01 dihedral pdb=" CA PRO I 178 " pdb=" C PRO I 178 " pdb=" N PRO I 179 " pdb=" CA PRO I 179 " ideal model delta harmonic sigma weight residual 180.00 135.41 44.59 0 5.00e+00 4.00e-02 7.95e+01 dihedral pdb=" CA PRO D 178 " pdb=" C PRO D 178 " pdb=" N PRO D 179 " pdb=" CA PRO D 179 " ideal model delta harmonic sigma weight residual 180.00 135.42 44.58 0 5.00e+00 4.00e-02 7.95e+01 ... (remaining 9506 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1546 0.037 - 0.073: 711 0.073 - 0.110: 279 0.110 - 0.146: 54 0.146 - 0.183: 20 Chirality restraints: 2610 Sorted by residual: chirality pdb=" CG LEU H 39 " pdb=" CB LEU H 39 " pdb=" CD1 LEU H 39 " pdb=" CD2 LEU H 39 " both_signs ideal model delta sigma weight residual False -2.59 -2.77 0.18 2.00e-01 2.50e+01 8.35e-01 chirality pdb=" CG LEU G 39 " pdb=" CB LEU G 39 " pdb=" CD1 LEU G 39 " pdb=" CD2 LEU G 39 " both_signs ideal model delta sigma weight residual False -2.59 -2.77 0.18 2.00e-01 2.50e+01 8.10e-01 chirality pdb=" CG LEU A 39 " pdb=" CB LEU A 39 " pdb=" CD1 LEU A 39 " pdb=" CD2 LEU A 39 " both_signs ideal model delta sigma weight residual False -2.59 -2.77 0.18 2.00e-01 2.50e+01 8.10e-01 ... (remaining 2607 not shown) Planarity restraints: 2700 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO H 178 " 0.048 5.00e-02 4.00e+02 7.26e-02 8.43e+00 pdb=" N PRO H 179 " -0.126 5.00e-02 4.00e+02 pdb=" CA PRO H 179 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO H 179 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 178 " -0.048 5.00e-02 4.00e+02 7.25e-02 8.42e+00 pdb=" N PRO C 179 " 0.125 5.00e-02 4.00e+02 pdb=" CA PRO C 179 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO C 179 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO J 178 " -0.048 5.00e-02 4.00e+02 7.25e-02 8.41e+00 pdb=" N PRO J 179 " 0.125 5.00e-02 4.00e+02 pdb=" CA PRO J 179 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO J 179 " -0.040 5.00e-02 4.00e+02 ... (remaining 2697 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 131 2.60 - 3.18: 13590 3.18 - 3.75: 24656 3.75 - 4.33: 30278 4.33 - 4.90: 50137 Nonbonded interactions: 118792 Sorted by model distance: nonbonded pdb=" SG CYS C 65 " pdb=" SG CYS C 175 " model vdw 2.031 3.760 nonbonded pdb=" SG CYS F 65 " pdb=" SG CYS F 175 " model vdw 2.031 3.760 nonbonded pdb=" SG CYS H 65 " pdb=" SG CYS H 175 " model vdw 2.031 3.760 nonbonded pdb=" SG CYS A 65 " pdb=" SG CYS A 175 " model vdw 2.031 3.760 nonbonded pdb=" SG CYS G 65 " pdb=" SG CYS G 175 " model vdw 2.031 3.760 ... (remaining 118787 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.17 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.680 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 33.510 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.120 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: 0.010 Load rotamer database and sin/cos tables:3.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6452 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 : 0.004 0.038 16163 Z= 0.169 Angle : 0.938 6.765 21986 Z= 0.512 Chirality : 0.048 0.183 2610 Planarity : 0.009 0.073 2700 Dihedral : 12.918 70.469 5760 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 9.09 % 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: -0.65 (0.19), residues: 1970 helix: 0.05 (0.15), residues: 1320 sheet: 2.14 (0.59), residues: 100 loop : -1.95 (0.24), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP J 25 HIS 0.002 0.000 HIS C 146 PHE 0.022 0.002 PHE E 52 TYR 0.025 0.003 TYR I 143 ARG 0.005 0.001 ARG D 190 Details of bonding type rmsd hydrogen bonds : bond 0.16428 ( 950) hydrogen bonds : angle 6.63581 ( 2820) SS BOND : bond 0.00957 ( 3) SS BOND : angle 2.41319 ( 6) covalent geometry : bond 0.00354 (16160) covalent geometry : angle 0.93728 (21980) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 815 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 815 time to evaluate : 2.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 224 MET cc_start: 0.5480 (mmp) cc_final: 0.5171 (tpp) REVERT: A 23 LYS cc_start: 0.8740 (mppt) cc_final: 0.8458 (mptt) REVERT: A 35 LEU cc_start: 0.8417 (tp) cc_final: 0.8187 (tt) REVERT: A 153 LEU cc_start: 0.8710 (mt) cc_final: 0.8448 (mt) REVERT: A 192 THR cc_start: 0.8458 (p) cc_final: 0.8223 (p) REVERT: B 7 LEU cc_start: 0.9306 (tp) cc_final: 0.8933 (tp) REVERT: B 47 ASP cc_start: 0.6583 (p0) cc_final: 0.5764 (t0) REVERT: B 184 VAL cc_start: 0.8243 (t) cc_final: 0.7734 (p) REVERT: B 198 MET cc_start: 0.7409 (ptt) cc_final: 0.6019 (ptt) REVERT: C 10 LEU cc_start: 0.8121 (tp) cc_final: 0.7771 (tp) REVERT: C 12 ILE cc_start: 0.8674 (mp) cc_final: 0.8280 (tp) REVERT: C 21 VAL cc_start: 0.8029 (t) cc_final: 0.7525 (p) REVERT: C 66 TYR cc_start: 0.7524 (t80) cc_final: 0.6759 (t80) REVERT: E 11 ILE cc_start: 0.8155 (pt) cc_final: 0.7947 (pt) REVERT: E 15 ASN cc_start: 0.8115 (t0) cc_final: 0.7609 (p0) REVERT: E 34 MET cc_start: 0.7400 (mmp) cc_final: 0.6788 (tmm) REVERT: E 53 VAL cc_start: 0.8005 (m) cc_final: 0.7713 (t) REVERT: E 161 HIS cc_start: 0.8819 (t-90) cc_final: 0.8374 (t70) REVERT: E 194 LYS cc_start: 0.8851 (mttt) cc_final: 0.8615 (ttmt) REVERT: E 201 LEU cc_start: 0.9293 (mm) cc_final: 0.8774 (tt) REVERT: F 20 MET cc_start: 0.7532 (ppp) cc_final: 0.7328 (ppp) REVERT: F 51 ARG cc_start: 0.7217 (mmm160) cc_final: 0.7014 (mmm160) REVERT: F 80 ILE cc_start: 0.8967 (pt) cc_final: 0.8662 (pt) REVERT: F 147 LEU cc_start: 0.8597 (mt) cc_final: 0.8355 (mt) REVERT: F 173 PHE cc_start: 0.6809 (t80) cc_final: 0.6599 (t80) REVERT: F 224 MET cc_start: 0.5914 (mmp) cc_final: 0.5671 (tpp) REVERT: G 11 ILE cc_start: 0.8661 (pt) cc_final: 0.8059 (mp) REVERT: G 23 LYS cc_start: 0.8900 (mppt) cc_final: 0.8465 (mptt) REVERT: G 31 LEU cc_start: 0.9169 (mm) cc_final: 0.8731 (mm) REVERT: G 35 LEU cc_start: 0.8529 (tp) cc_final: 0.8319 (tt) REVERT: G 52 PHE cc_start: 0.4726 (t80) cc_final: 0.4492 (t80) REVERT: G 153 LEU cc_start: 0.8814 (mt) cc_final: 0.8547 (mt) REVERT: H 33 ARG cc_start: 0.7692 (ttt180) cc_final: 0.7366 (ttt90) REVERT: H 34 MET cc_start: 0.8108 (mmp) cc_final: 0.7781 (mmm) REVERT: H 74 HIS cc_start: 0.7871 (p-80) cc_final: 0.7450 (p90) REVERT: H 184 VAL cc_start: 0.8428 (t) cc_final: 0.7857 (p) REVERT: H 201 LEU cc_start: 0.9308 (mm) cc_final: 0.8876 (tt) REVERT: H 202 TRP cc_start: 0.7556 (t-100) cc_final: 0.7087 (t60) REVERT: I 10 LEU cc_start: 0.7974 (tp) cc_final: 0.7701 (tp) REVERT: I 21 VAL cc_start: 0.8280 (t) cc_final: 0.7878 (p) REVERT: I 52 PHE cc_start: 0.3952 (t80) cc_final: 0.3694 (t80) REVERT: I 146 HIS cc_start: 0.8295 (t-90) cc_final: 0.8037 (t-170) REVERT: I 153 LEU cc_start: 0.8610 (mt) cc_final: 0.8141 (mt) REVERT: I 196 LEU cc_start: 0.8325 (tp) cc_final: 0.8115 (tt) REVERT: I 209 PHE cc_start: 0.8725 (t80) cc_final: 0.8429 (t80) REVERT: I 224 MET cc_start: 0.6562 (mmp) cc_final: 0.6118 (tmm) REVERT: J 148 LEU cc_start: 0.9180 (mt) cc_final: 0.8847 (mt) REVERT: J 194 LYS cc_start: 0.8845 (mttt) cc_final: 0.8555 (mtpt) outliers start: 0 outliers final: 0 residues processed: 815 average time/residue: 0.3625 time to fit residues: 423.4587 Evaluate side-chains 524 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 524 time to evaluate : 3.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 168 optimal weight: 0.9990 chunk 151 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 51 optimal weight: 6.9990 chunk 102 optimal weight: 3.9990 chunk 80 optimal weight: 4.9990 chunk 156 optimal weight: 0.6980 chunk 60 optimal weight: 2.9990 chunk 95 optimal weight: 9.9990 chunk 116 optimal weight: 5.9990 chunk 181 optimal weight: 0.3980 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 17 ASN D 49 GLN ** D 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 146 HIS ** A 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 17 ASN ** B 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 GLN B 55 ASN C 161 HIS F 17 ASN F 146 HIS ** G 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 55 ASN ** H 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 161 HIS J 98 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.140893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.111934 restraints weight = 44462.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.116289 restraints weight = 28943.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.119557 restraints weight = 20852.956| |-----------------------------------------------------------------------------| r_work (final): 0.4024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6853 moved from start: 0.4358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 16163 Z= 0.169 Angle : 0.881 13.228 21986 Z= 0.426 Chirality : 0.047 0.228 2610 Planarity : 0.008 0.103 2700 Dihedral : 6.116 53.889 2190 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 15.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 4.97 % Allowed : 19.31 % Favored : 75.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 9.09 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.19), residues: 1970 helix: 0.07 (0.15), residues: 1340 sheet: 1.41 (0.51), residues: 100 loop : -1.79 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP E 202 HIS 0.012 0.001 HIS F 146 PHE 0.028 0.002 PHE I 92 TYR 0.021 0.002 TYR F 66 ARG 0.011 0.001 ARG B 190 Details of bonding type rmsd hydrogen bonds : bond 0.04979 ( 950) hydrogen bonds : angle 4.52061 ( 2820) SS BOND : bond 0.00667 ( 3) SS BOND : angle 1.14010 ( 6) covalent geometry : bond 0.00375 (16160) covalent geometry : angle 0.88135 (21980) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 698 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 612 time to evaluate : 2.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 28 LEU cc_start: 0.9284 (mm) cc_final: 0.9015 (mm) REVERT: D 78 TRP cc_start: 0.6897 (m-10) cc_final: 0.5762 (m-90) REVERT: D 147 LEU cc_start: 0.9210 (mt) cc_final: 0.8940 (mt) REVERT: D 201 LEU cc_start: 0.9606 (OUTLIER) cc_final: 0.9308 (pp) REVERT: D 215 ASP cc_start: 0.8509 (m-30) cc_final: 0.8187 (m-30) REVERT: A 55 ASN cc_start: 0.8836 (p0) cc_final: 0.8344 (t0) REVERT: A 157 PHE cc_start: 0.8660 (m-80) cc_final: 0.8399 (m-80) REVERT: A 185 ASP cc_start: 0.8913 (p0) cc_final: 0.8046 (t0) REVERT: B 157 PHE cc_start: 0.8816 (m-80) cc_final: 0.8502 (m-80) REVERT: B 184 VAL cc_start: 0.8058 (t) cc_final: 0.7831 (p) REVERT: C 7 LEU cc_start: 0.8966 (mm) cc_final: 0.8513 (mp) REVERT: C 12 ILE cc_start: 0.9273 (mp) cc_final: 0.8939 (tp) REVERT: C 49 GLN cc_start: 0.8441 (mm110) cc_final: 0.8111 (mm110) REVERT: C 66 TYR cc_start: 0.7755 (t80) cc_final: 0.7498 (t80) REVERT: C 139 PHE cc_start: 0.6705 (m-10) cc_final: 0.6344 (m-10) REVERT: C 153 LEU cc_start: 0.8280 (mt) cc_final: 0.8045 (mt) REVERT: C 196 LEU cc_start: 0.9175 (mm) cc_final: 0.8826 (tt) REVERT: C 216 LEU cc_start: 0.8499 (tp) cc_final: 0.8067 (pp) REVERT: E 15 ASN cc_start: 0.9257 (t0) cc_final: 0.8262 (p0) REVERT: E 20 MET cc_start: 0.4647 (OUTLIER) cc_final: 0.4081 (mtp) REVERT: E 23 LYS cc_start: 0.8987 (ptpt) cc_final: 0.8328 (ptpp) REVERT: E 28 LEU cc_start: 0.9526 (mm) cc_final: 0.8870 (mm) REVERT: E 67 ASP cc_start: 0.7818 (t0) cc_final: 0.7015 (m-30) REVERT: E 190 ARG cc_start: 0.8168 (ptm160) cc_final: 0.7967 (ptm160) REVERT: E 202 TRP cc_start: 0.8352 (t60) cc_final: 0.7917 (t60) REVERT: F 20 MET cc_start: 0.8495 (ppp) cc_final: 0.8194 (ppp) REVERT: F 39 LEU cc_start: 0.9574 (mt) cc_final: 0.9241 (tp) REVERT: F 51 ARG cc_start: 0.8269 (mmm160) cc_final: 0.8013 (mmm160) REVERT: F 74 HIS cc_start: 0.7239 (OUTLIER) cc_final: 0.6991 (p-80) REVERT: F 147 LEU cc_start: 0.8892 (mt) cc_final: 0.8586 (mt) REVERT: G 20 MET cc_start: 0.6186 (ppp) cc_final: 0.5692 (mmm) REVERT: G 52 PHE cc_start: 0.5842 (t80) cc_final: 0.5337 (t80) REVERT: G 153 LEU cc_start: 0.9417 (mt) cc_final: 0.9094 (mt) REVERT: G 157 PHE cc_start: 0.8767 (m-80) cc_final: 0.8420 (m-80) REVERT: G 161 HIS cc_start: 0.8070 (t-90) cc_final: 0.7069 (m90) REVERT: H 5 ASP cc_start: 0.7790 (p0) cc_final: 0.7441 (p0) REVERT: H 184 VAL cc_start: 0.7848 (t) cc_final: 0.7640 (p) REVERT: H 201 LEU cc_start: 0.9692 (mm) cc_final: 0.9341 (tt) REVERT: H 223 ARG cc_start: 0.9025 (OUTLIER) cc_final: 0.8665 (tmm-80) REVERT: I 52 PHE cc_start: 0.4833 (t80) cc_final: 0.4083 (t80) REVERT: I 77 PHE cc_start: 0.9298 (OUTLIER) cc_final: 0.8984 (t80) REVERT: I 103 LEU cc_start: 0.9651 (mt) cc_final: 0.9392 (pp) REVERT: I 139 PHE cc_start: 0.7067 (m-10) cc_final: 0.6849 (m-10) REVERT: I 153 LEU cc_start: 0.8402 (mt) cc_final: 0.8159 (mt) REVERT: I 198 MET cc_start: 0.9017 (ptt) cc_final: 0.8770 (ptt) REVERT: J 7 LEU cc_start: 0.9005 (tp) cc_final: 0.8619 (pp) REVERT: J 20 MET cc_start: 0.4745 (OUTLIER) cc_final: 0.3787 (mmt) REVERT: J 23 LYS cc_start: 0.9044 (ptmt) cc_final: 0.8610 (ptmm) REVERT: J 51 ARG cc_start: 0.8294 (tpt170) cc_final: 0.7891 (tpt170) REVERT: J 81 GLN cc_start: 0.9036 (pt0) cc_final: 0.8558 (pt0) REVERT: J 162 TYR cc_start: 0.8390 (t80) cc_final: 0.7976 (t80) REVERT: J 202 TRP cc_start: 0.8329 (t60) cc_final: 0.7830 (t60) outliers start: 86 outliers final: 52 residues processed: 643 average time/residue: 0.3319 time to fit residues: 315.9600 Evaluate side-chains 525 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 467 time to evaluate : 2.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 11 ILE Chi-restraints excluded: chain D residue 52 PHE Chi-restraints excluded: chain D residue 187 TYR Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 224 MET Chi-restraints excluded: chain B residue 12 ILE Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 165 PHE Chi-restraints excluded: chain B residue 167 PHE Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 98 HIS Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 20 MET Chi-restraints excluded: chain E residue 74 HIS Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain E residue 149 LEU Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain F residue 74 HIS Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain F residue 146 HIS Chi-restraints excluded: chain G residue 15 ASN Chi-restraints excluded: chain G residue 207 LEU Chi-restraints excluded: chain G residue 224 MET Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 146 HIS Chi-restraints excluded: chain H residue 161 HIS Chi-restraints excluded: chain H residue 165 PHE Chi-restraints excluded: chain H residue 167 PHE Chi-restraints excluded: chain H residue 175 CYS Chi-restraints excluded: chain H residue 199 LEU Chi-restraints excluded: chain H residue 223 ARG Chi-restraints excluded: chain I residue 13 THR Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 77 PHE Chi-restraints excluded: chain I residue 134 LEU Chi-restraints excluded: chain I residue 197 LEU Chi-restraints excluded: chain I residue 199 LEU Chi-restraints excluded: chain I residue 213 LEU Chi-restraints excluded: chain J residue 10 LEU Chi-restraints excluded: chain J residue 20 MET Chi-restraints excluded: chain J residue 53 VAL Chi-restraints excluded: chain J residue 72 VAL Chi-restraints excluded: chain J residue 74 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 129 optimal weight: 4.9990 chunk 149 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 56 optimal weight: 10.0000 chunk 151 optimal weight: 8.9990 chunk 126 optimal weight: 5.9990 chunk 36 optimal weight: 7.9990 chunk 9 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 39 optimal weight: 0.6980 chunk 64 optimal weight: 0.8980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 146 HIS ** B 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 74 HIS C 17 ASN F 146 HIS ** H 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 74 HIS J 146 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.137543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.109591 restraints weight = 45897.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.113803 restraints weight = 30420.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.116896 restraints weight = 22093.267| |-----------------------------------------------------------------------------| r_work (final): 0.3974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6880 moved from start: 0.5220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16163 Z= 0.156 Angle : 0.852 13.702 21986 Z= 0.404 Chirality : 0.046 0.245 2610 Planarity : 0.007 0.099 2700 Dihedral : 5.810 50.744 2190 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 16.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 5.90 % Allowed : 24.10 % Favored : 70.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 9.09 % 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: -0.49 (0.19), residues: 1970 helix: 0.26 (0.15), residues: 1290 sheet: 0.96 (0.50), residues: 100 loop : -1.75 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 202 HIS 0.014 0.001 HIS F 146 PHE 0.047 0.002 PHE C 209 TYR 0.025 0.002 TYR J 143 ARG 0.007 0.001 ARG D 51 Details of bonding type rmsd hydrogen bonds : bond 0.04507 ( 950) hydrogen bonds : angle 4.36890 ( 2820) SS BOND : bond 0.00360 ( 3) SS BOND : angle 1.27726 ( 6) covalent geometry : bond 0.00344 (16160) covalent geometry : angle 0.85176 (21980) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 607 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 505 time to evaluate : 1.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 28 LEU cc_start: 0.9338 (mm) cc_final: 0.9017 (mm) REVERT: D 39 LEU cc_start: 0.9535 (mt) cc_final: 0.9140 (tp) REVERT: D 78 TRP cc_start: 0.6870 (m-10) cc_final: 0.5753 (m-90) REVERT: D 173 PHE cc_start: 0.7024 (t80) cc_final: 0.6667 (t80) REVERT: D 201 LEU cc_start: 0.9614 (OUTLIER) cc_final: 0.9263 (pp) REVERT: A 23 LYS cc_start: 0.8782 (mttp) cc_final: 0.8555 (mptt) REVERT: A 55 ASN cc_start: 0.8793 (p0) cc_final: 0.8379 (t0) REVERT: A 157 PHE cc_start: 0.8734 (m-80) cc_final: 0.8446 (m-80) REVERT: A 185 ASP cc_start: 0.8907 (p0) cc_final: 0.8071 (t0) REVERT: B 33 ARG cc_start: 0.8636 (ttt180) cc_final: 0.8311 (ttt90) REVERT: B 157 PHE cc_start: 0.8866 (m-80) cc_final: 0.8547 (m-80) REVERT: C 12 ILE cc_start: 0.9279 (mp) cc_final: 0.8959 (tp) REVERT: C 77 PHE cc_start: 0.9013 (OUTLIER) cc_final: 0.8773 (m-80) REVERT: C 138 ASP cc_start: 0.7724 (m-30) cc_final: 0.7298 (t0) REVERT: C 216 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8214 (pp) REVERT: E 15 ASN cc_start: 0.9254 (t0) cc_final: 0.8365 (p0) REVERT: E 20 MET cc_start: 0.4617 (OUTLIER) cc_final: 0.3861 (mtp) REVERT: E 23 LYS cc_start: 0.8919 (ptpt) cc_final: 0.8196 (ptpp) REVERT: E 81 GLN cc_start: 0.9130 (pt0) cc_final: 0.8841 (pt0) REVERT: E 98 HIS cc_start: 0.9520 (t70) cc_final: 0.9087 (t-170) REVERT: E 161 HIS cc_start: 0.9234 (t70) cc_final: 0.8979 (t70) REVERT: E 202 TRP cc_start: 0.8357 (t60) cc_final: 0.7895 (t60) REVERT: F 39 LEU cc_start: 0.9589 (mt) cc_final: 0.9274 (tp) REVERT: F 51 ARG cc_start: 0.8333 (mmm160) cc_final: 0.8071 (mmm160) REVERT: F 95 TYR cc_start: 0.6922 (t80) cc_final: 0.6663 (t80) REVERT: F 147 LEU cc_start: 0.8785 (mt) cc_final: 0.8487 (mt) REVERT: G 20 MET cc_start: 0.6279 (ppp) cc_final: 0.6076 (mmm) REVERT: G 23 LYS cc_start: 0.8932 (mppt) cc_final: 0.8684 (mttt) REVERT: G 30 MET cc_start: 0.9149 (tmm) cc_final: 0.8904 (tmm) REVERT: G 52 PHE cc_start: 0.6432 (t80) cc_final: 0.5689 (t80) REVERT: G 95 TYR cc_start: 0.7835 (t80) cc_final: 0.7343 (t80) REVERT: G 153 LEU cc_start: 0.9443 (mt) cc_final: 0.9174 (mt) REVERT: G 157 PHE cc_start: 0.8520 (m-80) cc_final: 0.8187 (m-80) REVERT: G 198 MET cc_start: 0.8362 (ptt) cc_final: 0.7265 (tpt) REVERT: G 226 ARG cc_start: 0.7762 (ptp-170) cc_final: 0.7549 (ptp-170) REVERT: H 33 ARG cc_start: 0.9078 (ttt180) cc_final: 0.8154 (ttt90) REVERT: H 34 MET cc_start: 0.8951 (mmm) cc_final: 0.8635 (mmm) REVERT: H 194 LYS cc_start: 0.9099 (mttp) cc_final: 0.8816 (mttp) REVERT: H 198 MET cc_start: 0.9057 (tmm) cc_final: 0.8560 (ppp) REVERT: H 201 LEU cc_start: 0.9706 (mm) cc_final: 0.9460 (tt) REVERT: H 223 ARG cc_start: 0.8996 (OUTLIER) cc_final: 0.8729 (ptm160) REVERT: I 34 MET cc_start: 0.9087 (mmp) cc_final: 0.8834 (mtp) REVERT: I 52 PHE cc_start: 0.4758 (t80) cc_final: 0.4030 (t80) REVERT: I 103 LEU cc_start: 0.9663 (mt) cc_final: 0.9433 (pp) REVERT: I 146 HIS cc_start: 0.9077 (t-170) cc_final: 0.8858 (t-170) REVERT: I 216 LEU cc_start: 0.8435 (OUTLIER) cc_final: 0.7898 (pp) REVERT: J 20 MET cc_start: 0.4407 (OUTLIER) cc_final: 0.3787 (tpp) REVERT: J 23 LYS cc_start: 0.9010 (ptmt) cc_final: 0.8567 (ptmm) REVERT: J 51 ARG cc_start: 0.8366 (tpt170) cc_final: 0.7846 (tpt170) REVERT: J 77 PHE cc_start: 0.9395 (t80) cc_final: 0.9094 (t80) REVERT: J 157 PHE cc_start: 0.9142 (m-80) cc_final: 0.8888 (t80) REVERT: J 202 TRP cc_start: 0.8319 (t60) cc_final: 0.7843 (t60) outliers start: 102 outliers final: 68 residues processed: 555 average time/residue: 0.2552 time to fit residues: 211.3699 Evaluate side-chains 538 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 463 time to evaluate : 1.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 11 ILE Chi-restraints excluded: chain D residue 54 CYS Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 187 TYR Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 224 MET Chi-restraints excluded: chain B residue 12 ILE Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 146 HIS Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 172 LYS Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 77 PHE Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 98 HIS Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 157 PHE Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 20 MET Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 74 HIS Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain G residue 14 LEU Chi-restraints excluded: chain G residue 63 ASN Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 207 LEU Chi-restraints excluded: chain G residue 224 MET Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 146 HIS Chi-restraints excluded: chain H residue 161 HIS Chi-restraints excluded: chain H residue 172 LYS Chi-restraints excluded: chain H residue 192 THR Chi-restraints excluded: chain H residue 215 ASP Chi-restraints excluded: chain H residue 223 ARG Chi-restraints excluded: chain I residue 39 LEU Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 98 HIS Chi-restraints excluded: chain I residue 134 LEU Chi-restraints excluded: chain I residue 161 HIS Chi-restraints excluded: chain I residue 197 LEU Chi-restraints excluded: chain I residue 199 LEU Chi-restraints excluded: chain I residue 213 LEU Chi-restraints excluded: chain I residue 216 LEU Chi-restraints excluded: chain J residue 10 LEU Chi-restraints excluded: chain J residue 20 MET Chi-restraints excluded: chain J residue 44 VAL Chi-restraints excluded: chain J residue 53 VAL Chi-restraints excluded: chain J residue 72 VAL Chi-restraints excluded: chain J residue 74 HIS Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 87 LEU Chi-restraints excluded: chain J residue 150 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 48 optimal weight: 3.9990 chunk 50 optimal weight: 9.9990 chunk 140 optimal weight: 9.9990 chunk 118 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 129 optimal weight: 0.8980 chunk 119 optimal weight: 7.9990 chunk 185 optimal weight: 0.0060 chunk 43 optimal weight: 3.9990 chunk 113 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 overall best weight: 1.9802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 146 HIS A 49 GLN ** A 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 46 GLN ** G 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.134918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.107487 restraints weight = 45960.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.111639 restraints weight = 29663.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.114708 restraints weight = 21367.883| |-----------------------------------------------------------------------------| r_work (final): 0.3927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7012 moved from start: 0.5875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 16163 Z= 0.182 Angle : 0.838 14.190 21986 Z= 0.404 Chirality : 0.045 0.192 2610 Planarity : 0.007 0.102 2700 Dihedral : 5.756 50.487 2190 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 17.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 7.69 % Allowed : 24.62 % Favored : 67.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 9.09 % 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: -0.40 (0.19), residues: 1970 helix: 0.37 (0.15), residues: 1290 sheet: 0.82 (0.50), residues: 100 loop : -1.78 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 202 HIS 0.008 0.001 HIS D 146 PHE 0.019 0.002 PHE E 77 TYR 0.026 0.002 TYR A 66 ARG 0.006 0.001 ARG E 33 Details of bonding type rmsd hydrogen bonds : bond 0.04321 ( 950) hydrogen bonds : angle 4.34322 ( 2820) SS BOND : bond 0.00365 ( 3) SS BOND : angle 1.34853 ( 6) covalent geometry : bond 0.00388 (16160) covalent geometry : angle 0.83774 (21980) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 607 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 474 time to evaluate : 1.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 28 LEU cc_start: 0.9370 (mm) cc_final: 0.9050 (mm) REVERT: D 39 LEU cc_start: 0.9544 (mt) cc_final: 0.9183 (tp) REVERT: D 46 GLN cc_start: 0.9401 (tm-30) cc_final: 0.8983 (tp40) REVERT: D 78 TRP cc_start: 0.6821 (m-10) cc_final: 0.5709 (m-90) REVERT: D 201 LEU cc_start: 0.9605 (OUTLIER) cc_final: 0.9229 (pp) REVERT: A 33 ARG cc_start: 0.8791 (tpt170) cc_final: 0.8394 (tpp80) REVERT: A 78 TRP cc_start: 0.8631 (m-10) cc_final: 0.8359 (m-10) REVERT: A 157 PHE cc_start: 0.8713 (m-80) cc_final: 0.8339 (m-80) REVERT: A 185 ASP cc_start: 0.8839 (p0) cc_final: 0.8274 (t0) REVERT: A 198 MET cc_start: 0.7583 (ptt) cc_final: 0.6679 (tpt) REVERT: B 33 ARG cc_start: 0.8647 (ttt180) cc_final: 0.8246 (ttt90) REVERT: B 157 PHE cc_start: 0.8918 (m-80) cc_final: 0.8591 (m-80) REVERT: C 12 ILE cc_start: 0.9345 (mp) cc_final: 0.9059 (tp) REVERT: C 77 PHE cc_start: 0.8977 (OUTLIER) cc_final: 0.8735 (m-80) REVERT: C 216 LEU cc_start: 0.8572 (OUTLIER) cc_final: 0.8167 (pp) REVERT: E 20 MET cc_start: 0.4675 (OUTLIER) cc_final: 0.3897 (mtp) REVERT: E 23 LYS cc_start: 0.8915 (ptpt) cc_final: 0.8425 (ptpp) REVERT: E 34 MET cc_start: 0.7837 (mmp) cc_final: 0.6585 (tmm) REVERT: E 39 LEU cc_start: 0.9662 (tp) cc_final: 0.9375 (pp) REVERT: E 81 GLN cc_start: 0.9067 (pt0) cc_final: 0.8588 (pt0) REVERT: E 98 HIS cc_start: 0.9534 (t70) cc_final: 0.9071 (t-170) REVERT: E 202 TRP cc_start: 0.8333 (t60) cc_final: 0.7898 (t60) REVERT: F 39 LEU cc_start: 0.9593 (mt) cc_final: 0.9249 (tp) REVERT: F 147 LEU cc_start: 0.8796 (mt) cc_final: 0.8575 (mt) REVERT: G 20 MET cc_start: 0.6278 (ppp) cc_final: 0.5771 (mmm) REVERT: G 52 PHE cc_start: 0.6679 (t80) cc_final: 0.5850 (t80) REVERT: G 77 PHE cc_start: 0.8760 (t80) cc_final: 0.8312 (t80) REVERT: G 153 LEU cc_start: 0.9399 (mt) cc_final: 0.9116 (mt) REVERT: G 157 PHE cc_start: 0.8620 (m-80) cc_final: 0.8189 (m-80) REVERT: G 198 MET cc_start: 0.8335 (ptt) cc_final: 0.7246 (tpt) REVERT: G 226 ARG cc_start: 0.7936 (ptp-170) cc_final: 0.7702 (ptp-170) REVERT: H 33 ARG cc_start: 0.9144 (ttt180) cc_final: 0.8838 (ttt180) REVERT: H 194 LYS cc_start: 0.9233 (mttp) cc_final: 0.8988 (mttp) REVERT: H 223 ARG cc_start: 0.9045 (OUTLIER) cc_final: 0.8690 (ptm160) REVERT: I 52 PHE cc_start: 0.5010 (t80) cc_final: 0.4215 (t80) REVERT: I 216 LEU cc_start: 0.8384 (OUTLIER) cc_final: 0.7900 (pp) REVERT: J 20 MET cc_start: 0.4484 (OUTLIER) cc_final: 0.3671 (tpp) REVERT: J 23 LYS cc_start: 0.8973 (ptmt) cc_final: 0.8338 (ptpp) REVERT: J 51 ARG cc_start: 0.8376 (tpt170) cc_final: 0.7822 (tpt170) REVERT: J 157 PHE cc_start: 0.9181 (OUTLIER) cc_final: 0.8951 (t80) REVERT: J 202 TRP cc_start: 0.8212 (t60) cc_final: 0.7674 (t60) outliers start: 133 outliers final: 99 residues processed: 545 average time/residue: 0.2645 time to fit residues: 216.4346 Evaluate side-chains 554 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 447 time to evaluate : 1.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 11 ILE Chi-restraints excluded: chain D residue 52 PHE Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 54 CYS Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 224 MET Chi-restraints excluded: chain B residue 12 ILE Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 146 HIS Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 175 CYS Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 77 PHE Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 98 HIS Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 157 PHE Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 20 MET Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 74 HIS Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain E residue 149 LEU Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 54 CYS Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain F residue 74 HIS Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain F residue 145 ILE Chi-restraints excluded: chain G residue 14 LEU Chi-restraints excluded: chain G residue 37 ILE Chi-restraints excluded: chain G residue 63 ASN Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 144 ILE Chi-restraints excluded: chain G residue 192 THR Chi-restraints excluded: chain G residue 207 LEU Chi-restraints excluded: chain G residue 224 MET Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 50 GLU Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 146 HIS Chi-restraints excluded: chain H residue 161 HIS Chi-restraints excluded: chain H residue 175 CYS Chi-restraints excluded: chain H residue 192 THR Chi-restraints excluded: chain H residue 199 LEU Chi-restraints excluded: chain H residue 215 ASP Chi-restraints excluded: chain H residue 223 ARG Chi-restraints excluded: chain I residue 39 LEU Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 69 PHE Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 98 HIS Chi-restraints excluded: chain I residue 134 LEU Chi-restraints excluded: chain I residue 161 HIS Chi-restraints excluded: chain I residue 175 CYS Chi-restraints excluded: chain I residue 197 LEU Chi-restraints excluded: chain I residue 199 LEU Chi-restraints excluded: chain I residue 213 LEU Chi-restraints excluded: chain I residue 216 LEU Chi-restraints excluded: chain J residue 7 LEU Chi-restraints excluded: chain J residue 10 LEU Chi-restraints excluded: chain J residue 20 MET Chi-restraints excluded: chain J residue 44 VAL Chi-restraints excluded: chain J residue 53 VAL Chi-restraints excluded: chain J residue 61 CYS Chi-restraints excluded: chain J residue 72 VAL Chi-restraints excluded: chain J residue 74 HIS Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 87 LEU Chi-restraints excluded: chain J residue 91 VAL Chi-restraints excluded: chain J residue 150 ARG Chi-restraints excluded: chain J residue 157 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 23 optimal weight: 0.6980 chunk 89 optimal weight: 0.9990 chunk 165 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 57 optimal weight: 4.9990 chunk 98 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 4 optimal weight: 0.3980 chunk 188 optimal weight: 0.8980 chunk 7 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 15 ASN ** G 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.137746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.109671 restraints weight = 45473.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.113955 restraints weight = 29364.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.117123 restraints weight = 21124.134| |-----------------------------------------------------------------------------| r_work (final): 0.3946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6964 moved from start: 0.6165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 16163 Z= 0.137 Angle : 0.833 14.918 21986 Z= 0.386 Chirality : 0.045 0.340 2610 Planarity : 0.006 0.098 2700 Dihedral : 5.601 47.819 2190 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 15.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 6.47 % Allowed : 27.92 % Favored : 65.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 9.09 % 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: -0.25 (0.19), residues: 1970 helix: 0.48 (0.15), residues: 1290 sheet: 0.84 (0.50), residues: 100 loop : -1.71 (0.27), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP J 78 HIS 0.006 0.001 HIS J 146 PHE 0.019 0.001 PHE A 26 TYR 0.024 0.002 TYR F 66 ARG 0.010 0.001 ARG D 51 Details of bonding type rmsd hydrogen bonds : bond 0.04048 ( 950) hydrogen bonds : angle 4.18162 ( 2820) SS BOND : bond 0.00908 ( 3) SS BOND : angle 1.28627 ( 6) covalent geometry : bond 0.00301 (16160) covalent geometry : angle 0.83281 (21980) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 589 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 477 time to evaluate : 1.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 28 LEU cc_start: 0.9404 (mm) cc_final: 0.9081 (mm) REVERT: D 34 MET cc_start: 0.8543 (mmm) cc_final: 0.8325 (mmm) REVERT: D 39 LEU cc_start: 0.9579 (mt) cc_final: 0.9199 (tp) REVERT: D 50 GLU cc_start: 0.8955 (mm-30) cc_final: 0.8736 (tp30) REVERT: D 51 ARG cc_start: 0.8380 (mtt180) cc_final: 0.7935 (mmt90) REVERT: D 78 TRP cc_start: 0.6765 (m-10) cc_final: 0.5693 (m-90) REVERT: D 86 LEU cc_start: 0.9263 (mm) cc_final: 0.8993 (mm) REVERT: D 201 LEU cc_start: 0.9575 (OUTLIER) cc_final: 0.9191 (pp) REVERT: D 211 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8618 (tt) REVERT: A 15 ASN cc_start: 0.8750 (t0) cc_final: 0.8247 (m110) REVERT: A 55 ASN cc_start: 0.8764 (p0) cc_final: 0.8365 (t0) REVERT: A 64 VAL cc_start: 0.8334 (OUTLIER) cc_final: 0.7980 (t) REVERT: A 78 TRP cc_start: 0.8641 (m-10) cc_final: 0.8428 (m-90) REVERT: A 185 ASP cc_start: 0.8809 (p0) cc_final: 0.8035 (t0) REVERT: A 198 MET cc_start: 0.7730 (ptt) cc_final: 0.6933 (tpp) REVERT: B 33 ARG cc_start: 0.8619 (ttt180) cc_final: 0.8380 (ttt90) REVERT: B 78 TRP cc_start: 0.8962 (m-10) cc_final: 0.8503 (m-10) REVERT: B 224 MET cc_start: 0.6030 (mmt) cc_final: 0.3639 (mmm) REVERT: C 12 ILE cc_start: 0.9289 (mp) cc_final: 0.8999 (tp) REVERT: C 77 PHE cc_start: 0.8945 (OUTLIER) cc_final: 0.8680 (m-80) REVERT: C 216 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8335 (pp) REVERT: E 20 MET cc_start: 0.4153 (OUTLIER) cc_final: 0.3514 (mtp) REVERT: E 23 LYS cc_start: 0.8844 (ptpt) cc_final: 0.8370 (pttm) REVERT: E 34 MET cc_start: 0.7703 (mmp) cc_final: 0.6581 (tmm) REVERT: E 81 GLN cc_start: 0.9001 (pt0) cc_final: 0.8774 (pt0) REVERT: E 98 HIS cc_start: 0.9505 (t70) cc_final: 0.9030 (t-170) REVERT: E 202 TRP cc_start: 0.8182 (t60) cc_final: 0.7707 (t60) REVERT: F 34 MET cc_start: 0.9217 (tpp) cc_final: 0.8896 (mmm) REVERT: F 39 LEU cc_start: 0.9579 (mt) cc_final: 0.9240 (tp) REVERT: F 51 ARG cc_start: 0.8388 (mmm160) cc_final: 0.8079 (mmm160) REVERT: F 54 CYS cc_start: 0.7831 (OUTLIER) cc_final: 0.7323 (t) REVERT: F 86 LEU cc_start: 0.9530 (mm) cc_final: 0.9276 (mm) REVERT: F 147 LEU cc_start: 0.8792 (mt) cc_final: 0.8538 (mt) REVERT: G 20 MET cc_start: 0.6267 (ppp) cc_final: 0.5961 (mmm) REVERT: G 52 PHE cc_start: 0.6590 (t80) cc_final: 0.5812 (t80) REVERT: G 153 LEU cc_start: 0.9357 (mt) cc_final: 0.9059 (mt) REVERT: G 157 PHE cc_start: 0.8694 (m-80) cc_final: 0.8242 (m-80) REVERT: G 198 MET cc_start: 0.8368 (ptt) cc_final: 0.7986 (ptt) REVERT: G 224 MET cc_start: 0.5148 (OUTLIER) cc_final: 0.4625 (mmp) REVERT: H 33 ARG cc_start: 0.9058 (ttt180) cc_final: 0.8166 (ttt90) REVERT: H 34 MET cc_start: 0.8729 (mmm) cc_final: 0.8284 (mmm) REVERT: H 76 ARG cc_start: 0.6881 (ppt170) cc_final: 0.6558 (ptm160) REVERT: H 154 GLU cc_start: 0.9222 (tp30) cc_final: 0.8570 (tm-30) REVERT: H 198 MET cc_start: 0.9125 (tmm) cc_final: 0.8513 (ppp) REVERT: I 52 PHE cc_start: 0.5106 (t80) cc_final: 0.4212 (t80) REVERT: I 216 LEU cc_start: 0.8343 (OUTLIER) cc_final: 0.7900 (pp) REVERT: J 23 LYS cc_start: 0.8951 (ptmt) cc_final: 0.8536 (ptmm) REVERT: J 51 ARG cc_start: 0.8346 (tpt170) cc_final: 0.7748 (tpt170) REVERT: J 81 GLN cc_start: 0.9117 (pp30) cc_final: 0.8630 (pp30) REVERT: J 157 PHE cc_start: 0.9161 (m-80) cc_final: 0.8889 (t80) REVERT: J 202 TRP cc_start: 0.8056 (t60) cc_final: 0.7502 (t60) outliers start: 112 outliers final: 80 residues processed: 537 average time/residue: 0.2581 time to fit residues: 207.6509 Evaluate side-chains 537 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 448 time to evaluate : 1.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 11 ILE Chi-restraints excluded: chain D residue 52 PHE Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 54 CYS Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 187 TYR Chi-restraints excluded: chain D residue 196 LEU Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 224 MET Chi-restraints excluded: chain B residue 12 ILE Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 146 HIS Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 175 CYS Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 77 PHE Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 98 HIS Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 157 PHE Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 11 ILE Chi-restraints excluded: chain E residue 20 MET Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 74 HIS Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 54 CYS Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain F residue 74 HIS Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain F residue 187 TYR Chi-restraints excluded: chain G residue 4 VAL Chi-restraints excluded: chain G residue 14 LEU Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 144 ILE Chi-restraints excluded: chain G residue 224 MET Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 50 GLU Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 146 HIS Chi-restraints excluded: chain H residue 161 HIS Chi-restraints excluded: chain H residue 175 CYS Chi-restraints excluded: chain H residue 184 VAL Chi-restraints excluded: chain H residue 215 ASP Chi-restraints excluded: chain H residue 223 ARG Chi-restraints excluded: chain I residue 13 THR Chi-restraints excluded: chain I residue 19 THR Chi-restraints excluded: chain I residue 39 LEU Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 69 PHE Chi-restraints excluded: chain I residue 98 HIS Chi-restraints excluded: chain I residue 134 LEU Chi-restraints excluded: chain I residue 153 LEU Chi-restraints excluded: chain I residue 161 HIS Chi-restraints excluded: chain I residue 198 MET Chi-restraints excluded: chain I residue 199 LEU Chi-restraints excluded: chain I residue 211 LEU Chi-restraints excluded: chain I residue 216 LEU Chi-restraints excluded: chain J residue 10 LEU Chi-restraints excluded: chain J residue 53 VAL Chi-restraints excluded: chain J residue 72 VAL Chi-restraints excluded: chain J residue 74 HIS Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 87 LEU Chi-restraints excluded: chain J residue 91 VAL Chi-restraints excluded: chain J residue 148 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 21 optimal weight: 0.3980 chunk 141 optimal weight: 0.9990 chunk 48 optimal weight: 0.8980 chunk 186 optimal weight: 8.9990 chunk 25 optimal weight: 8.9990 chunk 97 optimal weight: 1.9990 chunk 121 optimal weight: 0.9980 chunk 7 optimal weight: 9.9990 chunk 176 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 GLN ** D 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 46 GLN A 58 GLN ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 58 GLN ** H 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.136044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.108292 restraints weight = 45907.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.112324 restraints weight = 30231.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.115410 restraints weight = 22069.626| |-----------------------------------------------------------------------------| r_work (final): 0.3957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6920 moved from start: 0.6489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16163 Z= 0.134 Angle : 0.832 13.380 21986 Z= 0.386 Chirality : 0.045 0.236 2610 Planarity : 0.006 0.099 2700 Dihedral : 5.499 46.797 2190 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 6.13 % Allowed : 29.36 % Favored : 64.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 9.09 % 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: -0.22 (0.19), residues: 1970 helix: 0.52 (0.15), residues: 1290 sheet: 0.69 (0.51), residues: 100 loop : -1.69 (0.27), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 78 HIS 0.006 0.001 HIS J 146 PHE 0.025 0.001 PHE A 26 TYR 0.020 0.001 TYR F 66 ARG 0.006 0.001 ARG B 226 Details of bonding type rmsd hydrogen bonds : bond 0.03978 ( 950) hydrogen bonds : angle 4.19287 ( 2820) SS BOND : bond 0.00420 ( 3) SS BOND : angle 1.29714 ( 6) covalent geometry : bond 0.00299 (16160) covalent geometry : angle 0.83191 (21980) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 569 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 463 time to evaluate : 1.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 28 LEU cc_start: 0.9435 (mm) cc_final: 0.9116 (mm) REVERT: D 34 MET cc_start: 0.8613 (mmm) cc_final: 0.8335 (mmm) REVERT: D 39 LEU cc_start: 0.9544 (mt) cc_final: 0.9112 (tp) REVERT: D 46 GLN cc_start: 0.9374 (mm-40) cc_final: 0.8924 (tp40) REVERT: D 86 LEU cc_start: 0.9260 (mm) cc_final: 0.9004 (mm) REVERT: D 211 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8596 (tt) REVERT: A 15 ASN cc_start: 0.8750 (t0) cc_final: 0.8047 (m110) REVERT: A 20 MET cc_start: 0.6743 (mtp) cc_final: 0.5690 (mmt) REVERT: A 23 LYS cc_start: 0.8809 (mttp) cc_final: 0.8279 (mptt) REVERT: A 33 ARG cc_start: 0.8700 (tpt170) cc_final: 0.8262 (tpp80) REVERT: A 55 ASN cc_start: 0.8771 (p0) cc_final: 0.8411 (t0) REVERT: A 64 VAL cc_start: 0.8370 (OUTLIER) cc_final: 0.8043 (t) REVERT: A 78 TRP cc_start: 0.8699 (m-10) cc_final: 0.8201 (m-90) REVERT: A 185 ASP cc_start: 0.8934 (p0) cc_final: 0.8058 (t0) REVERT: A 198 MET cc_start: 0.7822 (ptt) cc_final: 0.6945 (tpt) REVERT: B 33 ARG cc_start: 0.8688 (ttt180) cc_final: 0.8124 (ttt90) REVERT: B 154 GLU cc_start: 0.8447 (tt0) cc_final: 0.8053 (tt0) REVERT: B 193 GLU cc_start: 0.9650 (mm-30) cc_final: 0.9310 (mm-30) REVERT: C 12 ILE cc_start: 0.9264 (mp) cc_final: 0.8991 (tp) REVERT: C 77 PHE cc_start: 0.8924 (OUTLIER) cc_final: 0.8664 (m-80) REVERT: C 216 LEU cc_start: 0.8719 (OUTLIER) cc_final: 0.8420 (pp) REVERT: E 20 MET cc_start: 0.4246 (OUTLIER) cc_final: 0.3610 (mtp) REVERT: E 23 LYS cc_start: 0.8845 (ptpt) cc_final: 0.8369 (pttm) REVERT: E 34 MET cc_start: 0.7671 (mmp) cc_final: 0.6656 (tmm) REVERT: E 39 LEU cc_start: 0.9669 (OUTLIER) cc_final: 0.9390 (pp) REVERT: E 81 GLN cc_start: 0.9047 (pt0) cc_final: 0.8798 (pt0) REVERT: E 98 HIS cc_start: 0.9508 (t70) cc_final: 0.9060 (t-170) REVERT: E 202 TRP cc_start: 0.8209 (t60) cc_final: 0.7830 (t60) REVERT: F 34 MET cc_start: 0.9205 (tpp) cc_final: 0.8295 (mmm) REVERT: F 39 LEU cc_start: 0.9578 (mt) cc_final: 0.9197 (tp) REVERT: F 42 ARG cc_start: 0.9218 (tpt90) cc_final: 0.8937 (tpt90) REVERT: F 51 ARG cc_start: 0.8505 (mmm160) cc_final: 0.8287 (mmm160) REVERT: F 86 LEU cc_start: 0.9538 (mm) cc_final: 0.9248 (mm) REVERT: F 147 LEU cc_start: 0.8694 (mt) cc_final: 0.8458 (mt) REVERT: G 4 VAL cc_start: 0.7239 (OUTLIER) cc_final: 0.6992 (p) REVERT: G 20 MET cc_start: 0.6386 (ppp) cc_final: 0.5878 (mmm) REVERT: G 52 PHE cc_start: 0.6634 (t80) cc_final: 0.5845 (t80) REVERT: G 77 PHE cc_start: 0.8719 (t80) cc_final: 0.8304 (t80) REVERT: G 153 LEU cc_start: 0.9369 (mt) cc_final: 0.9150 (pp) REVERT: G 157 PHE cc_start: 0.8797 (m-80) cc_final: 0.8310 (m-80) REVERT: G 198 MET cc_start: 0.8430 (ptt) cc_final: 0.8030 (ptt) REVERT: G 224 MET cc_start: 0.5045 (OUTLIER) cc_final: 0.3666 (ptm) REVERT: G 226 ARG cc_start: 0.7773 (ptp-170) cc_final: 0.7514 (ptp-170) REVERT: H 33 ARG cc_start: 0.9106 (ttt180) cc_final: 0.8103 (ttt90) REVERT: H 34 MET cc_start: 0.8790 (mmm) cc_final: 0.8366 (mmm) REVERT: H 76 ARG cc_start: 0.6856 (ppt170) cc_final: 0.6565 (ptm160) REVERT: H 154 GLU cc_start: 0.9251 (tp30) cc_final: 0.8552 (tm-30) REVERT: H 198 MET cc_start: 0.9048 (tmm) cc_final: 0.8593 (ppp) REVERT: H 201 LEU cc_start: 0.9731 (mm) cc_final: 0.9418 (tt) REVERT: I 52 PHE cc_start: 0.5228 (t80) cc_final: 0.4377 (t80) REVERT: I 77 PHE cc_start: 0.9185 (OUTLIER) cc_final: 0.8901 (m-80) REVERT: I 216 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.7955 (pp) REVERT: J 23 LYS cc_start: 0.8900 (ptmt) cc_final: 0.8578 (ptmm) REVERT: J 51 ARG cc_start: 0.8366 (tpt170) cc_final: 0.7760 (tpt170) REVERT: J 81 GLN cc_start: 0.9106 (pp30) cc_final: 0.8455 (pp30) REVERT: J 157 PHE cc_start: 0.9182 (m-80) cc_final: 0.8863 (t80) REVERT: J 202 TRP cc_start: 0.8075 (t60) cc_final: 0.7531 (t60) outliers start: 106 outliers final: 80 residues processed: 522 average time/residue: 0.2633 time to fit residues: 204.8334 Evaluate side-chains 540 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 450 time to evaluate : 1.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 11 ILE Chi-restraints excluded: chain D residue 52 PHE Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 54 CYS Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 187 TYR Chi-restraints excluded: chain D residue 196 LEU Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 224 MET Chi-restraints excluded: chain B residue 12 ILE Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 146 HIS Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 175 CYS Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 77 PHE Chi-restraints excluded: chain C residue 98 HIS Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 11 ILE Chi-restraints excluded: chain E residue 20 MET Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 74 HIS Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 149 LEU Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 54 CYS Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain F residue 74 HIS Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 4 VAL Chi-restraints excluded: chain G residue 14 LEU Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 144 ILE Chi-restraints excluded: chain G residue 207 LEU Chi-restraints excluded: chain G residue 215 ASP Chi-restraints excluded: chain G residue 224 MET Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 50 GLU Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 146 HIS Chi-restraints excluded: chain H residue 161 HIS Chi-restraints excluded: chain H residue 184 VAL Chi-restraints excluded: chain H residue 215 ASP Chi-restraints excluded: chain H residue 223 ARG Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 69 PHE Chi-restraints excluded: chain I residue 77 PHE Chi-restraints excluded: chain I residue 98 HIS Chi-restraints excluded: chain I residue 134 LEU Chi-restraints excluded: chain I residue 161 HIS Chi-restraints excluded: chain I residue 198 MET Chi-restraints excluded: chain I residue 199 LEU Chi-restraints excluded: chain I residue 211 LEU Chi-restraints excluded: chain I residue 213 LEU Chi-restraints excluded: chain I residue 216 LEU Chi-restraints excluded: chain J residue 10 LEU Chi-restraints excluded: chain J residue 44 VAL Chi-restraints excluded: chain J residue 53 VAL Chi-restraints excluded: chain J residue 72 VAL Chi-restraints excluded: chain J residue 74 HIS Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 87 LEU Chi-restraints excluded: chain J residue 91 VAL Chi-restraints excluded: chain J residue 150 ARG Chi-restraints excluded: chain J residue 216 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 94 optimal weight: 9.9990 chunk 191 optimal weight: 6.9990 chunk 100 optimal weight: 8.9990 chunk 8 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 chunk 45 optimal weight: 7.9990 chunk 169 optimal weight: 0.6980 chunk 95 optimal weight: 0.9980 chunk 68 optimal weight: 0.6980 chunk 190 optimal weight: 4.9990 chunk 4 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 46 GLN ** D 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 146 HIS ** A 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 GLN F 49 GLN ** G 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.135661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.107895 restraints weight = 45660.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.112028 restraints weight = 30057.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.115130 restraints weight = 21764.480| |-----------------------------------------------------------------------------| r_work (final): 0.3969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6956 moved from start: 0.6716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16163 Z= 0.136 Angle : 0.864 13.668 21986 Z= 0.396 Chirality : 0.046 0.388 2610 Planarity : 0.006 0.097 2700 Dihedral : 5.439 46.280 2190 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 15.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 6.01 % Allowed : 30.40 % Favored : 63.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 9.09 % 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 (0.20), residues: 1970 helix: 0.65 (0.15), residues: 1270 sheet: 0.64 (0.52), residues: 100 loop : -1.27 (0.28), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 78 HIS 0.006 0.001 HIS D 146 PHE 0.024 0.001 PHE G 92 TYR 0.019 0.002 TYR A 66 ARG 0.004 0.000 ARG I 150 Details of bonding type rmsd hydrogen bonds : bond 0.03882 ( 950) hydrogen bonds : angle 4.20701 ( 2820) SS BOND : bond 0.00548 ( 3) SS BOND : angle 1.31904 ( 6) covalent geometry : bond 0.00304 (16160) covalent geometry : angle 0.86365 (21980) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 566 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 462 time to evaluate : 1.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 28 LEU cc_start: 0.9445 (mm) cc_final: 0.9120 (mm) REVERT: D 34 MET cc_start: 0.8642 (mmm) cc_final: 0.8336 (mmm) REVERT: D 39 LEU cc_start: 0.9525 (mt) cc_final: 0.9080 (tp) REVERT: D 46 GLN cc_start: 0.9378 (OUTLIER) cc_final: 0.8937 (tp40) REVERT: D 86 LEU cc_start: 0.9279 (mm) cc_final: 0.9054 (mm) REVERT: D 211 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8613 (tt) REVERT: A 15 ASN cc_start: 0.8774 (t0) cc_final: 0.8283 (m110) REVERT: A 20 MET cc_start: 0.6679 (mtp) cc_final: 0.5839 (mmt) REVERT: A 55 ASN cc_start: 0.8878 (p0) cc_final: 0.8516 (t0) REVERT: A 64 VAL cc_start: 0.8343 (OUTLIER) cc_final: 0.7980 (t) REVERT: A 77 PHE cc_start: 0.8574 (t80) cc_final: 0.8229 (t80) REVERT: A 78 TRP cc_start: 0.8695 (m-10) cc_final: 0.8251 (m-90) REVERT: A 185 ASP cc_start: 0.8883 (p0) cc_final: 0.7911 (t0) REVERT: A 198 MET cc_start: 0.7832 (ptt) cc_final: 0.6973 (tpt) REVERT: B 33 ARG cc_start: 0.8454 (ttt180) cc_final: 0.7888 (ttm-80) REVERT: B 193 GLU cc_start: 0.9661 (mm-30) cc_final: 0.9276 (mm-30) REVERT: C 12 ILE cc_start: 0.9244 (mp) cc_final: 0.8976 (tp) REVERT: C 77 PHE cc_start: 0.8876 (OUTLIER) cc_final: 0.8621 (m-80) REVERT: C 216 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8383 (pp) REVERT: E 20 MET cc_start: 0.4250 (OUTLIER) cc_final: 0.3628 (mtp) REVERT: E 23 LYS cc_start: 0.8888 (ptpt) cc_final: 0.8395 (pttm) REVERT: E 34 MET cc_start: 0.7808 (mmp) cc_final: 0.6669 (tmm) REVERT: E 39 LEU cc_start: 0.9683 (OUTLIER) cc_final: 0.9400 (pp) REVERT: E 81 GLN cc_start: 0.9000 (pt0) cc_final: 0.8768 (pt0) REVERT: E 98 HIS cc_start: 0.9512 (t70) cc_final: 0.9040 (t-170) REVERT: E 202 TRP cc_start: 0.8216 (t60) cc_final: 0.7821 (t60) REVERT: F 34 MET cc_start: 0.9211 (tpp) cc_final: 0.8313 (mmm) REVERT: F 39 LEU cc_start: 0.9580 (mt) cc_final: 0.9164 (tp) REVERT: F 42 ARG cc_start: 0.9220 (tpt90) cc_final: 0.8931 (tpt90) REVERT: F 54 CYS cc_start: 0.7789 (OUTLIER) cc_final: 0.7320 (t) REVERT: F 86 LEU cc_start: 0.9536 (mm) cc_final: 0.9238 (mm) REVERT: F 147 LEU cc_start: 0.8653 (mt) cc_final: 0.8414 (mt) REVERT: G 4 VAL cc_start: 0.7299 (OUTLIER) cc_final: 0.7036 (p) REVERT: G 20 MET cc_start: 0.6366 (ppp) cc_final: 0.5875 (mmm) REVERT: G 23 LYS cc_start: 0.8862 (mppt) cc_final: 0.8640 (mttt) REVERT: G 52 PHE cc_start: 0.6436 (t80) cc_final: 0.5669 (t80) REVERT: G 77 PHE cc_start: 0.8741 (t80) cc_final: 0.8315 (t80) REVERT: G 153 LEU cc_start: 0.9386 (mt) cc_final: 0.9076 (pp) REVERT: G 157 PHE cc_start: 0.8872 (m-80) cc_final: 0.8411 (m-80) REVERT: G 198 MET cc_start: 0.8425 (ptt) cc_final: 0.8074 (ptt) REVERT: G 224 MET cc_start: 0.5061 (OUTLIER) cc_final: 0.3739 (ptm) REVERT: G 226 ARG cc_start: 0.7797 (ptp-170) cc_final: 0.7466 (ptp-170) REVERT: H 33 ARG cc_start: 0.8908 (ttt180) cc_final: 0.8105 (ttt90) REVERT: H 34 MET cc_start: 0.8816 (mmm) cc_final: 0.8350 (mmm) REVERT: H 76 ARG cc_start: 0.6972 (ppt170) cc_final: 0.6640 (ptm160) REVERT: H 154 GLU cc_start: 0.9199 (tp30) cc_final: 0.8624 (tm-30) REVERT: H 194 LYS cc_start: 0.9215 (mttp) cc_final: 0.8721 (mttt) REVERT: H 198 MET cc_start: 0.9058 (tmm) cc_final: 0.8546 (ppp) REVERT: I 34 MET cc_start: 0.9089 (mmp) cc_final: 0.8762 (mmm) REVERT: I 52 PHE cc_start: 0.5260 (t80) cc_final: 0.4352 (t80) REVERT: I 77 PHE cc_start: 0.9185 (OUTLIER) cc_final: 0.8889 (m-80) REVERT: I 216 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.8005 (pp) REVERT: J 23 LYS cc_start: 0.8868 (ptmt) cc_final: 0.8503 (ptmm) REVERT: J 51 ARG cc_start: 0.8368 (tpt170) cc_final: 0.7748 (tpt170) REVERT: J 157 PHE cc_start: 0.9189 (OUTLIER) cc_final: 0.8888 (t80) REVERT: J 202 TRP cc_start: 0.8123 (t60) cc_final: 0.7550 (t60) outliers start: 104 outliers final: 78 residues processed: 512 average time/residue: 0.2551 time to fit residues: 196.6569 Evaluate side-chains 541 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 450 time to evaluate : 1.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 11 ILE Chi-restraints excluded: chain D residue 46 GLN Chi-restraints excluded: chain D residue 52 PHE Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 54 CYS Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 224 MET Chi-restraints excluded: chain B residue 12 ILE Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 146 HIS Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 175 CYS Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 77 PHE Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 98 HIS Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 11 ILE Chi-restraints excluded: chain E residue 20 MET Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 74 HIS Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 197 LEU Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 54 CYS Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain F residue 74 HIS Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 4 VAL Chi-restraints excluded: chain G residue 14 LEU Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 144 ILE Chi-restraints excluded: chain G residue 154 GLU Chi-restraints excluded: chain G residue 207 LEU Chi-restraints excluded: chain G residue 215 ASP Chi-restraints excluded: chain G residue 224 MET Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 50 GLU Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 146 HIS Chi-restraints excluded: chain H residue 161 HIS Chi-restraints excluded: chain H residue 184 VAL Chi-restraints excluded: chain H residue 215 ASP Chi-restraints excluded: chain H residue 223 ARG Chi-restraints excluded: chain I residue 13 THR Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 69 PHE Chi-restraints excluded: chain I residue 77 PHE Chi-restraints excluded: chain I residue 98 HIS Chi-restraints excluded: chain I residue 161 HIS Chi-restraints excluded: chain I residue 198 MET Chi-restraints excluded: chain I residue 199 LEU Chi-restraints excluded: chain I residue 211 LEU Chi-restraints excluded: chain I residue 213 LEU Chi-restraints excluded: chain I residue 216 LEU Chi-restraints excluded: chain J residue 10 LEU Chi-restraints excluded: chain J residue 11 ILE Chi-restraints excluded: chain J residue 44 VAL Chi-restraints excluded: chain J residue 53 VAL Chi-restraints excluded: chain J residue 72 VAL Chi-restraints excluded: chain J residue 74 HIS Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 87 LEU Chi-restraints excluded: chain J residue 148 LEU Chi-restraints excluded: chain J residue 150 ARG Chi-restraints excluded: chain J residue 157 PHE Chi-restraints excluded: chain J residue 207 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 6 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 65 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 125 optimal weight: 0.7980 chunk 90 optimal weight: 8.9990 chunk 136 optimal weight: 7.9990 chunk 64 optimal weight: 0.3980 chunk 167 optimal weight: 2.9990 chunk 128 optimal weight: 0.5980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.134319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.106983 restraints weight = 45816.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.111002 restraints weight = 30013.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.114040 restraints weight = 21646.140| |-----------------------------------------------------------------------------| r_work (final): 0.3949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7033 moved from start: 0.7017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16163 Z= 0.150 Angle : 0.882 14.215 21986 Z= 0.406 Chirality : 0.047 0.444 2610 Planarity : 0.006 0.102 2700 Dihedral : 5.457 45.132 2190 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 16.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 6.53 % Allowed : 30.58 % Favored : 62.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 9.09 % 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: 0.17 (0.20), residues: 1970 helix: 0.64 (0.15), residues: 1320 sheet: 0.42 (0.51), residues: 100 loop : -1.04 (0.29), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 78 HIS 0.006 0.001 HIS F 98 PHE 0.023 0.001 PHE H 77 TYR 0.019 0.002 TYR J 143 ARG 0.005 0.001 ARG I 150 Details of bonding type rmsd hydrogen bonds : bond 0.03901 ( 950) hydrogen bonds : angle 4.28799 ( 2820) SS BOND : bond 0.00500 ( 3) SS BOND : angle 1.33623 ( 6) covalent geometry : bond 0.00327 (16160) covalent geometry : angle 0.88170 (21980) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 566 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 453 time to evaluate : 1.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 28 LEU cc_start: 0.9494 (mm) cc_final: 0.9103 (mm) REVERT: D 34 MET cc_start: 0.8633 (mmm) cc_final: 0.8342 (mmm) REVERT: D 39 LEU cc_start: 0.9515 (mt) cc_final: 0.9033 (tp) REVERT: D 42 ARG cc_start: 0.9197 (tpt90) cc_final: 0.8785 (ttt180) REVERT: D 46 GLN cc_start: 0.9407 (OUTLIER) cc_final: 0.9036 (mm-40) REVERT: D 86 LEU cc_start: 0.9309 (mm) cc_final: 0.9056 (mm) REVERT: D 211 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8408 (tt) REVERT: D 215 ASP cc_start: 0.8395 (m-30) cc_final: 0.7631 (m-30) REVERT: A 15 ASN cc_start: 0.8781 (t0) cc_final: 0.8290 (m110) REVERT: A 20 MET cc_start: 0.6639 (mtp) cc_final: 0.5764 (mmt) REVERT: A 30 MET cc_start: 0.9007 (tmm) cc_final: 0.8701 (tmm) REVERT: A 55 ASN cc_start: 0.8893 (p0) cc_final: 0.8580 (t0) REVERT: A 64 VAL cc_start: 0.8366 (OUTLIER) cc_final: 0.8011 (t) REVERT: A 77 PHE cc_start: 0.8667 (t80) cc_final: 0.8323 (t80) REVERT: A 78 TRP cc_start: 0.8748 (m-10) cc_final: 0.8177 (m-90) REVERT: A 185 ASP cc_start: 0.8862 (p0) cc_final: 0.7941 (t0) REVERT: A 198 MET cc_start: 0.7881 (ptt) cc_final: 0.6969 (tpt) REVERT: B 33 ARG cc_start: 0.8501 (ttt180) cc_final: 0.7890 (ttm-80) REVERT: B 193 GLU cc_start: 0.9657 (mm-30) cc_final: 0.9303 (mm-30) REVERT: B 198 MET cc_start: 0.9255 (tmm) cc_final: 0.8522 (ptt) REVERT: C 12 ILE cc_start: 0.9254 (OUTLIER) cc_final: 0.9001 (tp) REVERT: C 77 PHE cc_start: 0.8835 (OUTLIER) cc_final: 0.8580 (m-80) REVERT: E 20 MET cc_start: 0.4281 (OUTLIER) cc_final: 0.3858 (mtm) REVERT: E 23 LYS cc_start: 0.8960 (ptpt) cc_final: 0.8477 (pttm) REVERT: E 34 MET cc_start: 0.7716 (mmp) cc_final: 0.6764 (tmm) REVERT: E 39 LEU cc_start: 0.9707 (OUTLIER) cc_final: 0.9413 (pp) REVERT: E 67 ASP cc_start: 0.7788 (t0) cc_final: 0.6923 (m-30) REVERT: E 81 GLN cc_start: 0.9008 (pt0) cc_final: 0.8753 (pt0) REVERT: E 98 HIS cc_start: 0.9493 (t70) cc_final: 0.9004 (t-170) REVERT: E 202 TRP cc_start: 0.8180 (t60) cc_final: 0.7746 (t60) REVERT: F 34 MET cc_start: 0.9211 (tpp) cc_final: 0.8846 (mmm) REVERT: F 39 LEU cc_start: 0.9589 (mt) cc_final: 0.9158 (tp) REVERT: F 42 ARG cc_start: 0.9260 (tpt90) cc_final: 0.8965 (tpt90) REVERT: F 54 CYS cc_start: 0.7838 (OUTLIER) cc_final: 0.7278 (t) REVERT: F 86 LEU cc_start: 0.9548 (mm) cc_final: 0.9287 (mm) REVERT: F 147 LEU cc_start: 0.8603 (mt) cc_final: 0.8375 (mt) REVERT: G 4 VAL cc_start: 0.7318 (OUTLIER) cc_final: 0.7041 (p) REVERT: G 20 MET cc_start: 0.6263 (ppp) cc_final: 0.5666 (mmm) REVERT: G 23 LYS cc_start: 0.8894 (mppt) cc_final: 0.8452 (mttt) REVERT: G 31 LEU cc_start: 0.9568 (mm) cc_final: 0.9353 (mm) REVERT: G 52 PHE cc_start: 0.6550 (t80) cc_final: 0.5746 (t80) REVERT: G 77 PHE cc_start: 0.8764 (t80) cc_final: 0.8386 (t80) REVERT: G 153 LEU cc_start: 0.9409 (mt) cc_final: 0.9153 (pp) REVERT: G 157 PHE cc_start: 0.8794 (m-80) cc_final: 0.8350 (m-80) REVERT: G 198 MET cc_start: 0.8460 (ptt) cc_final: 0.8243 (ptt) REVERT: G 224 MET cc_start: 0.5408 (OUTLIER) cc_final: 0.4034 (ptp) REVERT: G 226 ARG cc_start: 0.7874 (ptp-170) cc_final: 0.7504 (ptp-170) REVERT: H 33 ARG cc_start: 0.8960 (ttt180) cc_final: 0.8201 (ttt90) REVERT: H 34 MET cc_start: 0.8823 (mmm) cc_final: 0.8411 (mmm) REVERT: H 76 ARG cc_start: 0.7019 (ppt170) cc_final: 0.6661 (ptm160) REVERT: H 154 GLU cc_start: 0.9259 (tp30) cc_final: 0.8734 (tm-30) REVERT: H 201 LEU cc_start: 0.9653 (mp) cc_final: 0.9223 (tt) REVERT: I 33 ARG cc_start: 0.7586 (ttt180) cc_final: 0.7035 (ttt180) REVERT: I 52 PHE cc_start: 0.5400 (t80) cc_final: 0.4441 (t80) REVERT: I 77 PHE cc_start: 0.9108 (OUTLIER) cc_final: 0.8839 (m-80) REVERT: I 187 TYR cc_start: 0.7058 (m-80) cc_final: 0.6731 (m-10) REVERT: I 216 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8139 (pp) REVERT: J 23 LYS cc_start: 0.8841 (ptmt) cc_final: 0.8527 (ptmm) REVERT: J 51 ARG cc_start: 0.8434 (tpt170) cc_final: 0.8183 (tpt170) REVERT: J 157 PHE cc_start: 0.9160 (OUTLIER) cc_final: 0.8887 (t80) REVERT: J 202 TRP cc_start: 0.8092 (t60) cc_final: 0.7489 (t60) outliers start: 113 outliers final: 86 residues processed: 506 average time/residue: 0.2533 time to fit residues: 189.6507 Evaluate side-chains 544 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 445 time to evaluate : 1.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 11 ILE Chi-restraints excluded: chain D residue 46 GLN Chi-restraints excluded: chain D residue 52 PHE Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 54 CYS Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 224 MET Chi-restraints excluded: chain B residue 12 ILE Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 146 HIS Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain C residue 12 ILE Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 77 PHE Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 98 HIS Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 11 ILE Chi-restraints excluded: chain E residue 20 MET Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 74 HIS Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 149 LEU Chi-restraints excluded: chain E residue 197 LEU Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 54 CYS Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain F residue 74 HIS Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain F residue 87 LEU Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 4 VAL Chi-restraints excluded: chain G residue 14 LEU Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 144 ILE Chi-restraints excluded: chain G residue 154 GLU Chi-restraints excluded: chain G residue 207 LEU Chi-restraints excluded: chain G residue 215 ASP Chi-restraints excluded: chain G residue 224 MET Chi-restraints excluded: chain H residue 12 ILE Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 50 GLU Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 146 HIS Chi-restraints excluded: chain H residue 161 HIS Chi-restraints excluded: chain H residue 184 VAL Chi-restraints excluded: chain H residue 215 ASP Chi-restraints excluded: chain H residue 223 ARG Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 69 PHE Chi-restraints excluded: chain I residue 77 PHE Chi-restraints excluded: chain I residue 98 HIS Chi-restraints excluded: chain I residue 161 HIS Chi-restraints excluded: chain I residue 198 MET Chi-restraints excluded: chain I residue 199 LEU Chi-restraints excluded: chain I residue 211 LEU Chi-restraints excluded: chain I residue 213 LEU Chi-restraints excluded: chain I residue 216 LEU Chi-restraints excluded: chain J residue 10 LEU Chi-restraints excluded: chain J residue 11 ILE Chi-restraints excluded: chain J residue 44 VAL Chi-restraints excluded: chain J residue 53 VAL Chi-restraints excluded: chain J residue 61 CYS Chi-restraints excluded: chain J residue 72 VAL Chi-restraints excluded: chain J residue 74 HIS Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 87 LEU Chi-restraints excluded: chain J residue 91 VAL Chi-restraints excluded: chain J residue 146 HIS Chi-restraints excluded: chain J residue 148 LEU Chi-restraints excluded: chain J residue 150 ARG Chi-restraints excluded: chain J residue 157 PHE Chi-restraints excluded: chain J residue 207 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 198 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 120 optimal weight: 0.0870 chunk 5 optimal weight: 2.9990 chunk 112 optimal weight: 6.9990 chunk 181 optimal weight: 0.2980 chunk 114 optimal weight: 4.9990 chunk 15 optimal weight: 0.9990 chunk 79 optimal weight: 6.9990 chunk 116 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 overall best weight: 1.0764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 146 HIS B 17 ASN ** E 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 17 ASN ** F 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 161 HIS ** J 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.138183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.110014 restraints weight = 46703.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.114134 restraints weight = 31176.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.117165 restraints weight = 22674.270| |-----------------------------------------------------------------------------| r_work (final): 0.3936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6996 moved from start: 0.7236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 16163 Z= 0.142 Angle : 0.896 15.285 21986 Z= 0.408 Chirality : 0.047 0.435 2610 Planarity : 0.006 0.101 2700 Dihedral : 5.405 45.102 2190 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 16.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 5.84 % Allowed : 31.73 % Favored : 62.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 9.09 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.20), residues: 1970 helix: 0.66 (0.15), residues: 1320 sheet: 0.33 (0.50), residues: 100 loop : -1.06 (0.29), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 78 HIS 0.007 0.001 HIS F 98 PHE 0.022 0.001 PHE H 77 TYR 0.020 0.002 TYR J 143 ARG 0.007 0.001 ARG A 51 Details of bonding type rmsd hydrogen bonds : bond 0.03860 ( 950) hydrogen bonds : angle 4.27449 ( 2820) SS BOND : bond 0.00379 ( 3) SS BOND : angle 1.26512 ( 6) covalent geometry : bond 0.00316 (16160) covalent geometry : angle 0.89557 (21980) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 543 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 442 time to evaluate : 1.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 28 LEU cc_start: 0.9424 (mm) cc_final: 0.9044 (mm) REVERT: D 34 MET cc_start: 0.8649 (mmm) cc_final: 0.8365 (mmm) REVERT: D 39 LEU cc_start: 0.9498 (mt) cc_final: 0.9010 (tp) REVERT: D 42 ARG cc_start: 0.9194 (tpt90) cc_final: 0.8793 (ttt180) REVERT: D 46 GLN cc_start: 0.9418 (tm-30) cc_final: 0.9101 (mm-40) REVERT: D 86 LEU cc_start: 0.9284 (mm) cc_final: 0.9042 (mm) REVERT: D 211 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8541 (tt) REVERT: A 15 ASN cc_start: 0.8746 (t0) cc_final: 0.8273 (m110) REVERT: A 20 MET cc_start: 0.6621 (mtp) cc_final: 0.5746 (mmt) REVERT: A 30 MET cc_start: 0.8985 (tmm) cc_final: 0.8652 (tmm) REVERT: A 55 ASN cc_start: 0.8848 (p0) cc_final: 0.8643 (t0) REVERT: A 64 VAL cc_start: 0.8412 (OUTLIER) cc_final: 0.8053 (t) REVERT: A 77 PHE cc_start: 0.8638 (t80) cc_final: 0.8306 (t80) REVERT: A 78 TRP cc_start: 0.8712 (m-10) cc_final: 0.8153 (m-90) REVERT: A 185 ASP cc_start: 0.8916 (p0) cc_final: 0.8024 (t0) REVERT: A 198 MET cc_start: 0.7815 (ptt) cc_final: 0.6978 (tpt) REVERT: B 33 ARG cc_start: 0.8490 (ttt180) cc_final: 0.7884 (ttm-80) REVERT: B 46 GLN cc_start: 0.9312 (pp30) cc_final: 0.8434 (pt0) REVERT: B 47 ASP cc_start: 0.8612 (p0) cc_final: 0.8019 (p0) REVERT: B 193 GLU cc_start: 0.9678 (mm-30) cc_final: 0.9349 (mm-30) REVERT: B 194 LYS cc_start: 0.9281 (mttp) cc_final: 0.8395 (mtmt) REVERT: B 198 MET cc_start: 0.9258 (tmm) cc_final: 0.8502 (ptt) REVERT: C 12 ILE cc_start: 0.9272 (OUTLIER) cc_final: 0.9035 (tp) REVERT: C 77 PHE cc_start: 0.8782 (OUTLIER) cc_final: 0.8531 (m-80) REVERT: E 23 LYS cc_start: 0.8772 (ptpt) cc_final: 0.8405 (pttt) REVERT: E 34 MET cc_start: 0.7823 (mmp) cc_final: 0.6702 (tmm) REVERT: E 39 LEU cc_start: 0.9706 (OUTLIER) cc_final: 0.9402 (pp) REVERT: E 67 ASP cc_start: 0.7774 (t0) cc_final: 0.6892 (m-30) REVERT: E 81 GLN cc_start: 0.8987 (pt0) cc_final: 0.8727 (pt0) REVERT: E 87 LEU cc_start: 0.9252 (tt) cc_final: 0.8607 (mt) REVERT: E 98 HIS cc_start: 0.9492 (t70) cc_final: 0.9012 (t-170) REVERT: E 202 TRP cc_start: 0.8182 (t60) cc_final: 0.7784 (t60) REVERT: F 34 MET cc_start: 0.9196 (tpp) cc_final: 0.8812 (mmm) REVERT: F 39 LEU cc_start: 0.9572 (mt) cc_final: 0.9117 (tp) REVERT: F 42 ARG cc_start: 0.9265 (tpt90) cc_final: 0.8957 (tpt90) REVERT: F 54 CYS cc_start: 0.7774 (OUTLIER) cc_final: 0.7142 (t) REVERT: F 86 LEU cc_start: 0.9553 (mm) cc_final: 0.9288 (mm) REVERT: F 147 LEU cc_start: 0.8540 (mt) cc_final: 0.8315 (mt) REVERT: G 20 MET cc_start: 0.6305 (ppp) cc_final: 0.5699 (tpt) REVERT: G 23 LYS cc_start: 0.8899 (mppt) cc_final: 0.8417 (mttt) REVERT: G 35 LEU cc_start: 0.9432 (tp) cc_final: 0.9162 (mm) REVERT: G 52 PHE cc_start: 0.6668 (t80) cc_final: 0.5945 (t80) REVERT: G 77 PHE cc_start: 0.8776 (t80) cc_final: 0.8319 (t80) REVERT: G 78 TRP cc_start: 0.9295 (OUTLIER) cc_final: 0.9044 (m-90) REVERT: G 153 LEU cc_start: 0.9396 (mt) cc_final: 0.9154 (pp) REVERT: G 157 PHE cc_start: 0.8824 (m-80) cc_final: 0.8406 (m-80) REVERT: G 224 MET cc_start: 0.5226 (OUTLIER) cc_final: 0.3971 (ptm) REVERT: G 226 ARG cc_start: 0.7854 (ptp-170) cc_final: 0.7473 (ptp-170) REVERT: H 33 ARG cc_start: 0.8989 (ttt180) cc_final: 0.8202 (ttt90) REVERT: H 34 MET cc_start: 0.8818 (mmm) cc_final: 0.8485 (mmm) REVERT: H 154 GLU cc_start: 0.9346 (tp30) cc_final: 0.8764 (tm-30) REVERT: H 198 MET cc_start: 0.9126 (tmm) cc_final: 0.8577 (ppp) REVERT: H 201 LEU cc_start: 0.9646 (mp) cc_final: 0.9272 (tt) REVERT: H 218 CYS cc_start: 0.9429 (t) cc_final: 0.8993 (p) REVERT: I 33 ARG cc_start: 0.7600 (ttt180) cc_final: 0.7026 (ttt180) REVERT: I 52 PHE cc_start: 0.5473 (t80) cc_final: 0.4444 (t80) REVERT: I 77 PHE cc_start: 0.9073 (OUTLIER) cc_final: 0.8804 (m-80) REVERT: I 187 TYR cc_start: 0.6966 (m-80) cc_final: 0.6651 (m-10) REVERT: I 216 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8161 (pp) REVERT: I 224 MET cc_start: 0.8837 (mmm) cc_final: 0.7810 (tmm) REVERT: J 23 LYS cc_start: 0.8843 (ptmt) cc_final: 0.8519 (ptmm) REVERT: J 51 ARG cc_start: 0.8449 (tpt170) cc_final: 0.8172 (tpt170) REVERT: J 157 PHE cc_start: 0.9148 (OUTLIER) cc_final: 0.8840 (t80) REVERT: J 202 TRP cc_start: 0.8086 (t60) cc_final: 0.7486 (t60) outliers start: 101 outliers final: 77 residues processed: 487 average time/residue: 0.2577 time to fit residues: 187.9400 Evaluate side-chains 522 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 434 time to evaluate : 1.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 11 ILE Chi-restraints excluded: chain D residue 52 PHE Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 54 CYS Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 224 MET Chi-restraints excluded: chain B residue 12 ILE Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 146 HIS Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain C residue 12 ILE Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 77 PHE Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 98 HIS Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 11 ILE Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 61 CYS Chi-restraints excluded: chain E residue 74 HIS Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 149 LEU Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 54 CYS Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain F residue 74 HIS Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 4 VAL Chi-restraints excluded: chain G residue 14 LEU Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 78 TRP Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 144 ILE Chi-restraints excluded: chain G residue 154 GLU Chi-restraints excluded: chain G residue 207 LEU Chi-restraints excluded: chain G residue 215 ASP Chi-restraints excluded: chain G residue 224 MET Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 50 GLU Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 146 HIS Chi-restraints excluded: chain H residue 161 HIS Chi-restraints excluded: chain H residue 184 VAL Chi-restraints excluded: chain H residue 215 ASP Chi-restraints excluded: chain H residue 223 ARG Chi-restraints excluded: chain I residue 13 THR Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 69 PHE Chi-restraints excluded: chain I residue 77 PHE Chi-restraints excluded: chain I residue 98 HIS Chi-restraints excluded: chain I residue 161 HIS Chi-restraints excluded: chain I residue 198 MET Chi-restraints excluded: chain I residue 199 LEU Chi-restraints excluded: chain I residue 211 LEU Chi-restraints excluded: chain I residue 213 LEU Chi-restraints excluded: chain I residue 216 LEU Chi-restraints excluded: chain J residue 10 LEU Chi-restraints excluded: chain J residue 11 ILE Chi-restraints excluded: chain J residue 53 VAL Chi-restraints excluded: chain J residue 72 VAL Chi-restraints excluded: chain J residue 74 HIS Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 87 LEU Chi-restraints excluded: chain J residue 91 VAL Chi-restraints excluded: chain J residue 148 LEU Chi-restraints excluded: chain J residue 150 ARG Chi-restraints excluded: chain J residue 157 PHE Chi-restraints excluded: chain J residue 207 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 63 optimal weight: 0.0040 chunk 195 optimal weight: 2.9990 chunk 104 optimal weight: 0.6980 chunk 159 optimal weight: 5.9990 chunk 154 optimal weight: 6.9990 chunk 189 optimal weight: 10.0000 chunk 89 optimal weight: 0.4980 chunk 2 optimal weight: 0.4980 chunk 145 optimal weight: 4.9990 chunk 148 optimal weight: 0.6980 chunk 134 optimal weight: 1.9990 overall best weight: 0.4792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 146 HIS ** A 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 46 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.137427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.109701 restraints weight = 45631.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.113907 restraints weight = 29837.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.117063 restraints weight = 21469.390| |-----------------------------------------------------------------------------| r_work (final): 0.3961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6915 moved from start: 0.7336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16163 Z= 0.136 Angle : 0.917 15.634 21986 Z= 0.410 Chirality : 0.047 0.433 2610 Planarity : 0.006 0.104 2700 Dihedral : 5.348 44.313 2190 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 14.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 4.86 % Allowed : 32.89 % Favored : 62.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 9.09 % 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: 0.16 (0.20), residues: 1970 helix: 0.64 (0.15), residues: 1320 sheet: 0.33 (0.50), residues: 100 loop : -1.07 (0.29), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP J 78 HIS 0.009 0.001 HIS H 161 PHE 0.020 0.001 PHE B 77 TYR 0.020 0.001 TYR J 143 ARG 0.009 0.001 ARG A 76 Details of bonding type rmsd hydrogen bonds : bond 0.03795 ( 950) hydrogen bonds : angle 4.24348 ( 2820) SS BOND : bond 0.00445 ( 3) SS BOND : angle 1.28294 ( 6) covalent geometry : bond 0.00303 (16160) covalent geometry : angle 0.91673 (21980) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 527 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 443 time to evaluate : 1.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 28 LEU cc_start: 0.9426 (mm) cc_final: 0.9069 (mm) REVERT: D 34 MET cc_start: 0.8641 (mmm) cc_final: 0.8345 (mmm) REVERT: D 39 LEU cc_start: 0.9483 (mt) cc_final: 0.9011 (tp) REVERT: D 42 ARG cc_start: 0.9180 (tpt90) cc_final: 0.8749 (ttt180) REVERT: D 46 GLN cc_start: 0.9436 (tm-30) cc_final: 0.9081 (mm-40) REVERT: D 78 TRP cc_start: 0.6856 (m-10) cc_final: 0.5559 (m-90) REVERT: D 86 LEU cc_start: 0.9270 (mm) cc_final: 0.9014 (mm) REVERT: D 211 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8384 (tt) REVERT: D 215 ASP cc_start: 0.8417 (OUTLIER) cc_final: 0.7689 (m-30) REVERT: A 20 MET cc_start: 0.6609 (mtp) cc_final: 0.5738 (mmt) REVERT: A 77 PHE cc_start: 0.8554 (t80) cc_final: 0.8243 (t80) REVERT: A 78 TRP cc_start: 0.8757 (m-10) cc_final: 0.8247 (m-90) REVERT: A 185 ASP cc_start: 0.9019 (p0) cc_final: 0.7947 (t0) REVERT: A 198 MET cc_start: 0.7925 (ptt) cc_final: 0.7089 (tpt) REVERT: B 33 ARG cc_start: 0.8484 (ttt180) cc_final: 0.7867 (ttm-80) REVERT: B 46 GLN cc_start: 0.9291 (pp30) cc_final: 0.8336 (pt0) REVERT: B 47 ASP cc_start: 0.8524 (p0) cc_final: 0.7950 (p0) REVERT: B 193 GLU cc_start: 0.9663 (mm-30) cc_final: 0.9342 (mm-30) REVERT: C 12 ILE cc_start: 0.9229 (OUTLIER) cc_final: 0.8970 (tp) REVERT: C 77 PHE cc_start: 0.8771 (OUTLIER) cc_final: 0.8510 (m-80) REVERT: E 20 MET cc_start: 0.4637 (ttm) cc_final: 0.4292 (tpp) REVERT: E 23 LYS cc_start: 0.8688 (ptpt) cc_final: 0.8330 (pttt) REVERT: E 34 MET cc_start: 0.7801 (mmp) cc_final: 0.6716 (tmm) REVERT: E 39 LEU cc_start: 0.9702 (OUTLIER) cc_final: 0.9386 (pp) REVERT: E 54 CYS cc_start: 0.8264 (p) cc_final: 0.7597 (p) REVERT: E 81 GLN cc_start: 0.8983 (pt0) cc_final: 0.8719 (pt0) REVERT: E 87 LEU cc_start: 0.9212 (tt) cc_final: 0.8574 (mt) REVERT: E 98 HIS cc_start: 0.9479 (t70) cc_final: 0.9019 (t-170) REVERT: E 202 TRP cc_start: 0.8148 (t60) cc_final: 0.7749 (t60) REVERT: F 34 MET cc_start: 0.9201 (tpp) cc_final: 0.8280 (mmm) REVERT: F 39 LEU cc_start: 0.9548 (mt) cc_final: 0.9126 (tp) REVERT: F 42 ARG cc_start: 0.9252 (tpt90) cc_final: 0.8938 (tpt90) REVERT: F 86 LEU cc_start: 0.9535 (mm) cc_final: 0.9209 (mm) REVERT: F 147 LEU cc_start: 0.8519 (mt) cc_final: 0.8289 (mt) REVERT: G 20 MET cc_start: 0.6287 (ppp) cc_final: 0.5814 (tpt) REVERT: G 23 LYS cc_start: 0.8830 (mppt) cc_final: 0.8314 (mttt) REVERT: G 35 LEU cc_start: 0.9412 (tp) cc_final: 0.9193 (mm) REVERT: G 52 PHE cc_start: 0.6634 (t80) cc_final: 0.5945 (t80) REVERT: G 77 PHE cc_start: 0.8748 (t80) cc_final: 0.8317 (t80) REVERT: G 78 TRP cc_start: 0.9283 (m-90) cc_final: 0.9032 (m-90) REVERT: G 153 LEU cc_start: 0.9415 (mt) cc_final: 0.9165 (pp) REVERT: G 157 PHE cc_start: 0.8831 (m-80) cc_final: 0.8441 (m-80) REVERT: G 224 MET cc_start: 0.5174 (OUTLIER) cc_final: 0.3956 (ptt) REVERT: G 226 ARG cc_start: 0.7769 (ptp-170) cc_final: 0.7423 (ptp-170) REVERT: H 33 ARG cc_start: 0.8984 (ttt180) cc_final: 0.8402 (ttm-80) REVERT: H 76 ARG cc_start: 0.6860 (ppt170) cc_final: 0.6548 (ptm160) REVERT: H 198 MET cc_start: 0.9140 (tmm) cc_final: 0.8587 (ppp) REVERT: H 201 LEU cc_start: 0.9629 (mp) cc_final: 0.9214 (tt) REVERT: H 218 CYS cc_start: 0.9352 (t) cc_final: 0.8919 (p) REVERT: I 33 ARG cc_start: 0.7567 (ttt180) cc_final: 0.6997 (ttt180) REVERT: I 52 PHE cc_start: 0.5474 (t80) cc_final: 0.4382 (t80) REVERT: I 77 PHE cc_start: 0.9051 (OUTLIER) cc_final: 0.8796 (m-80) REVERT: I 187 TYR cc_start: 0.6855 (m-80) cc_final: 0.6580 (m-10) REVERT: I 216 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8156 (pp) REVERT: I 224 MET cc_start: 0.8783 (mmm) cc_final: 0.7829 (tmm) REVERT: J 23 LYS cc_start: 0.8785 (ptmt) cc_final: 0.8544 (ptmm) REVERT: J 51 ARG cc_start: 0.8418 (tpt170) cc_final: 0.8072 (tpt170) REVERT: J 157 PHE cc_start: 0.9156 (OUTLIER) cc_final: 0.8860 (t80) REVERT: J 202 TRP cc_start: 0.8009 (t60) cc_final: 0.7470 (t60) outliers start: 84 outliers final: 69 residues processed: 482 average time/residue: 0.2536 time to fit residues: 182.7795 Evaluate side-chains 511 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 433 time to evaluate : 1.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 11 ILE Chi-restraints excluded: chain D residue 54 CYS Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 215 ASP Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 224 MET Chi-restraints excluded: chain B residue 12 ILE Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 146 HIS Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain C residue 12 ILE Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 77 PHE Chi-restraints excluded: chain C residue 98 HIS Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 11 ILE Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 74 HIS Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 149 LEU Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain F residue 74 HIS Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain G residue 4 VAL Chi-restraints excluded: chain G residue 14 LEU Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 154 GLU Chi-restraints excluded: chain G residue 224 MET Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 50 GLU Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 146 HIS Chi-restraints excluded: chain H residue 161 HIS Chi-restraints excluded: chain H residue 215 ASP Chi-restraints excluded: chain H residue 223 ARG Chi-restraints excluded: chain I residue 10 LEU Chi-restraints excluded: chain I residue 13 THR Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 69 PHE Chi-restraints excluded: chain I residue 77 PHE Chi-restraints excluded: chain I residue 98 HIS Chi-restraints excluded: chain I residue 161 HIS Chi-restraints excluded: chain I residue 198 MET Chi-restraints excluded: chain I residue 199 LEU Chi-restraints excluded: chain I residue 211 LEU Chi-restraints excluded: chain I residue 213 LEU Chi-restraints excluded: chain I residue 216 LEU Chi-restraints excluded: chain J residue 10 LEU Chi-restraints excluded: chain J residue 11 ILE Chi-restraints excluded: chain J residue 72 VAL Chi-restraints excluded: chain J residue 74 HIS Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 87 LEU Chi-restraints excluded: chain J residue 146 HIS Chi-restraints excluded: chain J residue 148 LEU Chi-restraints excluded: chain J residue 150 ARG Chi-restraints excluded: chain J residue 157 PHE Chi-restraints excluded: chain J residue 207 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 120 optimal weight: 3.9990 chunk 40 optimal weight: 0.1980 chunk 130 optimal weight: 20.0000 chunk 36 optimal weight: 5.9990 chunk 7 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 chunk 54 optimal weight: 0.7980 chunk 186 optimal weight: 5.9990 chunk 148 optimal weight: 0.9980 chunk 138 optimal weight: 0.7980 chunk 117 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 146 HIS ** A 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 74 HIS ** E 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 49 GLN ** G 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 161 HIS J 46 GLN ** J 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.137188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.109671 restraints weight = 45749.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.113864 restraints weight = 29988.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.116942 restraints weight = 21696.642| |-----------------------------------------------------------------------------| r_work (final): 0.3962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6927 moved from start: 0.7547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16163 Z= 0.137 Angle : 0.921 16.901 21986 Z= 0.413 Chirality : 0.047 0.415 2610 Planarity : 0.006 0.105 2700 Dihedral : 5.260 44.138 2190 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 14.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 4.86 % Allowed : 33.41 % Favored : 61.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 9.09 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.20), residues: 1970 helix: 0.60 (0.15), residues: 1340 sheet: 0.31 (0.51), residues: 100 loop : -1.52 (0.28), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP F 78 HIS 0.011 0.001 HIS D 146 PHE 0.021 0.001 PHE H 77 TYR 0.019 0.001 TYR J 143 ARG 0.008 0.001 ARG G 76 Details of bonding type rmsd hydrogen bonds : bond 0.03699 ( 950) hydrogen bonds : angle 4.23619 ( 2820) SS BOND : bond 0.00363 ( 3) SS BOND : angle 1.22030 ( 6) covalent geometry : bond 0.00305 (16160) covalent geometry : angle 0.92083 (21980) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6981.69 seconds wall clock time: 124 minutes 2.95 seconds (7442.95 seconds total)