Starting phenix.real_space_refine on Tue Dec 31 13:10:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gnb_34159/12_2024/8gnb_34159.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gnb_34159/12_2024/8gnb_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_34159/12_2024/8gnb_34159.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gnb_34159/12_2024/8gnb_34159.map" model { file = "/net/cci-nas-00/data/ceres_data/8gnb_34159/12_2024/8gnb_34159.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gnb_34159/12_2024/8gnb_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-5532/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: 5.16, per 1000 atoms: 0.33 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: 4.01 Conformation dependent library (CDL) restraints added in 2.1 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: 1.49 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: 4.42 Time building geometry restraints manager: 4.59 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' 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: 10.320 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: 0.000 Extract box with map and model: 0.230 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 31.100 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.500 ------------------------------------------------------------------------------- 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 16160 Z= 0.228 Angle : 0.937 6.765 21980 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 *********************** 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 : 1.740 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: 0.3062 time to fit residues: 354.4695 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 : 1.894 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6767 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 16160 Z= 0.247 Angle : 0.881 13.228 21980 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 *********************** 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 : 1.897 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 21 VAL cc_start: 0.8288 (t) cc_final: 0.8085 (t) REVERT: D 28 LEU cc_start: 0.9023 (mm) cc_final: 0.8746 (mm) REVERT: D 78 TRP cc_start: 0.7575 (m-10) cc_final: 0.6149 (m-90) REVERT: D 147 LEU cc_start: 0.8945 (mt) cc_final: 0.8712 (mt) REVERT: D 201 LEU cc_start: 0.9270 (OUTLIER) cc_final: 0.9070 (pp) REVERT: D 215 ASP cc_start: 0.7885 (m-30) cc_final: 0.7536 (m-30) REVERT: A 55 ASN cc_start: 0.8639 (p0) cc_final: 0.7804 (t0) REVERT: A 92 PHE cc_start: 0.8160 (t80) cc_final: 0.7748 (t80) REVERT: A 185 ASP cc_start: 0.7950 (p0) cc_final: 0.7657 (t0) REVERT: C 7 LEU cc_start: 0.9070 (mm) cc_final: 0.8553 (mp) REVERT: C 10 LEU cc_start: 0.8179 (tp) cc_final: 0.7970 (tp) REVERT: C 12 ILE cc_start: 0.8780 (mp) cc_final: 0.8407 (tp) REVERT: C 49 GLN cc_start: 0.8082 (mm110) cc_final: 0.7763 (mm110) REVERT: C 153 LEU cc_start: 0.8173 (mt) cc_final: 0.7882 (mt) REVERT: C 196 LEU cc_start: 0.9304 (mm) cc_final: 0.8882 (tt) REVERT: E 15 ASN cc_start: 0.8401 (t0) cc_final: 0.7789 (p0) REVERT: E 20 MET cc_start: 0.3755 (OUTLIER) cc_final: 0.3379 (mtp) REVERT: E 23 LYS cc_start: 0.9076 (ptpt) cc_final: 0.8347 (ptpp) REVERT: E 28 LEU cc_start: 0.9121 (mm) cc_final: 0.8625 (mm) REVERT: E 161 HIS cc_start: 0.9084 (t-90) cc_final: 0.8665 (t70) REVERT: E 202 TRP cc_start: 0.7642 (t60) cc_final: 0.7206 (t60) REVERT: F 20 MET cc_start: 0.7981 (ppp) cc_final: 0.7604 (ppp) REVERT: F 24 LEU cc_start: 0.8754 (mp) cc_final: 0.8532 (tt) REVERT: F 39 LEU cc_start: 0.9385 (mt) cc_final: 0.9057 (tp) REVERT: F 74 HIS cc_start: 0.7853 (OUTLIER) cc_final: 0.7582 (p-80) REVERT: F 147 LEU cc_start: 0.8644 (mt) cc_final: 0.8419 (mt) REVERT: G 52 PHE cc_start: 0.5357 (t80) cc_final: 0.4872 (t80) REVERT: G 153 LEU cc_start: 0.8988 (mt) cc_final: 0.8745 (mt) REVERT: G 157 PHE cc_start: 0.7876 (m-80) cc_final: 0.7603 (m-80) REVERT: H 5 ASP cc_start: 0.7826 (p0) cc_final: 0.7553 (p0) REVERT: H 21 VAL cc_start: 0.8753 (m) cc_final: 0.8523 (p) REVERT: H 201 LEU cc_start: 0.9299 (mm) cc_final: 0.8936 (tt) REVERT: I 21 VAL cc_start: 0.8328 (t) cc_final: 0.8105 (t) REVERT: I 52 PHE cc_start: 0.4164 (t80) cc_final: 0.3692 (t80) REVERT: I 77 PHE cc_start: 0.8476 (OUTLIER) cc_final: 0.8186 (t80) REVERT: I 103 LEU cc_start: 0.9420 (mt) cc_final: 0.9158 (pp) REVERT: I 153 LEU cc_start: 0.8423 (mt) cc_final: 0.8068 (mt) REVERT: I 198 MET cc_start: 0.8170 (ptt) cc_final: 0.7770 (ptt) REVERT: J 20 MET cc_start: 0.3408 (OUTLIER) cc_final: 0.2673 (mmt) REVERT: J 23 LYS cc_start: 0.9163 (ptmt) cc_final: 0.8776 (ptmm) REVERT: J 81 GLN cc_start: 0.8731 (pt0) cc_final: 0.8175 (pt0) REVERT: J 162 TYR cc_start: 0.7775 (t80) cc_final: 0.7457 (t80) REVERT: J 202 TRP cc_start: 0.7600 (t60) cc_final: 0.7087 (t60) outliers start: 86 outliers final: 52 residues processed: 643 average time/residue: 0.2833 time to fit residues: 266.1352 Evaluate side-chains 525 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 468 time to evaluate : 1.898 ------------------------------------------------------------------------------- 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 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 100 optimal weight: 8.9990 chunk 56 optimal weight: 10.0000 chunk 151 optimal weight: 4.9990 chunk 123 optimal weight: 0.6980 chunk 50 optimal weight: 0.4980 chunk 181 optimal weight: 6.9990 chunk 196 optimal weight: 0.6980 chunk 162 optimal weight: 0.9980 chunk 180 optimal weight: 0.8980 chunk 62 optimal weight: 4.9990 chunk 145 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 74 HIS C 17 ASN F 146 HIS ** G 81 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 74 HIS H 98 HIS J 146 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6787 moved from start: 0.5182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16160 Z= 0.217 Angle : 0.856 14.082 21980 Z= 0.402 Chirality : 0.045 0.243 2610 Planarity : 0.007 0.098 2700 Dihedral : 5.820 50.278 2190 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 16.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 5.61 % Allowed : 24.97 % Favored : 69.42 % 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: -0.53 (0.19), residues: 1970 helix: 0.23 (0.15), residues: 1290 sheet: 1.01 (0.48), residues: 100 loop : -1.78 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 202 HIS 0.015 0.001 HIS G 161 PHE 0.045 0.002 PHE C 209 TYR 0.024 0.002 TYR J 143 ARG 0.008 0.001 ARG G 76 *********************** 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 618 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 521 time to evaluate : 1.861 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 21 VAL cc_start: 0.8404 (t) cc_final: 0.8175 (t) REVERT: D 28 LEU cc_start: 0.9034 (mm) cc_final: 0.8733 (mm) REVERT: D 39 LEU cc_start: 0.9408 (mt) cc_final: 0.9011 (tp) REVERT: D 78 TRP cc_start: 0.7461 (m-10) cc_final: 0.6094 (m-90) REVERT: D 201 LEU cc_start: 0.9266 (OUTLIER) cc_final: 0.9027 (pp) REVERT: D 215 ASP cc_start: 0.7806 (m-30) cc_final: 0.7429 (m-30) REVERT: A 23 LYS cc_start: 0.8996 (mttp) cc_final: 0.8515 (mptt) REVERT: A 55 ASN cc_start: 0.8549 (p0) cc_final: 0.7794 (t0) REVERT: A 185 ASP cc_start: 0.7906 (p0) cc_final: 0.7653 (t0) REVERT: A 197 LEU cc_start: 0.8333 (tp) cc_final: 0.8083 (tt) REVERT: A 201 LEU cc_start: 0.8889 (mt) cc_final: 0.8473 (pp) REVERT: B 33 ARG cc_start: 0.7225 (ttt180) cc_final: 0.6954 (ttt90) REVERT: C 10 LEU cc_start: 0.8221 (tp) cc_final: 0.8015 (tp) REVERT: C 12 ILE cc_start: 0.8795 (mp) cc_final: 0.8452 (tp) REVERT: C 49 GLN cc_start: 0.8098 (mm110) cc_final: 0.7858 (mm110) REVERT: C 153 LEU cc_start: 0.8131 (mt) cc_final: 0.7800 (mt) REVERT: E 15 ASN cc_start: 0.8401 (t0) cc_final: 0.7793 (p0) REVERT: E 20 MET cc_start: 0.3613 (OUTLIER) cc_final: 0.3081 (mtp) REVERT: E 23 LYS cc_start: 0.9006 (ptpt) cc_final: 0.8183 (ptpp) REVERT: E 81 GLN cc_start: 0.8670 (pt0) cc_final: 0.8459 (pt0) REVERT: E 98 HIS cc_start: 0.8779 (t70) cc_final: 0.8551 (t-170) REVERT: E 149 LEU cc_start: 0.9354 (OUTLIER) cc_final: 0.9043 (tp) REVERT: E 161 HIS cc_start: 0.9032 (t-90) cc_final: 0.8674 (t70) REVERT: E 202 TRP cc_start: 0.7608 (t60) cc_final: 0.7110 (t60) REVERT: E 210 LEU cc_start: 0.8467 (tp) cc_final: 0.8058 (tt) REVERT: F 20 MET cc_start: 0.7985 (ppp) cc_final: 0.7626 (ppp) REVERT: F 24 LEU cc_start: 0.8697 (mp) cc_final: 0.8346 (tt) REVERT: F 28 LEU cc_start: 0.9166 (mm) cc_final: 0.8940 (mm) REVERT: F 39 LEU cc_start: 0.9392 (mt) cc_final: 0.9118 (tp) REVERT: F 147 LEU cc_start: 0.8576 (mt) cc_final: 0.8357 (mt) REVERT: G 30 MET cc_start: 0.8207 (tmm) cc_final: 0.7999 (tmm) REVERT: G 52 PHE cc_start: 0.5767 (t80) cc_final: 0.5203 (t80) REVERT: G 95 TYR cc_start: 0.7061 (t80) cc_final: 0.6513 (t80) REVERT: G 153 LEU cc_start: 0.8980 (mt) cc_final: 0.8706 (mt) REVERT: G 198 MET cc_start: 0.7043 (ptt) cc_final: 0.6720 (tpt) REVERT: H 5 ASP cc_start: 0.7492 (p0) cc_final: 0.7236 (p0) REVERT: H 33 ARG cc_start: 0.7720 (ttt180) cc_final: 0.7403 (ttt90) REVERT: H 34 MET cc_start: 0.8198 (mmm) cc_final: 0.7728 (mmm) REVERT: H 194 LYS cc_start: 0.9001 (mttp) cc_final: 0.8683 (mttp) REVERT: H 201 LEU cc_start: 0.9351 (mm) cc_final: 0.9076 (tt) REVERT: I 21 VAL cc_start: 0.8451 (t) cc_final: 0.8220 (t) REVERT: I 30 MET cc_start: 0.8744 (mmp) cc_final: 0.7530 (tpt) REVERT: I 52 PHE cc_start: 0.4147 (t80) cc_final: 0.3602 (t80) REVERT: I 103 LEU cc_start: 0.9456 (mt) cc_final: 0.9249 (pp) REVERT: I 146 HIS cc_start: 0.8307 (t-170) cc_final: 0.8058 (t-170) REVERT: J 20 MET cc_start: 0.3018 (OUTLIER) cc_final: 0.2641 (tpp) REVERT: J 23 LYS cc_start: 0.9066 (ptmt) cc_final: 0.8667 (ptmm) REVERT: J 77 PHE cc_start: 0.8356 (t80) cc_final: 0.8011 (t80) REVERT: J 202 TRP cc_start: 0.7507 (t60) cc_final: 0.6977 (t60) outliers start: 97 outliers final: 63 residues processed: 564 average time/residue: 0.2609 time to fit residues: 219.2923 Evaluate side-chains 534 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 467 time to evaluate : 1.771 ------------------------------------------------------------------------------- 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 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 57 LEU 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 175 CYS 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 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 211 LEU Chi-restraints excluded: chain C residue 213 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 87 LEU Chi-restraints excluded: chain E residue 149 LEU Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain G residue 15 ASN Chi-restraints excluded: chain G residue 106 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 215 ASP 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 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 87 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 179 optimal weight: 6.9990 chunk 136 optimal weight: 6.9990 chunk 94 optimal weight: 9.9990 chunk 20 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 chunk 122 optimal weight: 5.9990 chunk 182 optimal weight: 1.9990 chunk 193 optimal weight: 7.9990 chunk 95 optimal weight: 3.9990 chunk 173 optimal weight: 1.9990 chunk 52 optimal weight: 10.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 81 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: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7050 moved from start: 0.6315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 16160 Z= 0.332 Angle : 0.932 14.919 21980 Z= 0.465 Chirality : 0.047 0.193 2610 Planarity : 0.007 0.105 2700 Dihedral : 6.050 53.343 2190 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 22.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 9.13 % Allowed : 23.47 % Favored : 67.40 % 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: -0.73 (0.19), residues: 1970 helix: 0.10 (0.14), residues: 1290 sheet: 0.35 (0.48), residues: 100 loop : -1.79 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP G 78 HIS 0.010 0.002 HIS J 146 PHE 0.031 0.002 PHE C 209 TYR 0.030 0.003 TYR F 66 ARG 0.011 0.001 ARG E 33 *********************** 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 633 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 475 time to evaluate : 1.812 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: D 20 MET cc_start: 0.7978 (ppp) cc_final: 0.7702 (ppp) REVERT: D 28 LEU cc_start: 0.9209 (mm) cc_final: 0.8895 (mm) REVERT: D 39 LEU cc_start: 0.9459 (mt) cc_final: 0.9037 (tp) REVERT: D 78 TRP cc_start: 0.7549 (m-10) cc_final: 0.6214 (m-90) REVERT: D 201 LEU cc_start: 0.9312 (OUTLIER) cc_final: 0.8946 (pp) REVERT: A 30 MET cc_start: 0.8392 (tmm) cc_final: 0.8013 (tmm) REVERT: A 33 ARG cc_start: 0.8380 (tpt170) cc_final: 0.8066 (tpp80) REVERT: A 35 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8356 (mm) REVERT: A 198 MET cc_start: 0.6444 (ptt) cc_final: 0.5858 (tpt) REVERT: B 33 ARG cc_start: 0.7387 (ttt180) cc_final: 0.6931 (ttt90) REVERT: B 160 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8796 (mt) REVERT: C 12 ILE cc_start: 0.8973 (mp) cc_final: 0.8690 (tp) REVERT: C 157 PHE cc_start: 0.8985 (OUTLIER) cc_final: 0.8271 (t80) REVERT: E 20 MET cc_start: 0.3668 (OUTLIER) cc_final: 0.3155 (mtp) REVERT: E 23 LYS cc_start: 0.9077 (ptpt) cc_final: 0.8548 (ptpp) REVERT: E 81 GLN cc_start: 0.8727 (pt0) cc_final: 0.8105 (pt0) REVERT: E 87 LEU cc_start: 0.9105 (OUTLIER) cc_final: 0.8723 (mm) REVERT: E 98 HIS cc_start: 0.8773 (t70) cc_final: 0.8509 (t-170) REVERT: E 161 HIS cc_start: 0.9127 (t-90) cc_final: 0.8750 (t70) REVERT: E 202 TRP cc_start: 0.7748 (t60) cc_final: 0.7262 (t60) REVERT: F 39 LEU cc_start: 0.9466 (mt) cc_final: 0.9052 (tp) REVERT: G 23 LYS cc_start: 0.9040 (mttt) cc_final: 0.8566 (mmtm) REVERT: G 31 LEU cc_start: 0.9285 (mm) cc_final: 0.8992 (mm) REVERT: G 198 MET cc_start: 0.7267 (ptt) cc_final: 0.7065 (ptt) REVERT: G 226 ARG cc_start: 0.7999 (ptp-170) cc_final: 0.7705 (ptp-170) REVERT: H 33 ARG cc_start: 0.7980 (ttt180) cc_final: 0.7688 (ttt180) REVERT: I 30 MET cc_start: 0.8483 (mmp) cc_final: 0.8017 (mmp) REVERT: I 39 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.7050 (tt) REVERT: I 52 PHE cc_start: 0.4606 (t80) cc_final: 0.3922 (t80) REVERT: I 103 LEU cc_start: 0.9576 (mt) cc_final: 0.9368 (pp) REVERT: I 146 HIS cc_start: 0.8360 (t-170) cc_final: 0.8158 (t-170) REVERT: J 20 MET cc_start: 0.3381 (OUTLIER) cc_final: 0.3092 (mtp) REVERT: J 23 LYS cc_start: 0.9055 (ptmt) cc_final: 0.8593 (ptpp) REVERT: J 202 TRP cc_start: 0.7636 (t60) cc_final: 0.7042 (t60) outliers start: 158 outliers final: 116 residues processed: 560 average time/residue: 0.2661 time to fit residues: 221.8605 Evaluate side-chains 566 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 442 time to evaluate : 1.818 ------------------------------------------------------------------------------- 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 87 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 D residue 210 LEU Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 17 ASN Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 49 GLN 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 149 LEU Chi-restraints excluded: chain A residue 153 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 A residue 226 ARG Chi-restraints excluded: chain B residue 12 ILE Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 146 HIS Chi-restraints excluded: chain B residue 160 LEU 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 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 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 E residue 7 LEU Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 20 MET Chi-restraints excluded: chain E residue 30 MET Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 61 CYS 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 87 LEU Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 149 LEU Chi-restraints excluded: chain E residue 175 CYS Chi-restraints excluded: chain F residue 4 VAL 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 87 LEU Chi-restraints excluded: chain F residue 145 ILE Chi-restraints excluded: chain G residue 4 VAL Chi-restraints excluded: chain G residue 10 LEU 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 183 VAL 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 19 THR 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 192 THR Chi-restraints excluded: chain H residue 195 SER Chi-restraints excluded: chain H residue 199 LEU Chi-restraints excluded: chain H residue 215 ASP Chi-restraints excluded: chain H residue 216 LEU Chi-restraints excluded: chain I residue 19 THR Chi-restraints excluded: chain I residue 36 VAL 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 211 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 148 LEU Chi-restraints excluded: chain J residue 150 ARG Chi-restraints excluded: chain J residue 184 VAL Chi-restraints excluded: chain J residue 185 ASP Chi-restraints excluded: chain J residue 192 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 161 optimal weight: 0.0270 chunk 109 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 143 optimal weight: 4.9990 chunk 79 optimal weight: 0.9990 chunk 164 optimal weight: 2.9990 chunk 133 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 98 optimal weight: 1.9990 chunk 173 optimal weight: 0.9990 chunk 48 optimal weight: 0.8980 overall best weight: 0.7844 ------------------------------------------------------------------------------- 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** ** A 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 49 GLN A 74 HIS ** B 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 146 HIS ** G 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 81 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6931 moved from start: 0.6514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 16160 Z= 0.209 Angle : 0.855 13.285 21980 Z= 0.402 Chirality : 0.045 0.265 2610 Planarity : 0.007 0.099 2700 Dihedral : 5.741 49.096 2190 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 16.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 6.07 % Allowed : 28.96 % Favored : 64.97 % 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: -0.41 (0.19), residues: 1970 helix: 0.37 (0.14), residues: 1290 sheet: 0.44 (0.49), residues: 100 loop : -1.74 (0.27), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP A 78 HIS 0.008 0.001 HIS A 74 PHE 0.029 0.002 PHE C 209 TYR 0.026 0.002 TYR A 66 ARG 0.007 0.001 ARG A 76 *********************** 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 588 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 483 time to evaluate : 1.932 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: D 28 LEU cc_start: 0.9165 (mm) cc_final: 0.8822 (mm) REVERT: D 39 LEU cc_start: 0.9443 (mt) cc_final: 0.9023 (tp) REVERT: D 78 TRP cc_start: 0.7427 (m-10) cc_final: 0.6175 (m-90) REVERT: D 86 LEU cc_start: 0.9051 (mm) cc_final: 0.8818 (mm) REVERT: D 201 LEU cc_start: 0.9263 (OUTLIER) cc_final: 0.8907 (pp) REVERT: D 211 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8282 (tt) REVERT: D 215 ASP cc_start: 0.7676 (m-30) cc_final: 0.7049 (m-30) REVERT: A 20 MET cc_start: 0.5439 (mtp) cc_final: 0.5153 (mmt) REVERT: A 30 MET cc_start: 0.8345 (tmm) cc_final: 0.7976 (tmm) REVERT: A 35 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8392 (mm) REVERT: A 55 ASN cc_start: 0.8469 (p0) cc_final: 0.7795 (t0) REVERT: B 34 MET cc_start: 0.7411 (mmm) cc_final: 0.7201 (mpp) REVERT: B 86 LEU cc_start: 0.8842 (mt) cc_final: 0.8590 (mt) REVERT: B 160 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8723 (mt) REVERT: C 12 ILE cc_start: 0.8936 (mp) cc_final: 0.8637 (tp) REVERT: E 20 MET cc_start: 0.3120 (OUTLIER) cc_final: 0.2737 (mtp) REVERT: E 23 LYS cc_start: 0.8966 (ptpt) cc_final: 0.8470 (pttp) REVERT: E 34 MET cc_start: 0.7245 (mmp) cc_final: 0.6907 (tmm) REVERT: E 51 ARG cc_start: 0.7598 (tpt170) cc_final: 0.7373 (tpt170) REVERT: E 81 GLN cc_start: 0.8558 (pt0) cc_final: 0.8278 (pt0) REVERT: E 98 HIS cc_start: 0.8735 (t70) cc_final: 0.8529 (t-170) REVERT: E 161 HIS cc_start: 0.8955 (t-90) cc_final: 0.8688 (t70) REVERT: E 202 TRP cc_start: 0.7495 (t60) cc_final: 0.7077 (t60) REVERT: F 39 LEU cc_start: 0.9465 (mt) cc_final: 0.9081 (tp) REVERT: F 86 LEU cc_start: 0.9345 (mm) cc_final: 0.9129 (mm) REVERT: G 23 LYS cc_start: 0.9102 (mttt) cc_final: 0.8612 (mmtm) REVERT: G 52 PHE cc_start: 0.6195 (t80) cc_final: 0.5533 (t80) REVERT: G 224 MET cc_start: 0.4727 (OUTLIER) cc_final: 0.4235 (mmp) REVERT: H 34 MET cc_start: 0.7941 (mmm) cc_final: 0.7324 (mmm) REVERT: H 76 ARG cc_start: 0.6456 (ppt170) cc_final: 0.6127 (ptm160) REVERT: I 30 MET cc_start: 0.8270 (mmp) cc_final: 0.7754 (mmp) REVERT: I 52 PHE cc_start: 0.4581 (t80) cc_final: 0.3920 (t80) REVERT: I 146 HIS cc_start: 0.8283 (t-170) cc_final: 0.8061 (t-170) REVERT: J 23 LYS cc_start: 0.8957 (ptmt) cc_final: 0.8541 (ptmm) REVERT: J 81 GLN cc_start: 0.8831 (pp30) cc_final: 0.8517 (pp30) REVERT: J 202 TRP cc_start: 0.7458 (t60) cc_final: 0.6843 (t60) outliers start: 105 outliers final: 76 residues processed: 532 average time/residue: 0.2671 time to fit residues: 212.6632 Evaluate side-chains 531 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 449 time to evaluate : 1.871 ------------------------------------------------------------------------------- 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 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 35 LEU Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 149 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 A residue 226 ARG 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 160 LEU Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain C residue 64 VAL 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 211 LEU Chi-restraints excluded: chain C residue 213 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 136 VAL Chi-restraints excluded: chain F residue 4 VAL 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 F residue 187 TYR 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 215 ASP 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 61 CYS 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 199 LEU Chi-restraints excluded: chain H residue 215 ASP Chi-restraints excluded: chain I residue 13 THR Chi-restraints excluded: chain I residue 19 THR Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain I residue 39 LEU 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 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 150 ARG Chi-restraints excluded: chain J residue 216 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 65 optimal weight: 9.9990 chunk 174 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 chunk 113 optimal weight: 0.3980 chunk 47 optimal weight: 0.7980 chunk 193 optimal weight: 0.7980 chunk 160 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 16 optimal weight: 4.9990 chunk 64 optimal weight: 0.9980 chunk 101 optimal weight: 0.0270 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 49 GLN ** D 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 58 GLN A 74 HIS B 74 HIS E 15 ASN ** G 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 81 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6906 moved from start: 0.6773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16160 Z= 0.199 Angle : 0.881 14.982 21980 Z= 0.403 Chirality : 0.046 0.320 2610 Planarity : 0.007 0.104 2700 Dihedral : 5.630 47.463 2190 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 15.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 6.18 % Allowed : 29.31 % 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: -0.33 (0.19), residues: 1970 helix: 0.43 (0.15), residues: 1290 sheet: 0.50 (0.49), residues: 100 loop : -1.71 (0.27), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP A 78 HIS 0.006 0.001 HIS B 74 PHE 0.027 0.002 PHE D 173 TYR 0.021 0.001 TYR A 66 ARG 0.007 0.001 ARG G 76 *********************** 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 577 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 470 time to evaluate : 2.024 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: D 28 LEU cc_start: 0.9171 (mm) cc_final: 0.8853 (mm) REVERT: D 34 MET cc_start: 0.8262 (mmm) cc_final: 0.8037 (mmm) REVERT: D 39 LEU cc_start: 0.9425 (mt) cc_final: 0.8973 (tp) REVERT: D 78 TRP cc_start: 0.7345 (m-10) cc_final: 0.6128 (m-90) REVERT: D 86 LEU cc_start: 0.9070 (mm) cc_final: 0.8827 (mm) REVERT: D 201 LEU cc_start: 0.9228 (OUTLIER) cc_final: 0.8907 (pp) REVERT: D 211 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8300 (tt) REVERT: D 215 ASP cc_start: 0.7589 (m-30) cc_final: 0.7261 (m-30) REVERT: A 20 MET cc_start: 0.5635 (mtp) cc_final: 0.5290 (mmm) REVERT: A 55 ASN cc_start: 0.8383 (p0) cc_final: 0.7829 (t0) REVERT: A 64 VAL cc_start: 0.7893 (OUTLIER) cc_final: 0.7347 (t) REVERT: B 78 TRP cc_start: 0.9045 (m-10) cc_final: 0.8607 (m-90) REVERT: B 160 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8682 (mt) REVERT: B 193 GLU cc_start: 0.8500 (mm-30) cc_final: 0.8246 (mm-30) REVERT: C 12 ILE cc_start: 0.8931 (mp) cc_final: 0.8627 (tp) REVERT: C 34 MET cc_start: 0.7339 (OUTLIER) cc_final: 0.7132 (pmm) REVERT: C 207 LEU cc_start: 0.9026 (mm) cc_final: 0.8764 (mp) REVERT: E 20 MET cc_start: 0.3037 (OUTLIER) cc_final: 0.2774 (mtp) REVERT: E 23 LYS cc_start: 0.8917 (ptpt) cc_final: 0.8405 (pttm) REVERT: E 34 MET cc_start: 0.7198 (mmp) cc_final: 0.6897 (tmm) REVERT: E 81 GLN cc_start: 0.8542 (pt0) cc_final: 0.8271 (pt0) REVERT: E 98 HIS cc_start: 0.8762 (t70) cc_final: 0.8526 (t-170) REVERT: E 202 TRP cc_start: 0.7497 (t60) cc_final: 0.6987 (t60) REVERT: E 210 LEU cc_start: 0.8544 (tp) cc_final: 0.8152 (tt) REVERT: F 39 LEU cc_start: 0.9452 (mt) cc_final: 0.9057 (tp) REVERT: F 86 LEU cc_start: 0.9352 (mm) cc_final: 0.9122 (mm) REVERT: G 20 MET cc_start: 0.4461 (mmt) cc_final: 0.3350 (mmt) REVERT: G 23 LYS cc_start: 0.9134 (mttt) cc_final: 0.8404 (mptt) REVERT: G 31 LEU cc_start: 0.9248 (mm) cc_final: 0.8975 (mm) REVERT: G 52 PHE cc_start: 0.6225 (t80) cc_final: 0.5519 (t80) REVERT: G 224 MET cc_start: 0.4418 (OUTLIER) cc_final: 0.3425 (ptm) REVERT: H 76 ARG cc_start: 0.6401 (ppt170) cc_final: 0.6076 (ptm160) REVERT: H 194 LYS cc_start: 0.8886 (mttp) cc_final: 0.8618 (mttt) REVERT: I 30 MET cc_start: 0.8240 (mmp) cc_final: 0.7708 (mmp) REVERT: I 52 PHE cc_start: 0.4525 (t80) cc_final: 0.3908 (t80) REVERT: I 146 HIS cc_start: 0.8270 (t-170) cc_final: 0.8034 (t-170) REVERT: J 23 LYS cc_start: 0.8927 (ptmt) cc_final: 0.8563 (ptmm) REVERT: J 81 GLN cc_start: 0.8777 (pp30) cc_final: 0.8336 (pp30) REVERT: J 202 TRP cc_start: 0.7464 (t60) cc_final: 0.6780 (t60) outliers start: 107 outliers final: 75 residues processed: 537 average time/residue: 0.2616 time to fit residues: 211.2205 Evaluate side-chains 527 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 445 time to evaluate : 1.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 11 ILE 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 196 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 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 149 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 A residue 226 ARG 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 160 LEU 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 34 MET 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 144 ILE Chi-restraints excluded: chain C residue 199 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 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 136 VAL Chi-restraints excluded: chain F residue 4 VAL 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 F residue 187 TYR Chi-restraints excluded: chain G residue 4 VAL Chi-restraints excluded: chain G residue 11 ILE 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 19 THR 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 I residue 13 THR Chi-restraints excluded: chain I residue 36 VAL 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 161 HIS Chi-restraints excluded: chain I residue 198 MET Chi-restraints excluded: chain I residue 199 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 87 LEU Chi-restraints excluded: chain J residue 91 VAL Chi-restraints excluded: chain J residue 150 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 186 optimal weight: 0.5980 chunk 21 optimal weight: 2.9990 chunk 110 optimal weight: 9.9990 chunk 141 optimal weight: 0.2980 chunk 109 optimal weight: 0.7980 chunk 162 optimal weight: 9.9990 chunk 108 optimal weight: 1.9990 chunk 192 optimal weight: 2.9990 chunk 120 optimal weight: 6.9990 chunk 117 optimal weight: 0.9980 chunk 88 optimal weight: 6.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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** B 17 ASN ** B 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 81 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** ** I 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6926 moved from start: 0.7061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16160 Z= 0.205 Angle : 0.896 15.633 21980 Z= 0.410 Chirality : 0.047 0.364 2610 Planarity : 0.007 0.103 2700 Dihedral : 5.519 45.626 2190 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 16.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 6.30 % Allowed : 31.04 % Favored : 62.66 % 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: -0.27 (0.19), residues: 1970 helix: 0.52 (0.15), residues: 1290 sheet: 0.42 (0.50), residues: 100 loop : -1.78 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 78 HIS 0.006 0.001 HIS B 74 PHE 0.025 0.001 PHE D 173 TYR 0.019 0.001 TYR F 66 ARG 0.010 0.001 ARG H 33 *********************** 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 576 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 467 time to evaluate : 1.849 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: 0.9243 (mm) cc_final: 0.8919 (mm) REVERT: D 34 MET cc_start: 0.8395 (mmm) cc_final: 0.8143 (mmm) REVERT: D 39 LEU cc_start: 0.9405 (mt) cc_final: 0.8913 (tp) REVERT: D 86 LEU cc_start: 0.9112 (mm) cc_final: 0.8888 (mm) REVERT: D 211 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8262 (tt) REVERT: D 215 ASP cc_start: 0.7655 (m-30) cc_final: 0.7294 (m-30) REVERT: A 15 ASN cc_start: 0.8109 (t0) cc_final: 0.7903 (m110) REVERT: A 35 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8484 (mm) REVERT: A 55 ASN cc_start: 0.8450 (p0) cc_final: 0.7915 (t0) REVERT: A 64 VAL cc_start: 0.8008 (OUTLIER) cc_final: 0.7485 (t) REVERT: B 78 TRP cc_start: 0.9068 (m-10) cc_final: 0.8827 (m-90) REVERT: B 160 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8683 (mt) REVERT: B 193 GLU cc_start: 0.8518 (mm-30) cc_final: 0.8272 (mm-30) REVERT: C 12 ILE cc_start: 0.8891 (mp) cc_final: 0.8579 (tp) REVERT: E 20 MET cc_start: 0.3071 (OUTLIER) cc_final: 0.2797 (mtp) REVERT: E 23 LYS cc_start: 0.8938 (ptpt) cc_final: 0.8426 (pttm) REVERT: E 34 MET cc_start: 0.7200 (mmp) cc_final: 0.6812 (tmm) REVERT: E 81 GLN cc_start: 0.8620 (pt0) cc_final: 0.8354 (pt0) REVERT: E 87 LEU cc_start: 0.9050 (tt) cc_final: 0.8527 (mm) REVERT: E 98 HIS cc_start: 0.8727 (t70) cc_final: 0.8484 (t-170) REVERT: E 202 TRP cc_start: 0.7484 (t60) cc_final: 0.6916 (t60) REVERT: F 34 MET cc_start: 0.8914 (mmm) cc_final: 0.8643 (tpp) REVERT: F 39 LEU cc_start: 0.9454 (mt) cc_final: 0.9013 (tp) REVERT: F 86 LEU cc_start: 0.9311 (mm) cc_final: 0.9060 (mm) REVERT: G 23 LYS cc_start: 0.9144 (mttt) cc_final: 0.8650 (mmtm) REVERT: G 30 MET cc_start: 0.8428 (tmm) cc_final: 0.8196 (tmm) REVERT: G 31 LEU cc_start: 0.9258 (OUTLIER) cc_final: 0.8940 (mm) REVERT: G 52 PHE cc_start: 0.6381 (t80) cc_final: 0.5645 (t80) REVERT: G 224 MET cc_start: 0.4584 (OUTLIER) cc_final: 0.3627 (ptm) REVERT: G 226 ARG cc_start: 0.7718 (ptp-170) cc_final: 0.7459 (ptp-170) REVERT: H 23 LYS cc_start: 0.9128 (mppt) cc_final: 0.8752 (mptt) REVERT: H 76 ARG cc_start: 0.6583 (ppt170) cc_final: 0.6188 (ptm160) REVERT: I 30 MET cc_start: 0.8258 (mmp) cc_final: 0.7613 (mmp) REVERT: I 52 PHE cc_start: 0.4600 (t80) cc_final: 0.3946 (t80) REVERT: J 23 LYS cc_start: 0.8858 (ptmt) cc_final: 0.8416 (ptmm) REVERT: J 81 GLN cc_start: 0.8729 (pp30) cc_final: 0.8316 (pp30) REVERT: J 87 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8314 (mp) REVERT: J 202 TRP cc_start: 0.7495 (t60) cc_final: 0.6780 (t60) outliers start: 109 outliers final: 83 residues processed: 523 average time/residue: 0.2673 time to fit residues: 208.8251 Evaluate side-chains 537 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 446 time to evaluate : 2.362 ------------------------------------------------------------------------------- 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 54 CYS Chi-restraints excluded: chain D residue 75 LEU 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 7 LEU Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 35 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 172 LYS Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 224 MET Chi-restraints excluded: chain A residue 226 ARG Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 160 LEU 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 27 VAL Chi-restraints excluded: chain C residue 36 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 144 ILE Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 213 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 61 CYS Chi-restraints excluded: chain E residue 72 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 136 VAL 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 F residue 187 TYR Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 14 LEU Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 63 ASN 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 224 MET Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 50 GLU Chi-restraints excluded: chain H residue 61 CYS 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 199 LEU Chi-restraints excluded: chain H residue 215 ASP Chi-restraints excluded: chain I residue 13 THR Chi-restraints excluded: chain I residue 19 THR Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 67 ASP 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 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 J residue 10 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 119 optimal weight: 6.9990 chunk 76 optimal weight: 0.8980 chunk 115 optimal weight: 0.0170 chunk 58 optimal weight: 5.9990 chunk 37 optimal weight: 0.6980 chunk 122 optimal weight: 6.9990 chunk 131 optimal weight: 2.9990 chunk 95 optimal weight: 10.0000 chunk 17 optimal weight: 1.9990 chunk 151 optimal weight: 0.0070 chunk 175 optimal weight: 2.9990 overall best weight: 0.7238 ------------------------------------------------------------------------------- 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 F 49 GLN ** F 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 58 GLN ** G 81 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 98 HIS J 98 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6908 moved from start: 0.7302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16160 Z= 0.200 Angle : 0.932 14.660 21980 Z= 0.422 Chirality : 0.048 0.430 2610 Planarity : 0.007 0.103 2700 Dihedral : 5.455 45.287 2190 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 16.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 5.26 % Allowed : 33.12 % Favored : 61.62 % 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: -0.33 (0.19), residues: 1970 helix: 0.47 (0.15), residues: 1290 sheet: 0.53 (0.51), residues: 100 loop : -1.82 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 78 HIS 0.007 0.001 HIS D 146 PHE 0.027 0.001 PHE F 9 TYR 0.019 0.001 TYR H 66 ARG 0.011 0.000 ARG H 33 *********************** 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 544 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 453 time to evaluate : 1.934 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: D 28 LEU cc_start: 0.9269 (mm) cc_final: 0.8938 (mm) REVERT: D 34 MET cc_start: 0.8352 (mmm) cc_final: 0.8128 (mmm) REVERT: D 39 LEU cc_start: 0.9408 (mt) cc_final: 0.8902 (tp) REVERT: D 86 LEU cc_start: 0.9060 (mm) cc_final: 0.8811 (mm) REVERT: D 211 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8157 (tt) REVERT: D 215 ASP cc_start: 0.7587 (m-30) cc_final: 0.6905 (m-30) REVERT: A 7 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8702 (mp) REVERT: A 51 ARG cc_start: 0.8124 (OUTLIER) cc_final: 0.7729 (ttm170) REVERT: A 55 ASN cc_start: 0.8453 (p0) cc_final: 0.8037 (t0) REVERT: A 64 VAL cc_start: 0.7988 (OUTLIER) cc_final: 0.7469 (t) REVERT: A 77 PHE cc_start: 0.8476 (t80) cc_final: 0.8006 (t80) REVERT: A 78 TRP cc_start: 0.8494 (m-90) cc_final: 0.7693 (m-90) REVERT: B 23 LYS cc_start: 0.9076 (mttp) cc_final: 0.8357 (mptt) REVERT: B 160 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8625 (mt) REVERT: C 12 ILE cc_start: 0.8838 (mp) cc_final: 0.8516 (tp) REVERT: E 23 LYS cc_start: 0.8939 (ptpt) cc_final: 0.8494 (pttt) REVERT: E 34 MET cc_start: 0.7209 (mmp) cc_final: 0.6819 (tmm) REVERT: E 45 TYR cc_start: 0.7918 (m-10) cc_final: 0.7677 (m-10) REVERT: E 81 GLN cc_start: 0.8601 (pt0) cc_final: 0.8322 (pt0) REVERT: E 87 LEU cc_start: 0.9052 (tt) cc_final: 0.8500 (mt) REVERT: E 202 TRP cc_start: 0.7476 (t60) cc_final: 0.6962 (t60) REVERT: F 23 LYS cc_start: 0.9126 (mppt) cc_final: 0.8648 (mmmt) REVERT: F 34 MET cc_start: 0.8901 (mmm) cc_final: 0.8672 (tpp) REVERT: F 39 LEU cc_start: 0.9432 (mt) cc_final: 0.8970 (tp) REVERT: F 86 LEU cc_start: 0.9272 (mm) cc_final: 0.9010 (mm) REVERT: G 20 MET cc_start: 0.4083 (mmm) cc_final: 0.3863 (mmm) REVERT: G 23 LYS cc_start: 0.9166 (mttt) cc_final: 0.8889 (mmtp) REVERT: G 30 MET cc_start: 0.8485 (tmm) cc_final: 0.8061 (tmm) REVERT: G 35 LEU cc_start: 0.9158 (tp) cc_final: 0.8940 (mm) REVERT: G 52 PHE cc_start: 0.6427 (t80) cc_final: 0.5846 (t80) REVERT: G 202 TRP cc_start: 0.8855 (t-100) cc_final: 0.8640 (t-100) REVERT: G 224 MET cc_start: 0.4509 (OUTLIER) cc_final: 0.3633 (ptt) REVERT: H 23 LYS cc_start: 0.9184 (mppt) cc_final: 0.8799 (mptt) REVERT: H 76 ARG cc_start: 0.6580 (ppt170) cc_final: 0.6199 (ptm160) REVERT: I 30 MET cc_start: 0.8231 (mmp) cc_final: 0.7520 (mmp) REVERT: I 52 PHE cc_start: 0.4698 (t80) cc_final: 0.3961 (t80) REVERT: J 23 LYS cc_start: 0.8845 (ptmt) cc_final: 0.8470 (ptmm) REVERT: J 81 GLN cc_start: 0.8751 (pp30) cc_final: 0.8308 (pp30) REVERT: J 202 TRP cc_start: 0.7442 (t60) cc_final: 0.6727 (t60) outliers start: 91 outliers final: 72 residues processed: 498 average time/residue: 0.2918 time to fit residues: 219.2562 Evaluate side-chains 522 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 444 time to evaluate : 2.311 ------------------------------------------------------------------------------- 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 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 7 LEU Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 51 ARG 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 172 LYS Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 224 MET Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 160 LEU 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 13 THR 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 144 ILE Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 11 ILE Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 72 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 136 VAL 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 F residue 187 TYR Chi-restraints excluded: chain G residue 11 ILE 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 144 ILE 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 19 THR 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 199 LEU Chi-restraints excluded: chain H residue 215 ASP Chi-restraints excluded: chain I residue 13 THR Chi-restraints excluded: chain I residue 19 THR 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 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 J residue 10 LEU 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 145 ILE Chi-restraints excluded: chain J residue 150 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 184 optimal weight: 0.9990 chunk 168 optimal weight: 0.9980 chunk 179 optimal weight: 9.9990 chunk 108 optimal weight: 0.2980 chunk 78 optimal weight: 0.9990 chunk 141 optimal weight: 2.9990 chunk 55 optimal weight: 0.0370 chunk 162 optimal weight: 6.9990 chunk 169 optimal weight: 2.9990 chunk 117 optimal weight: 6.9990 chunk 189 optimal weight: 0.9990 overall best weight: 0.6662 ------------------------------------------------------------------------------- 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** ** E 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 HIS ** G 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 81 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6895 moved from start: 0.7491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 16160 Z= 0.212 Angle : 0.953 14.902 21980 Z= 0.428 Chirality : 0.048 0.435 2610 Planarity : 0.007 0.104 2700 Dihedral : 5.430 45.033 2190 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 15.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 5.09 % Allowed : 33.58 % Favored : 61.33 % 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: 0.45 (0.15), residues: 1340 sheet: 0.56 (0.52), residues: 100 loop : -1.52 (0.28), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP J 78 HIS 0.008 0.001 HIS E 98 PHE 0.028 0.001 PHE F 9 TYR 0.018 0.001 TYR F 66 ARG 0.007 0.001 ARG H 33 *********************** 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 537 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 449 time to evaluate : 1.796 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: 0.9292 (mm) cc_final: 0.8970 (mm) REVERT: D 34 MET cc_start: 0.8294 (mmm) cc_final: 0.8012 (mmm) REVERT: D 39 LEU cc_start: 0.9405 (mt) cc_final: 0.8797 (tp) REVERT: D 86 LEU cc_start: 0.9098 (mm) cc_final: 0.8834 (mm) REVERT: D 211 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.8148 (tt) REVERT: D 215 ASP cc_start: 0.7547 (m-30) cc_final: 0.6891 (m-30) REVERT: A 20 MET cc_start: 0.5020 (mmt) cc_final: 0.4616 (mmt) REVERT: A 35 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8553 (mm) REVERT: A 55 ASN cc_start: 0.8420 (p0) cc_final: 0.8053 (t0) REVERT: A 64 VAL cc_start: 0.8008 (OUTLIER) cc_final: 0.7482 (t) REVERT: A 78 TRP cc_start: 0.8310 (m-90) cc_final: 0.7901 (m-90) REVERT: B 23 LYS cc_start: 0.9130 (mttp) cc_final: 0.8391 (mptt) REVERT: B 160 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8649 (mt) REVERT: B 193 GLU cc_start: 0.8549 (mm-30) cc_final: 0.8297 (mm-30) REVERT: B 194 LYS cc_start: 0.9200 (mtmm) cc_final: 0.8409 (mtmt) REVERT: B 202 TRP cc_start: 0.8106 (t60) cc_final: 0.7797 (t60) REVERT: C 12 ILE cc_start: 0.8831 (mp) cc_final: 0.8481 (tp) REVERT: E 23 LYS cc_start: 0.8713 (ptpt) cc_final: 0.8252 (pttm) REVERT: E 34 MET cc_start: 0.7156 (mmp) cc_final: 0.6884 (tmm) REVERT: E 81 GLN cc_start: 0.8593 (pt0) cc_final: 0.8315 (pt0) REVERT: E 87 LEU cc_start: 0.9033 (tt) cc_final: 0.8487 (mt) REVERT: E 202 TRP cc_start: 0.7458 (t60) cc_final: 0.6948 (t60) REVERT: F 23 LYS cc_start: 0.9122 (mppt) cc_final: 0.8630 (mmmt) REVERT: F 39 LEU cc_start: 0.9412 (mt) cc_final: 0.8964 (tp) REVERT: F 86 LEU cc_start: 0.9270 (mm) cc_final: 0.9048 (mm) REVERT: G 20 MET cc_start: 0.4030 (mmm) cc_final: 0.3744 (mmm) REVERT: G 23 LYS cc_start: 0.9166 (mttt) cc_final: 0.8882 (mmtp) REVERT: G 30 MET cc_start: 0.8529 (tmm) cc_final: 0.8068 (tmm) REVERT: G 52 PHE cc_start: 0.6215 (t80) cc_final: 0.5741 (t80) REVERT: G 224 MET cc_start: 0.4395 (OUTLIER) cc_final: 0.3611 (ptt) REVERT: G 226 ARG cc_start: 0.7503 (ptp-170) cc_final: 0.7232 (ptp-170) REVERT: H 76 ARG cc_start: 0.6554 (ppt170) cc_final: 0.6198 (ptm160) REVERT: I 30 MET cc_start: 0.8210 (mmp) cc_final: 0.7475 (mmp) REVERT: I 52 PHE cc_start: 0.4773 (t80) cc_final: 0.4008 (t80) REVERT: I 77 PHE cc_start: 0.8423 (m-80) cc_final: 0.8068 (m-80) REVERT: J 20 MET cc_start: 0.2058 (mmt) cc_final: 0.1755 (mmt) REVERT: J 23 LYS cc_start: 0.8821 (ptmt) cc_final: 0.8312 (ptmm) REVERT: J 87 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8385 (mt) REVERT: J 202 TRP cc_start: 0.7372 (t60) cc_final: 0.6670 (t60) outliers start: 88 outliers final: 70 residues processed: 496 average time/residue: 0.2590 time to fit residues: 193.1062 Evaluate side-chains 504 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 428 time to evaluate : 1.802 ------------------------------------------------------------------------------- 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 54 CYS Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 35 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 172 LYS Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 224 MET Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 160 LEU 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 13 THR 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 144 ILE Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 61 CYS Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 72 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 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 F residue 187 TYR Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 14 LEU Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 75 LEU 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 19 THR Chi-restraints excluded: chain H residue 50 GLU Chi-restraints excluded: chain H residue 61 CYS 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 199 LEU Chi-restraints excluded: chain H residue 215 ASP Chi-restraints excluded: chain I residue 13 THR Chi-restraints excluded: chain I residue 19 THR 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 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 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 87 LEU Chi-restraints excluded: chain J residue 91 VAL Chi-restraints excluded: chain J residue 145 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 115 optimal weight: 1.9990 chunk 90 optimal weight: 0.6980 chunk 132 optimal weight: 5.9990 chunk 199 optimal weight: 0.7980 chunk 183 optimal weight: 2.9990 chunk 158 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 122 optimal weight: 0.4980 chunk 97 optimal weight: 0.9990 chunk 126 optimal weight: 0.5980 chunk 169 optimal weight: 0.2980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 F 17 ASN ** G 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 81 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6883 moved from start: 0.7691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16160 Z= 0.202 Angle : 0.966 15.621 21980 Z= 0.430 Chirality : 0.048 0.434 2610 Planarity : 0.007 0.106 2700 Dihedral : 5.387 44.505 2190 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 15.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 4.51 % Allowed : 34.62 % Favored : 60.87 % 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: -0.19 (0.20), residues: 1970 helix: 0.43 (0.15), residues: 1340 sheet: 0.54 (0.53), residues: 100 loop : -1.51 (0.28), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP J 78 HIS 0.008 0.001 HIS D 98 PHE 0.025 0.001 PHE A 209 TYR 0.019 0.001 TYR I 187 ARG 0.010 0.001 ARG H 223 ********************** 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 521 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 443 time to evaluate : 1.915 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: 0.9278 (mm) cc_final: 0.8945 (mm) REVERT: D 34 MET cc_start: 0.8315 (mmm) cc_final: 0.8093 (mmm) REVERT: D 39 LEU cc_start: 0.9339 (mt) cc_final: 0.8758 (tp) REVERT: D 86 LEU cc_start: 0.9112 (mm) cc_final: 0.8867 (mm) REVERT: D 211 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8220 (tt) REVERT: A 15 ASN cc_start: 0.7996 (t0) cc_final: 0.7735 (m110) REVERT: A 20 MET cc_start: 0.5059 (mmt) cc_final: 0.4228 (mmt) REVERT: A 23 LYS cc_start: 0.8948 (mmtt) cc_final: 0.8161 (mptt) REVERT: A 55 ASN cc_start: 0.8439 (p0) cc_final: 0.8161 (t0) REVERT: A 77 PHE cc_start: 0.8325 (t80) cc_final: 0.8103 (t80) REVERT: B 160 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8607 (mt) REVERT: B 194 LYS cc_start: 0.9169 (mtmm) cc_final: 0.8814 (mtmt) REVERT: B 202 TRP cc_start: 0.8095 (t60) cc_final: 0.7840 (t60) REVERT: E 20 MET cc_start: 0.2538 (tpp) cc_final: 0.2277 (mmt) REVERT: E 23 LYS cc_start: 0.8764 (ptpt) cc_final: 0.8240 (ptpp) REVERT: E 34 MET cc_start: 0.7142 (mmp) cc_final: 0.6897 (tmm) REVERT: E 54 CYS cc_start: 0.7151 (p) cc_final: 0.6511 (p) REVERT: E 81 GLN cc_start: 0.8596 (pt0) cc_final: 0.8316 (pt0) REVERT: E 87 LEU cc_start: 0.9028 (tt) cc_final: 0.8477 (mt) REVERT: E 202 TRP cc_start: 0.7434 (t60) cc_final: 0.6960 (t60) REVERT: E 210 LEU cc_start: 0.8542 (tp) cc_final: 0.8183 (tt) REVERT: F 39 LEU cc_start: 0.9382 (mt) cc_final: 0.8933 (tp) REVERT: F 86 LEU cc_start: 0.9269 (mm) cc_final: 0.9053 (mm) REVERT: F 168 LEU cc_start: 0.8163 (tp) cc_final: 0.7763 (pt) REVERT: G 20 MET cc_start: 0.4122 (mmm) cc_final: 0.3821 (mmm) REVERT: G 23 LYS cc_start: 0.9193 (mttt) cc_final: 0.8914 (mmtp) REVERT: G 52 PHE cc_start: 0.6170 (t80) cc_final: 0.5674 (t80) REVERT: G 224 MET cc_start: 0.4411 (OUTLIER) cc_final: 0.3562 (ptt) REVERT: H 76 ARG cc_start: 0.6541 (ppt170) cc_final: 0.6174 (ptm160) REVERT: I 30 MET cc_start: 0.8120 (mmp) cc_final: 0.7369 (mmp) REVERT: I 52 PHE cc_start: 0.4823 (t80) cc_final: 0.4005 (t80) REVERT: I 77 PHE cc_start: 0.8380 (m-80) cc_final: 0.8018 (m-80) REVERT: J 20 MET cc_start: 0.2020 (mmt) cc_final: 0.1708 (mmt) REVERT: J 23 LYS cc_start: 0.8783 (ptmt) cc_final: 0.8287 (ptmm) REVERT: J 87 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8362 (mt) REVERT: J 202 TRP cc_start: 0.7335 (t60) cc_final: 0.6673 (t60) outliers start: 78 outliers final: 66 residues processed: 480 average time/residue: 0.2477 time to fit residues: 180.9178 Evaluate side-chains 501 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 431 time to evaluate : 1.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 52 PHE Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain A residue 14 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 172 LYS Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 224 MET Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 160 LEU 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 13 THR 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 144 ILE Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 213 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 61 CYS Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 72 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 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 11 ILE Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 75 LEU 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 19 THR 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 199 LEU Chi-restraints excluded: chain H residue 215 ASP 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 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 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 87 LEU Chi-restraints excluded: chain J residue 91 VAL Chi-restraints excluded: chain J residue 145 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 48 optimal weight: 0.0060 chunk 146 optimal weight: 0.8980 chunk 23 optimal weight: 6.9990 chunk 44 optimal weight: 0.0070 chunk 158 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 163 optimal weight: 2.9990 chunk 20 optimal weight: 0.0670 chunk 29 optimal weight: 0.9990 chunk 139 optimal weight: 0.4980 chunk 9 optimal weight: 5.9990 overall best weight: 0.2952 ------------------------------------------------------------------------------- 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 46 GLN ** E 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.140913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.112498 restraints weight = 45761.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.116607 restraints weight = 30848.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.119651 restraints weight = 22692.020| |-----------------------------------------------------------------------------| r_work (final): 0.3981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6890 moved from start: 0.7806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16160 Z= 0.200 Angle : 0.988 17.860 21980 Z= 0.436 Chirality : 0.049 0.421 2610 Planarity : 0.007 0.105 2700 Dihedral : 5.341 43.912 2190 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 15.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 3.87 % Allowed : 35.14 % Favored : 60.98 % 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: 0.22 (0.14), residues: 1350 sheet: 0.52 (0.53), residues: 100 loop : -2.20 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.002 TRP G 78 HIS 0.007 0.001 HIS D 98 PHE 0.027 0.001 PHE A 209 TYR 0.017 0.001 TYR E 143 ARG 0.014 0.001 ARG H 223 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4370.84 seconds wall clock time: 81 minutes 33.39 seconds (4893.39 seconds total)