Starting phenix.real_space_refine on Sun Aug 24 00:33:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gnb_34159/08_2025/8gnb_34159.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gnb_34159/08_2025/8gnb_34159.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gnb_34159/08_2025/8gnb_34159.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gnb_34159/08_2025/8gnb_34159.map" model { file = "/net/cci-nas-00/data/ceres_data/8gnb_34159/08_2025/8gnb_34159.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gnb_34159/08_2025/8gnb_34159.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15770 Number of models: 1 Model: "" Number of chains: 1 Chain: "D" 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: A, B, C, E, F, G, H, I, J Time building chain proxies: 2.09, per 1000 atoms: 0.13 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=30, 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 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 186 " distance=2.05 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 186 " distance=2.05 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 186 " distance=2.05 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 186 " distance=2.04 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 186 " distance=2.05 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 186 " distance=2.05 Simple disulfide: pdb=" SG CYS H 54 " - pdb=" SG CYS H 186 " distance=2.04 Simple disulfide: pdb=" SG CYS I 54 " - pdb=" SG CYS I 186 " distance=2.05 Simple disulfide: pdb=" SG CYS J 54 " - pdb=" SG CYS J 186 " distance=2.04 Simple disulfide: pdb=" SG CYS A 61 " - pdb=" SG CYS A 180 " distance=2.04 Simple disulfide: pdb=" SG CYS B 61 " - pdb=" SG CYS B 180 " distance=2.04 Simple disulfide: pdb=" SG CYS C 61 " - pdb=" SG CYS C 180 " distance=2.04 Simple disulfide: pdb=" SG CYS E 61 " - pdb=" SG CYS E 180 " distance=2.04 Simple disulfide: pdb=" SG CYS F 61 " - pdb=" SG CYS F 180 " distance=2.04 Simple disulfide: pdb=" SG CYS G 61 " - pdb=" SG CYS G 180 " distance=2.04 Simple disulfide: pdb=" SG CYS H 61 " - pdb=" SG CYS H 180 " distance=2.04 Simple disulfide: pdb=" SG CYS I 61 " - pdb=" SG CYS I 180 " distance=2.04 Simple disulfide: pdb=" SG CYS J 61 " - pdb=" SG CYS J 180 " distance=2.04 Simple disulfide: pdb=" SG CYS A 65 " - pdb=" SG CYS A 175 " distance=2.03 Simple disulfide: pdb=" SG CYS B 65 " - pdb=" SG CYS B 175 " distance=2.03 Simple disulfide: pdb=" SG CYS C 65 " - pdb=" SG CYS C 175 " distance=2.03 Simple disulfide: pdb=" SG CYS E 65 " - pdb=" SG CYS E 175 " distance=2.03 Simple disulfide: pdb=" SG CYS F 65 " - pdb=" SG CYS F 175 " distance=2.03 Simple disulfide: pdb=" SG CYS G 65 " - pdb=" SG CYS G 175 " distance=2.03 Simple disulfide: pdb=" SG CYS H 65 " - pdb=" SG CYS H 175 " distance=2.03 Simple disulfide: pdb=" SG CYS I 65 " - pdb=" SG CYS I 175 " distance=2.03 Simple disulfide: pdb=" SG CYS J 65 " - pdb=" SG CYS J 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: 1.03 Conformation dependent library (CDL) restraints added in 600.2 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.26 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: 1.70 Time building geometry restraints manager: 1.40 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: 8516 14.09 - 28.19: 764 28.19 - 42.28: 193 42.28 - 56.38: 77 56.38 - 70.47: 40 Dihedral angle restraints: 9590 sinusoidal: 3800 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 9587 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: 2.23 - 2.76: 2636 2.76 - 3.30: 15693 3.30 - 3.83: 25483 3.83 - 4.37: 27763 4.37 - 4.90: 47136 Nonbonded interactions: 118711 Sorted by model distance: nonbonded pdb=" NH2 ARG B 221 " pdb=" O ASP I 138 " model vdw 2.231 3.120 nonbonded pdb=" O THR J 13 " pdb=" ND2 ASN J 17 " model vdw 2.263 3.120 nonbonded pdb=" O THR E 13 " pdb=" ND2 ASN E 17 " model vdw 2.263 3.120 nonbonded pdb=" O THR H 13 " pdb=" ND2 ASN H 17 " model vdw 2.263 3.120 nonbonded pdb=" O THR G 13 " pdb=" ND2 ASN G 17 " model vdw 2.263 3.120 ... (remaining 118706 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: 0.05 Found NCS groups: ncs_group { reference = chain 'D' selection = chain 'A' selection = chain 'B' selection = chain 'C' 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: 0.010 Normalize map: mean=0, sd=1: 6.510 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 11.590 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 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:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.740 ------------------------------------------------------------------------------- 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 16190 Z= 0.170 Angle : 0.944 6.765 22040 Z= 0.515 Chirality : 0.048 0.183 2610 Planarity : 0.009 0.073 2700 Dihedral : 12.918 70.469 5760 Min Nonbonded Distance : 2.231 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.005 0.001 ARG D 190 TYR 0.025 0.003 TYR I 143 PHE 0.022 0.002 PHE E 52 TRP 0.006 0.001 TRP J 25 HIS 0.002 0.000 HIS C 146 Details of bonding type rmsd covalent geometry : bond 0.00354 (16160) covalent geometry : angle 0.93728 (21980) SS BOND : bond 0.00960 ( 30) SS BOND : angle 2.41976 ( 60) hydrogen bonds : bond 0.16428 ( 950) hydrogen bonds : angle 6.63581 ( 2820) *********************** 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 : 0.529 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: 0.1309 time to fit residues: 153.0545 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 : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 0.9980 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.0770 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 0.0370 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 17 ASN ** 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 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 161 HIS F 17 ASN ** F 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 146 HIS G 46 GLN ** 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 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 161 HIS J 98 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.143147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.113630 restraints weight = 43984.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.118060 restraints weight = 29018.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.121421 restraints weight = 21047.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.123964 restraints weight = 16221.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.125934 restraints weight = 13053.105| |-----------------------------------------------------------------------------| r_work (final): 0.4089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6770 moved from start: 0.4251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16190 Z= 0.157 Angle : 0.881 12.714 22040 Z= 0.423 Chirality : 0.047 0.221 2610 Planarity : 0.008 0.097 2700 Dihedral : 6.243 56.527 2190 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 15.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 4.91 % Allowed : 18.90 % Favored : 76.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 9.09 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.53 (0.19), residues: 1970 helix: 0.11 (0.15), residues: 1340 sheet: 2.27 (0.58), residues: 100 loop : -1.89 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG J 190 TYR 0.021 0.002 TYR I 66 PHE 0.027 0.002 PHE I 92 TRP 0.023 0.002 TRP E 202 HIS 0.012 0.001 HIS F 146 Details of bonding type rmsd covalent geometry : bond 0.00340 (16160) covalent geometry : angle 0.87999 (21980) SS BOND : bond 0.00532 ( 30) SS BOND : angle 1.25332 ( 60) hydrogen bonds : bond 0.05052 ( 950) hydrogen bonds : angle 4.56401 ( 2820) *********************** 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 704 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 619 time to evaluate : 0.578 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: D 28 LEU cc_start: 0.9261 (mm) cc_final: 0.8991 (mm) REVERT: D 78 TRP cc_start: 0.6869 (m-10) cc_final: 0.5691 (m-90) REVERT: D 143 TYR cc_start: 0.8788 (t80) cc_final: 0.8523 (t80) REVERT: D 147 LEU cc_start: 0.9198 (mt) cc_final: 0.8871 (mt) REVERT: D 201 LEU cc_start: 0.9593 (OUTLIER) cc_final: 0.9309 (pp) REVERT: D 215 ASP cc_start: 0.8487 (m-30) cc_final: 0.8216 (m-30) REVERT: D 216 LEU cc_start: 0.9641 (tp) cc_final: 0.9318 (tp) REVERT: A 15 ASN cc_start: 0.8570 (t0) cc_final: 0.7866 (m110) REVERT: A 20 MET cc_start: 0.5617 (pmm) cc_final: 0.5340 (mtm) REVERT: A 23 LYS cc_start: 0.8722 (mppt) cc_final: 0.8314 (mptt) REVERT: A 157 PHE cc_start: 0.8579 (m-80) cc_final: 0.8331 (m-80) REVERT: B 184 VAL cc_start: 0.7794 (t) cc_final: 0.7334 (p) REVERT: B 224 MET cc_start: 0.4115 (mmt) cc_final: 0.1534 (mmp) REVERT: C 12 ILE cc_start: 0.9252 (mp) cc_final: 0.8917 (tp) REVERT: C 17 ASN cc_start: 0.9158 (t0) cc_final: 0.8914 (t0) REVERT: C 49 GLN cc_start: 0.8455 (mm110) cc_final: 0.7890 (mm110) REVERT: C 52 PHE cc_start: 0.6434 (t80) cc_final: 0.5367 (t80) REVERT: C 139 PHE cc_start: 0.6729 (m-10) cc_final: 0.6327 (m-10) REVERT: C 153 LEU cc_start: 0.8313 (mt) cc_final: 0.7996 (mt) REVERT: C 216 LEU cc_start: 0.8475 (tp) cc_final: 0.8061 (pp) REVERT: E 7 LEU cc_start: 0.8926 (tp) cc_final: 0.8605 (pp) REVERT: E 15 ASN cc_start: 0.9251 (t0) cc_final: 0.8236 (p0) REVERT: E 20 MET cc_start: 0.4515 (OUTLIER) cc_final: 0.3644 (mtp) REVERT: E 23 LYS cc_start: 0.8987 (ptpt) cc_final: 0.8186 (pttp) REVERT: E 28 LEU cc_start: 0.9523 (mm) cc_final: 0.8924 (mm) REVERT: E 34 MET cc_start: 0.8221 (mmp) cc_final: 0.6994 (tmm) REVERT: E 39 LEU cc_start: 0.9614 (tp) cc_final: 0.9390 (pp) REVERT: E 67 ASP cc_start: 0.7592 (t0) cc_final: 0.6799 (m-30) REVERT: E 161 HIS cc_start: 0.9198 (t-90) cc_final: 0.8980 (t70) REVERT: E 202 TRP cc_start: 0.8313 (t60) cc_final: 0.7906 (t60) REVERT: E 224 MET cc_start: 0.6644 (tpp) cc_final: 0.5865 (ttt) REVERT: F 20 MET cc_start: 0.8365 (ppp) cc_final: 0.8037 (ppp) REVERT: F 39 LEU cc_start: 0.9594 (mt) cc_final: 0.9260 (tp) REVERT: F 51 ARG cc_start: 0.8249 (mmm160) cc_final: 0.7921 (mmm160) REVERT: F 89 SER cc_start: 0.9199 (m) cc_final: 0.8988 (p) REVERT: F 147 LEU cc_start: 0.8858 (mt) cc_final: 0.8547 (mt) REVERT: G 20 MET cc_start: 0.6115 (ppp) cc_final: 0.5521 (mmm) REVERT: G 23 LYS cc_start: 0.8882 (mppt) cc_final: 0.8458 (mptt) REVERT: G 46 GLN cc_start: 0.9235 (OUTLIER) cc_final: 0.8855 (pp30) REVERT: G 153 LEU cc_start: 0.9407 (mt) cc_final: 0.9078 (mt) REVERT: G 157 PHE cc_start: 0.8673 (m-80) cc_final: 0.8309 (m-80) REVERT: G 161 HIS cc_start: 0.8037 (t-90) cc_final: 0.7137 (m90) REVERT: G 198 MET cc_start: 0.8099 (ptt) cc_final: 0.7225 (tpt) REVERT: H 5 ASP cc_start: 0.7777 (p0) cc_final: 0.7441 (p0) REVERT: H 21 VAL cc_start: 0.8738 (m) cc_final: 0.8474 (p) REVERT: H 74 HIS cc_start: 0.8283 (p-80) cc_final: 0.8017 (p90) REVERT: H 201 LEU cc_start: 0.9693 (mm) cc_final: 0.9366 (tt) REVERT: H 223 ARG cc_start: 0.8970 (OUTLIER) cc_final: 0.8645 (tmm-80) REVERT: I 52 PHE cc_start: 0.4699 (t80) cc_final: 0.3962 (t80) REVERT: I 77 PHE cc_start: 0.9293 (OUTLIER) cc_final: 0.8982 (t80) REVERT: I 139 PHE cc_start: 0.7079 (m-10) cc_final: 0.6870 (m-10) REVERT: I 143 TYR cc_start: 0.9456 (t80) cc_final: 0.9229 (t80) REVERT: I 146 HIS cc_start: 0.9045 (t-90) cc_final: 0.8711 (t-170) REVERT: I 147 LEU cc_start: 0.9735 (mt) cc_final: 0.9529 (tp) REVERT: I 153 LEU cc_start: 0.8420 (mt) cc_final: 0.8175 (mt) REVERT: J 7 LEU cc_start: 0.8961 (tp) cc_final: 0.8586 (pp) REVERT: J 20 MET cc_start: 0.4485 (OUTLIER) cc_final: 0.3578 (mmt) REVERT: J 23 LYS cc_start: 0.9030 (ptmt) cc_final: 0.8591 (ptmm) REVERT: J 51 ARG cc_start: 0.8196 (tpt170) cc_final: 0.7865 (tpt170) REVERT: J 81 GLN cc_start: 0.9077 (pt0) cc_final: 0.8603 (pt0) REVERT: J 162 TYR cc_start: 0.8367 (t80) cc_final: 0.7965 (t80) REVERT: J 202 TRP cc_start: 0.8294 (t60) cc_final: 0.7815 (t60) outliers start: 85 outliers final: 44 residues processed: 654 average time/residue: 0.1218 time to fit residues: 118.2275 Evaluate side-chains 520 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 470 time to evaluate : 0.637 ------------------------------------------------------------------------------- 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 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 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 180 CYS Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 146 HIS Chi-restraints excluded: chain G residue 15 ASN Chi-restraints excluded: chain G residue 46 GLN 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 199 LEU Chi-restraints excluded: chain H residue 223 ARG Chi-restraints excluded: chain I residue 13 THR Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 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 72 VAL Chi-restraints excluded: chain J residue 74 HIS Chi-restraints excluded: chain J residue 180 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 3 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 181 optimal weight: 7.9990 chunk 199 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 30 optimal weight: 9.9990 chunk 197 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 146 optimal weight: 0.9980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 GLN ** D 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 146 HIS B 46 GLN B 74 HIS B 81 GLN ** C 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 146 HIS ** F 161 HIS ** 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 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.138250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.109581 restraints weight = 45660.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.113911 restraints weight = 30534.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.117189 restraints weight = 22162.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.119602 restraints weight = 17061.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.121427 restraints weight = 13733.741| |-----------------------------------------------------------------------------| r_work (final): 0.4042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6875 moved from start: 0.5151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 16190 Z= 0.164 Angle : 0.876 13.850 22040 Z= 0.421 Chirality : 0.047 0.272 2610 Planarity : 0.007 0.104 2700 Dihedral : 5.965 52.476 2190 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 16.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 6.30 % Allowed : 23.76 % Favored : 69.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 9.09 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.38 (0.19), residues: 1970 helix: 0.30 (0.15), residues: 1290 sheet: 1.62 (0.54), residues: 100 loop : -1.72 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 223 TYR 0.024 0.002 TYR F 66 PHE 0.046 0.002 PHE C 209 TRP 0.023 0.001 TRP B 202 HIS 0.015 0.001 HIS F 146 Details of bonding type rmsd covalent geometry : bond 0.00362 (16160) covalent geometry : angle 0.87077 (21980) SS BOND : bond 0.00603 ( 30) SS BOND : angle 2.03947 ( 60) hydrogen bonds : bond 0.04591 ( 950) hydrogen bonds : angle 4.43991 ( 2820) *********************** 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 620 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 511 time to evaluate : 0.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 28 LEU cc_start: 0.9281 (mm) cc_final: 0.8995 (mm) REVERT: D 39 LEU cc_start: 0.9535 (mt) cc_final: 0.9145 (tp) REVERT: D 78 TRP cc_start: 0.6952 (m-10) cc_final: 0.5802 (m-90) REVERT: D 147 LEU cc_start: 0.9132 (mt) cc_final: 0.8906 (mt) REVERT: D 201 LEU cc_start: 0.9594 (OUTLIER) cc_final: 0.9243 (pp) REVERT: A 23 LYS cc_start: 0.8672 (mppt) cc_final: 0.8459 (mttp) REVERT: A 157 PHE cc_start: 0.8686 (m-80) cc_final: 0.8257 (m-80) REVERT: B 33 ARG cc_start: 0.8567 (ttt180) cc_final: 0.7979 (ttm-80) REVERT: B 78 TRP cc_start: 0.8969 (m-10) cc_final: 0.8555 (m-10) REVERT: B 184 VAL cc_start: 0.8038 (t) cc_final: 0.7555 (p) REVERT: B 201 LEU cc_start: 0.9373 (tt) cc_final: 0.9162 (pp) REVERT: C 12 ILE cc_start: 0.9260 (mp) cc_final: 0.8945 (tp) REVERT: C 52 PHE cc_start: 0.6509 (t80) cc_final: 0.5372 (t80) REVERT: C 77 PHE cc_start: 0.9046 (OUTLIER) cc_final: 0.8805 (m-80) REVERT: C 139 PHE cc_start: 0.6757 (m-10) cc_final: 0.6549 (m-10) REVERT: C 216 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8108 (pp) REVERT: E 15 ASN cc_start: 0.9267 (t0) cc_final: 0.8330 (p0) REVERT: E 20 MET cc_start: 0.4595 (OUTLIER) cc_final: 0.3811 (mtp) REVERT: E 23 LYS cc_start: 0.8968 (OUTLIER) cc_final: 0.8230 (ptpp) REVERT: E 39 LEU cc_start: 0.9643 (tp) cc_final: 0.9413 (pp) REVERT: E 81 GLN cc_start: 0.9058 (pt0) cc_final: 0.8750 (pt0) REVERT: E 98 HIS cc_start: 0.9531 (t70) cc_final: 0.9095 (t-170) REVERT: E 161 HIS cc_start: 0.9251 (t-90) cc_final: 0.9025 (t70) REVERT: E 202 TRP cc_start: 0.8322 (t60) cc_final: 0.7852 (t60) REVERT: F 28 LEU cc_start: 0.9426 (mm) cc_final: 0.9136 (mm) REVERT: F 39 LEU cc_start: 0.9586 (mt) cc_final: 0.9274 (tp) REVERT: F 51 ARG cc_start: 0.8366 (mmm160) cc_final: 0.7836 (mmm160) REVERT: F 95 TYR cc_start: 0.6982 (t80) cc_final: 0.6754 (t80) REVERT: F 147 LEU cc_start: 0.8765 (mt) cc_final: 0.8460 (mt) REVERT: G 23 LYS cc_start: 0.8955 (mppt) cc_final: 0.8750 (mttt) REVERT: G 95 TYR cc_start: 0.7815 (t80) cc_final: 0.7592 (t80) REVERT: G 153 LEU cc_start: 0.9413 (mt) cc_final: 0.9129 (mt) REVERT: G 157 PHE cc_start: 0.8469 (m-80) cc_final: 0.8113 (m-80) REVERT: G 198 MET cc_start: 0.8326 (ptt) cc_final: 0.7269 (tpt) REVERT: G 226 ARG cc_start: 0.7649 (ptp-170) cc_final: 0.7373 (ptp-170) REVERT: H 33 ARG cc_start: 0.9078 (ttt180) cc_final: 0.8118 (ttt90) REVERT: H 34 MET cc_start: 0.8936 (mmm) cc_final: 0.8591 (mmm) REVERT: H 74 HIS cc_start: 0.8618 (p-80) cc_final: 0.8206 (p90) REVERT: H 194 LYS cc_start: 0.9127 (mttp) cc_final: 0.8802 (mttp) REVERT: H 198 MET cc_start: 0.9147 (tmm) cc_final: 0.8503 (ppp) REVERT: H 223 ARG cc_start: 0.9055 (OUTLIER) cc_final: 0.8779 (ptm160) REVERT: I 34 MET cc_start: 0.9083 (mmp) cc_final: 0.8799 (mtp) REVERT: I 36 VAL cc_start: 0.9639 (p) cc_final: 0.9412 (m) REVERT: I 39 LEU cc_start: 0.9277 (OUTLIER) cc_final: 0.8679 (tt) REVERT: I 52 PHE cc_start: 0.4999 (t80) cc_final: 0.4091 (t80) REVERT: I 146 HIS cc_start: 0.9136 (t-90) cc_final: 0.8885 (t-170) REVERT: J 20 MET cc_start: 0.4176 (OUTLIER) cc_final: 0.3546 (tpp) REVERT: J 23 LYS cc_start: 0.8998 (ptmt) cc_final: 0.8576 (ptmm) REVERT: J 45 TYR cc_start: 0.8797 (m-10) cc_final: 0.7931 (m-10) REVERT: J 51 ARG cc_start: 0.8252 (tpt170) cc_final: 0.7769 (tpt170) REVERT: J 77 PHE cc_start: 0.9375 (t80) cc_final: 0.9058 (t80) REVERT: J 157 PHE cc_start: 0.9119 (m-80) cc_final: 0.8880 (t80) REVERT: J 202 TRP cc_start: 0.8275 (t60) cc_final: 0.7789 (t60) outliers start: 109 outliers final: 78 residues processed: 560 average time/residue: 0.1222 time to fit residues: 103.1663 Evaluate side-chains 555 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 469 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 11 ILE Chi-restraints excluded: chain D residue 54 CYS Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 187 TYR Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 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 186 CYS 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 197 LEU Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 77 PHE Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 98 HIS Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 157 PHE Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 20 MET Chi-restraints excluded: chain E residue 23 LYS Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 74 HIS Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain E residue 180 CYS Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain G residue 14 LEU Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 149 LEU Chi-restraints excluded: chain G residue 186 CYS 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 30 MET Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 54 CYS 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 195 SER Chi-restraints excluded: chain H residue 215 ASP Chi-restraints excluded: chain H residue 223 ARG Chi-restraints excluded: chain I residue 39 LEU Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 67 ASP 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 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 44 VAL Chi-restraints excluded: chain J residue 53 VAL Chi-restraints excluded: chain J residue 72 VAL Chi-restraints excluded: chain J residue 74 HIS Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 87 LEU Chi-restraints excluded: chain J residue 149 LEU Chi-restraints excluded: chain J residue 180 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 105 optimal weight: 0.8980 chunk 3 optimal weight: 0.7980 chunk 2 optimal weight: 0.0770 chunk 152 optimal weight: 8.9990 chunk 160 optimal weight: 3.9990 chunk 15 optimal weight: 0.0570 chunk 142 optimal weight: 9.9990 chunk 167 optimal weight: 7.9990 chunk 181 optimal weight: 0.6980 chunk 60 optimal weight: 9.9990 chunk 63 optimal weight: 2.9990 overall best weight: 0.5056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 GLN ** D 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 146 HIS A 49 GLN A 58 GLN B 46 GLN ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 161 HIS ** G 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 58 GLN ** H 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.144478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.114146 restraints weight = 44508.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.118440 restraints weight = 29815.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.121754 restraints weight = 21994.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.124271 restraints weight = 17174.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.126190 restraints weight = 13975.464| |-----------------------------------------------------------------------------| r_work (final): 0.4061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6811 moved from start: 0.5618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16190 Z= 0.135 Angle : 0.834 13.405 22040 Z= 0.394 Chirality : 0.045 0.319 2610 Planarity : 0.007 0.103 2700 Dihedral : 5.864 52.177 2190 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 14.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 6.36 % Allowed : 25.78 % Favored : 67.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 9.09 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.29 (0.19), residues: 1970 helix: 0.38 (0.15), residues: 1290 sheet: 1.45 (0.52), residues: 100 loop : -1.69 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 51 TYR 0.025 0.002 TYR A 66 PHE 0.023 0.001 PHE A 26 TRP 0.013 0.001 TRP H 25 HIS 0.010 0.001 HIS D 146 Details of bonding type rmsd covalent geometry : bond 0.00300 (16160) covalent geometry : angle 0.82943 (21980) SS BOND : bond 0.00445 ( 30) SS BOND : angle 1.91463 ( 60) hydrogen bonds : bond 0.04184 ( 950) hydrogen bonds : angle 4.24548 ( 2820) *********************** 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 609 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 499 time to evaluate : 0.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 28 LEU cc_start: 0.9323 (mm) cc_final: 0.9005 (mm) REVERT: D 34 MET cc_start: 0.8520 (mmm) cc_final: 0.8280 (mmm) REVERT: D 39 LEU cc_start: 0.9530 (mt) cc_final: 0.9147 (tp) REVERT: D 42 ARG cc_start: 0.9077 (tpt90) cc_final: 0.8563 (ttt180) REVERT: D 46 GLN cc_start: 0.9370 (tm-30) cc_final: 0.9054 (mm-40) REVERT: D 66 TYR cc_start: 0.7204 (t80) cc_final: 0.6994 (t80) REVERT: D 69 PHE cc_start: 0.8419 (t80) cc_final: 0.8209 (t80) REVERT: D 78 TRP cc_start: 0.6711 (m-10) cc_final: 0.5630 (m-90) REVERT: D 86 LEU cc_start: 0.9232 (mm) cc_final: 0.8977 (mm) REVERT: D 147 LEU cc_start: 0.9143 (mt) cc_final: 0.8872 (mt) REVERT: D 201 LEU cc_start: 0.9595 (OUTLIER) cc_final: 0.9259 (pp) REVERT: A 15 ASN cc_start: 0.8440 (t0) cc_final: 0.8064 (m110) REVERT: A 33 ARG cc_start: 0.8720 (tpt170) cc_final: 0.8341 (tpp80) REVERT: A 157 PHE cc_start: 0.8699 (m-80) cc_final: 0.8474 (m-80) REVERT: A 198 MET cc_start: 0.7597 (ptt) cc_final: 0.6942 (tpt) REVERT: B 33 ARG cc_start: 0.8535 (ttt180) cc_final: 0.7909 (ttm-80) REVERT: B 78 TRP cc_start: 0.8953 (m-10) cc_final: 0.8509 (m-10) REVERT: C 12 ILE cc_start: 0.9211 (mp) cc_final: 0.8926 (tp) REVERT: C 52 PHE cc_start: 0.6573 (t80) cc_final: 0.5619 (t80) REVERT: C 77 PHE cc_start: 0.8930 (OUTLIER) cc_final: 0.8684 (m-80) REVERT: C 138 ASP cc_start: 0.7695 (m-30) cc_final: 0.7191 (t0) REVERT: C 216 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8249 (pp) REVERT: E 15 ASN cc_start: 0.9264 (t0) cc_final: 0.8512 (p0) REVERT: E 20 MET cc_start: 0.4465 (OUTLIER) cc_final: 0.3974 (tpp) REVERT: E 23 LYS cc_start: 0.8792 (ptpt) cc_final: 0.8479 (ptpt) REVERT: E 34 MET cc_start: 0.7547 (mmp) cc_final: 0.6427 (tmm) REVERT: E 39 LEU cc_start: 0.9681 (tp) cc_final: 0.9436 (pp) REVERT: E 67 ASP cc_start: 0.7608 (t0) cc_final: 0.6828 (m-30) REVERT: E 81 GLN cc_start: 0.9066 (pt0) cc_final: 0.8745 (pt0) REVERT: E 98 HIS cc_start: 0.9539 (t70) cc_final: 0.9073 (t-170) REVERT: E 202 TRP cc_start: 0.8262 (t60) cc_final: 0.7842 (t60) REVERT: F 39 LEU cc_start: 0.9575 (mt) cc_final: 0.9243 (tp) REVERT: F 51 ARG cc_start: 0.8359 (mmm160) cc_final: 0.8120 (mmm160) REVERT: F 95 TYR cc_start: 0.6694 (t80) cc_final: 0.6485 (t80) REVERT: F 147 LEU cc_start: 0.8835 (mt) cc_final: 0.8600 (mt) REVERT: F 207 LEU cc_start: 0.7680 (tt) cc_final: 0.7451 (pp) REVERT: G 46 GLN cc_start: 0.8984 (tm-30) cc_final: 0.8288 (pp30) REVERT: G 143 TYR cc_start: 0.9244 (t80) cc_final: 0.8817 (t80) REVERT: G 153 LEU cc_start: 0.9336 (mt) cc_final: 0.9030 (mt) REVERT: G 157 PHE cc_start: 0.8509 (m-80) cc_final: 0.8048 (m-80) REVERT: G 183 VAL cc_start: 0.3805 (OUTLIER) cc_final: 0.3335 (m) REVERT: G 198 MET cc_start: 0.8323 (ptt) cc_final: 0.7327 (tpt) REVERT: G 224 MET cc_start: 0.4535 (OUTLIER) cc_final: 0.3459 (ptt) REVERT: G 226 ARG cc_start: 0.7640 (ptp-170) cc_final: 0.7389 (ptp-170) REVERT: H 33 ARG cc_start: 0.9149 (ttt180) cc_final: 0.8085 (ttt90) REVERT: H 34 MET cc_start: 0.8879 (mmm) cc_final: 0.8594 (mmm) REVERT: H 74 HIS cc_start: 0.8552 (p-80) cc_final: 0.8197 (p-80) REVERT: H 154 GLU cc_start: 0.9336 (tp30) cc_final: 0.9134 (tp30) REVERT: H 194 LYS cc_start: 0.9082 (mttp) cc_final: 0.8718 (mttt) REVERT: H 198 MET cc_start: 0.9074 (tmm) cc_final: 0.8537 (ppp) REVERT: H 201 LEU cc_start: 0.9654 (mp) cc_final: 0.9304 (tt) REVERT: I 52 PHE cc_start: 0.5003 (t80) cc_final: 0.4331 (t80) REVERT: I 77 PHE cc_start: 0.9251 (OUTLIER) cc_final: 0.8967 (t80) REVERT: I 146 HIS cc_start: 0.8978 (t-90) cc_final: 0.8729 (t-170) REVERT: J 23 LYS cc_start: 0.8957 (ptmt) cc_final: 0.8581 (ptmm) REVERT: J 51 ARG cc_start: 0.8296 (tpt170) cc_final: 0.7790 (tpt170) REVERT: J 77 PHE cc_start: 0.9372 (t80) cc_final: 0.9014 (t80) REVERT: J 157 PHE cc_start: 0.9140 (m-80) cc_final: 0.8890 (t80) REVERT: J 202 TRP cc_start: 0.8131 (t60) cc_final: 0.7648 (t60) REVERT: J 210 LEU cc_start: 0.8874 (tp) cc_final: 0.8655 (tt) outliers start: 110 outliers final: 70 residues processed: 562 average time/residue: 0.1220 time to fit residues: 103.2210 Evaluate side-chains 535 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 458 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 68 VAL Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 186 CYS Chi-restraints excluded: chain A residue 189 SER 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 54 CYS 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 210 LEU Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 77 PHE Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 98 HIS Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 157 PHE Chi-restraints excluded: chain C residue 186 CYS Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 20 MET Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 74 HIS Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 180 CYS Chi-restraints excluded: chain E residue 197 LEU 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 187 TYR Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 183 VAL Chi-restraints excluded: chain G residue 186 CYS Chi-restraints excluded: chain G residue 224 MET Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 30 MET 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 215 ASP Chi-restraints excluded: chain H residue 223 ARG Chi-restraints excluded: chain I residue 39 LEU Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 77 PHE Chi-restraints excluded: chain I residue 98 HIS Chi-restraints excluded: chain I residue 134 LEU Chi-restraints excluded: chain I residue 161 HIS Chi-restraints excluded: chain I residue 198 MET Chi-restraints excluded: chain I residue 211 LEU Chi-restraints excluded: chain J residue 10 LEU Chi-restraints excluded: chain J residue 44 VAL Chi-restraints excluded: chain J residue 53 VAL Chi-restraints excluded: chain J residue 54 CYS Chi-restraints excluded: chain J residue 72 VAL Chi-restraints excluded: chain J residue 74 HIS Chi-restraints excluded: chain J residue 180 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 153 optimal weight: 5.9990 chunk 132 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 185 optimal weight: 6.9990 chunk 145 optimal weight: 4.9990 chunk 54 optimal weight: 6.9990 chunk 193 optimal weight: 2.9990 chunk 138 optimal weight: 0.9980 chunk 197 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 175 optimal weight: 6.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 146 HIS A 46 GLN B 46 GLN ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 98 HIS ** G 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.133431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.105726 restraints weight = 47224.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.109730 restraints weight = 31312.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.112718 restraints weight = 22840.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.114954 restraints weight = 17759.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.116674 restraints weight = 14430.454| |-----------------------------------------------------------------------------| r_work (final): 0.3966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7033 moved from start: 0.6350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16190 Z= 0.210 Angle : 0.887 12.413 22040 Z= 0.442 Chirality : 0.047 0.229 2610 Planarity : 0.007 0.107 2700 Dihedral : 6.119 55.437 2190 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 20.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 9.19 % Allowed : 25.61 % Favored : 65.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 9.09 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.30 (0.19), residues: 1970 helix: 0.41 (0.14), residues: 1290 sheet: 0.99 (0.50), residues: 100 loop : -1.70 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG J 222 TYR 0.028 0.002 TYR F 66 PHE 0.028 0.002 PHE D 173 TRP 0.037 0.002 TRP A 78 HIS 0.026 0.002 HIS A 74 Details of bonding type rmsd covalent geometry : bond 0.00433 (16160) covalent geometry : angle 0.88141 (21980) SS BOND : bond 0.00523 ( 30) SS BOND : angle 2.06973 ( 60) hydrogen bonds : bond 0.04472 ( 950) hydrogen bonds : angle 4.45356 ( 2820) *********************** 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 619 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 460 time to evaluate : 0.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 28 LEU cc_start: 0.9439 (mm) cc_final: 0.9118 (mm) REVERT: D 34 MET cc_start: 0.8708 (mmm) cc_final: 0.8424 (mmm) REVERT: D 39 LEU cc_start: 0.9544 (mt) cc_final: 0.9166 (tp) REVERT: D 42 ARG cc_start: 0.9208 (tpt90) cc_final: 0.8785 (ttt180) REVERT: D 46 GLN cc_start: 0.9421 (tm-30) cc_final: 0.9105 (mm-40) REVERT: D 78 TRP cc_start: 0.7014 (m-10) cc_final: 0.5952 (m-90) REVERT: D 86 LEU cc_start: 0.9375 (mm) cc_final: 0.9134 (mm) REVERT: D 147 LEU cc_start: 0.9110 (mt) cc_final: 0.8905 (mt) REVERT: D 201 LEU cc_start: 0.9586 (OUTLIER) cc_final: 0.9209 (pp) REVERT: D 211 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8490 (tt) REVERT: D 215 ASP cc_start: 0.8370 (m-30) cc_final: 0.7440 (m-30) REVERT: D 224 MET cc_start: 0.6434 (tpp) cc_final: 0.6198 (tpp) REVERT: A 30 MET cc_start: 0.9033 (tmm) cc_final: 0.8707 (tmm) REVERT: A 45 TYR cc_start: 0.9285 (m-10) cc_final: 0.8983 (m-10) REVERT: A 157 PHE cc_start: 0.8807 (m-80) cc_final: 0.8248 (m-80) REVERT: B 33 ARG cc_start: 0.8556 (ttt180) cc_final: 0.8285 (ttm-80) REVERT: B 34 MET cc_start: 0.8104 (mmm) cc_final: 0.7792 (mpp) REVERT: B 202 TRP cc_start: 0.9371 (t60) cc_final: 0.8926 (t60) REVERT: C 12 ILE cc_start: 0.9350 (mp) cc_final: 0.9101 (tp) REVERT: C 48 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7665 (pm20) REVERT: C 52 PHE cc_start: 0.7063 (t80) cc_final: 0.5761 (t80) REVERT: C 77 PHE cc_start: 0.8898 (OUTLIER) cc_final: 0.8615 (m-80) REVERT: C 216 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8240 (pp) REVERT: E 20 MET cc_start: 0.4529 (OUTLIER) cc_final: 0.3742 (mtp) REVERT: E 23 LYS cc_start: 0.8985 (ptpt) cc_final: 0.8475 (pttp) REVERT: E 34 MET cc_start: 0.7771 (mmp) cc_final: 0.6612 (tmm) REVERT: E 39 LEU cc_start: 0.9683 (tp) cc_final: 0.9400 (pp) REVERT: E 51 ARG cc_start: 0.8440 (tpt170) cc_final: 0.8173 (tpt170) REVERT: E 81 GLN cc_start: 0.9046 (pt0) cc_final: 0.8543 (pt0) REVERT: E 98 HIS cc_start: 0.9529 (t70) cc_final: 0.9032 (t-170) REVERT: E 202 TRP cc_start: 0.8209 (t60) cc_final: 0.7829 (t60) REVERT: F 20 MET cc_start: 0.8510 (ppp) cc_final: 0.8247 (pmm) REVERT: F 23 LYS cc_start: 0.9067 (mmtt) cc_final: 0.8667 (mmtt) REVERT: F 39 LEU cc_start: 0.9597 (mt) cc_final: 0.9246 (tp) REVERT: F 42 ARG cc_start: 0.9229 (tpt90) cc_final: 0.8969 (tpt90) REVERT: F 51 ARG cc_start: 0.8583 (mmm160) cc_final: 0.8339 (mmm160) REVERT: F 147 LEU cc_start: 0.8735 (mt) cc_final: 0.8484 (mt) REVERT: G 20 MET cc_start: 0.5997 (mmt) cc_final: 0.5627 (mmm) REVERT: G 31 LEU cc_start: 0.9577 (mm) cc_final: 0.9372 (mm) REVERT: G 77 PHE cc_start: 0.8844 (t80) cc_final: 0.8385 (t80) REVERT: G 153 LEU cc_start: 0.9360 (mt) cc_final: 0.9101 (pp) REVERT: G 157 PHE cc_start: 0.8715 (m-80) cc_final: 0.8231 (m-80) REVERT: G 173 PHE cc_start: 0.7839 (OUTLIER) cc_final: 0.7364 (t80) REVERT: G 198 MET cc_start: 0.8436 (ptt) cc_final: 0.8048 (ptt) REVERT: G 226 ARG cc_start: 0.7958 (ptp-170) cc_final: 0.7691 (ptp-170) REVERT: H 33 ARG cc_start: 0.9046 (ttt180) cc_final: 0.8765 (ttt180) REVERT: H 34 MET cc_start: 0.8952 (mmm) cc_final: 0.8747 (mmm) REVERT: H 74 HIS cc_start: 0.8634 (p-80) cc_final: 0.8269 (p90) REVERT: H 76 ARG cc_start: 0.6965 (ppt170) cc_final: 0.6657 (ptm160) REVERT: H 193 GLU cc_start: 0.9579 (mm-30) cc_final: 0.9273 (mm-30) REVERT: I 52 PHE cc_start: 0.5234 (t80) cc_final: 0.4305 (t80) REVERT: I 77 PHE cc_start: 0.9321 (OUTLIER) cc_final: 0.8973 (t80) REVERT: I 146 HIS cc_start: 0.8942 (t-90) cc_final: 0.8721 (t-170) REVERT: I 224 MET cc_start: 0.8977 (mmm) cc_final: 0.7578 (tmm) REVERT: J 23 LYS cc_start: 0.8924 (ptmt) cc_final: 0.8561 (ptmm) REVERT: J 51 ARG cc_start: 0.8342 (tpt170) cc_final: 0.7802 (tpt170) REVERT: J 77 PHE cc_start: 0.9352 (t80) cc_final: 0.9001 (t80) REVERT: J 157 PHE cc_start: 0.9182 (OUTLIER) cc_final: 0.8926 (t80) REVERT: J 202 TRP cc_start: 0.8104 (t60) cc_final: 0.7542 (t60) outliers start: 159 outliers final: 118 residues processed: 549 average time/residue: 0.1128 time to fit residues: 94.4353 Evaluate side-chains 560 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 433 time to evaluate : 0.554 ------------------------------------------------------------------------------- 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 145 ILE 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 210 LEU Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 185 ASP 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 36 VAL Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 146 HIS Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 48 GLU Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 77 PHE Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 98 HIS Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 157 PHE Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 186 CYS Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 20 MET Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 54 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 86 LEU Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 149 LEU Chi-restraints excluded: chain E residue 180 CYS Chi-restraints excluded: chain E residue 197 LEU Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 54 CYS Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain F residue 74 HIS Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain F residue 87 LEU Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain F residue 186 CYS Chi-restraints excluded: chain G residue 4 VAL Chi-restraints excluded: chain G residue 14 LEU Chi-restraints excluded: chain G residue 15 ASN Chi-restraints excluded: chain G residue 53 VAL 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 173 PHE Chi-restraints excluded: chain G residue 186 CYS Chi-restraints excluded: chain G residue 192 THR 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 36 VAL Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 50 GLU Chi-restraints excluded: chain H residue 54 CYS 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 199 LEU Chi-restraints excluded: chain H residue 215 ASP Chi-restraints excluded: chain H residue 223 ARG Chi-restraints excluded: chain I residue 19 THR Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain I residue 39 LEU Chi-restraints excluded: chain I residue 56 THR 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 77 PHE Chi-restraints excluded: chain I residue 98 HIS Chi-restraints excluded: chain I residue 134 LEU Chi-restraints excluded: chain I residue 161 HIS Chi-restraints excluded: chain I residue 186 CYS Chi-restraints excluded: chain I residue 197 LEU Chi-restraints excluded: chain I residue 198 MET Chi-restraints excluded: chain I residue 211 LEU Chi-restraints excluded: chain I residue 213 LEU Chi-restraints excluded: chain J residue 10 LEU Chi-restraints excluded: chain J residue 44 VAL Chi-restraints excluded: chain J residue 53 VAL Chi-restraints excluded: chain J residue 54 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 149 LEU Chi-restraints excluded: chain J residue 157 PHE Chi-restraints excluded: chain J residue 180 CYS Chi-restraints excluded: chain J residue 192 THR Chi-restraints excluded: chain J residue 198 MET 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 192 optimal weight: 0.9990 chunk 141 optimal weight: 4.9990 chunk 182 optimal weight: 4.9990 chunk 140 optimal weight: 5.9990 chunk 15 optimal weight: 0.7980 chunk 187 optimal weight: 6.9990 chunk 157 optimal weight: 0.8980 chunk 91 optimal weight: 7.9990 chunk 59 optimal weight: 0.9990 chunk 19 optimal weight: 6.9990 chunk 184 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 46 GLN ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 81 GLN ** I 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.137255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.108043 restraints weight = 47289.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.112148 restraints weight = 31992.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.115267 restraints weight = 23661.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.117598 restraints weight = 18543.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.119366 restraints weight = 15178.058| |-----------------------------------------------------------------------------| r_work (final): 0.3990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6967 moved from start: 0.6682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16190 Z= 0.155 Angle : 0.859 14.429 22040 Z= 0.412 Chirality : 0.046 0.256 2610 Planarity : 0.007 0.111 2700 Dihedral : 6.035 53.108 2190 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 16.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 7.57 % Allowed : 28.79 % Favored : 63.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 9.09 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.10 (0.19), residues: 1970 helix: 0.48 (0.15), residues: 1340 sheet: 0.75 (0.51), residues: 100 loop : -1.46 (0.28), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG J 190 TYR 0.025 0.002 TYR A 66 PHE 0.023 0.002 PHE A 26 TRP 0.056 0.002 TRP A 78 HIS 0.007 0.001 HIS H 98 Details of bonding type rmsd covalent geometry : bond 0.00338 (16160) covalent geometry : angle 0.85299 (21980) SS BOND : bond 0.00521 ( 30) SS BOND : angle 2.08910 ( 60) hydrogen bonds : bond 0.04147 ( 950) hydrogen bonds : angle 4.34200 ( 2820) *********************** 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 600 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 469 time to evaluate : 0.654 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: 0.9438 (mm) cc_final: 0.9091 (mm) REVERT: D 34 MET cc_start: 0.8706 (mmm) cc_final: 0.8461 (mmm) REVERT: D 39 LEU cc_start: 0.9542 (mt) cc_final: 0.9127 (tp) REVERT: D 42 ARG cc_start: 0.9219 (tpt90) cc_final: 0.8866 (ttt180) REVERT: D 46 GLN cc_start: 0.9427 (tm-30) cc_final: 0.9111 (mm-40) REVERT: D 47 ASP cc_start: 0.9086 (p0) cc_final: 0.8829 (p0) REVERT: D 86 LEU cc_start: 0.9327 (mm) cc_final: 0.9086 (mm) REVERT: D 147 LEU cc_start: 0.9096 (mt) cc_final: 0.8890 (mt) REVERT: D 211 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8593 (tt) REVERT: A 23 LYS cc_start: 0.8778 (mmtt) cc_final: 0.8326 (mmtp) REVERT: A 30 MET cc_start: 0.9104 (tmm) cc_final: 0.8755 (tmm) REVERT: A 49 GLN cc_start: 0.7247 (OUTLIER) cc_final: 0.6746 (mp10) REVERT: B 33 ARG cc_start: 0.8604 (ttt180) cc_final: 0.8310 (ttt90) REVERT: B 193 GLU cc_start: 0.9653 (mm-30) cc_final: 0.9277 (mm-30) REVERT: B 202 TRP cc_start: 0.9352 (t60) cc_final: 0.8917 (t60) REVERT: C 12 ILE cc_start: 0.9316 (mp) cc_final: 0.9075 (tp) REVERT: C 48 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.7808 (pm20) REVERT: C 52 PHE cc_start: 0.6955 (t80) cc_final: 0.5619 (t80) REVERT: C 77 PHE cc_start: 0.8824 (OUTLIER) cc_final: 0.8580 (m-80) REVERT: E 20 MET cc_start: 0.4181 (OUTLIER) cc_final: 0.3560 (mtp) REVERT: E 23 LYS cc_start: 0.8897 (ptpt) cc_final: 0.8432 (pttm) REVERT: E 34 MET cc_start: 0.7727 (mmp) cc_final: 0.6709 (tmm) REVERT: E 51 ARG cc_start: 0.8371 (tpt170) cc_final: 0.8116 (tpt170) REVERT: E 81 GLN cc_start: 0.9035 (pt0) cc_final: 0.8799 (pt0) REVERT: E 87 LEU cc_start: 0.9332 (tt) cc_final: 0.8723 (mm) REVERT: E 98 HIS cc_start: 0.9528 (t70) cc_final: 0.9056 (t-170) REVERT: E 202 TRP cc_start: 0.8216 (t60) cc_final: 0.7771 (t60) REVERT: F 20 MET cc_start: 0.8584 (ppp) cc_final: 0.8191 (pmm) REVERT: F 23 LYS cc_start: 0.9210 (mmtt) cc_final: 0.8737 (mmtt) REVERT: F 39 LEU cc_start: 0.9589 (mt) cc_final: 0.9169 (tp) REVERT: F 42 ARG cc_start: 0.9218 (tpt90) cc_final: 0.8940 (tpt90) REVERT: F 51 ARG cc_start: 0.8554 (mmm160) cc_final: 0.8337 (mmm160) REVERT: F 147 LEU cc_start: 0.8688 (mt) cc_final: 0.8434 (mt) REVERT: G 77 PHE cc_start: 0.8816 (t80) cc_final: 0.8398 (t80) REVERT: G 157 PHE cc_start: 0.8796 (m-80) cc_final: 0.8343 (m-80) REVERT: G 173 PHE cc_start: 0.7797 (OUTLIER) cc_final: 0.7446 (t80) REVERT: G 198 MET cc_start: 0.8497 (ptt) cc_final: 0.8132 (ptt) REVERT: G 226 ARG cc_start: 0.7963 (ptp-170) cc_final: 0.7695 (ptp-170) REVERT: H 33 ARG cc_start: 0.9065 (ttt180) cc_final: 0.8196 (ttt90) REVERT: H 34 MET cc_start: 0.8949 (mmm) cc_final: 0.8645 (mmm) REVERT: H 74 HIS cc_start: 0.8520 (p-80) cc_final: 0.8312 (p-80) REVERT: H 76 ARG cc_start: 0.6979 (ppt170) cc_final: 0.6645 (ptm160) REVERT: H 194 LYS cc_start: 0.9220 (mttp) cc_final: 0.8763 (mttt) REVERT: H 198 MET cc_start: 0.9231 (tmm) cc_final: 0.8612 (ppp) REVERT: H 201 LEU cc_start: 0.9653 (mp) cc_final: 0.9298 (tt) REVERT: I 52 PHE cc_start: 0.5371 (t80) cc_final: 0.4370 (t80) REVERT: I 77 PHE cc_start: 0.9264 (OUTLIER) cc_final: 0.8892 (t80) REVERT: J 20 MET cc_start: 0.4486 (tpp) cc_final: 0.4076 (mmt) REVERT: J 23 LYS cc_start: 0.8769 (ptmt) cc_final: 0.8373 (ptmm) REVERT: J 34 MET cc_start: 0.6514 (ttt) cc_final: 0.6287 (tpt) REVERT: J 51 ARG cc_start: 0.8385 (tpt170) cc_final: 0.7791 (tpt170) REVERT: J 157 PHE cc_start: 0.9173 (m-80) cc_final: 0.8967 (t80) REVERT: J 202 TRP cc_start: 0.8140 (t60) cc_final: 0.7574 (t60) outliers start: 131 outliers final: 91 residues processed: 541 average time/residue: 0.1235 time to fit residues: 99.8764 Evaluate side-chains 535 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 437 time to evaluate : 0.637 ------------------------------------------------------------------------------- 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 207 LEU Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain A residue 14 LEU 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 91 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 185 ASP 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 54 CYS Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 146 HIS Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain C residue 34 MET Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 48 GLU Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 77 PHE Chi-restraints excluded: chain C residue 98 HIS Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 186 CYS Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain E residue 7 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 54 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 86 LEU Chi-restraints excluded: chain E residue 149 LEU Chi-restraints excluded: chain E residue 180 CYS Chi-restraints excluded: chain E residue 197 LEU Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 54 CYS Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain F residue 74 HIS Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 4 VAL Chi-restraints excluded: chain G residue 14 LEU Chi-restraints excluded: chain G residue 53 VAL 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 173 PHE 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 54 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 215 ASP Chi-restraints excluded: chain H residue 223 ARG Chi-restraints excluded: chain I residue 39 LEU Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 69 PHE Chi-restraints excluded: chain I residue 77 PHE Chi-restraints excluded: chain I residue 98 HIS Chi-restraints excluded: chain I residue 161 HIS Chi-restraints excluded: chain I residue 186 CYS Chi-restraints excluded: chain I residue 198 MET Chi-restraints excluded: chain I residue 199 LEU Chi-restraints excluded: chain I residue 211 LEU Chi-restraints excluded: chain I residue 213 LEU Chi-restraints excluded: chain J residue 7 LEU Chi-restraints excluded: chain J residue 10 LEU Chi-restraints excluded: chain J residue 44 VAL Chi-restraints excluded: chain J residue 54 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 91 VAL Chi-restraints excluded: chain J residue 149 LEU Chi-restraints excluded: chain J residue 180 CYS Chi-restraints excluded: chain J residue 216 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 136 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 131 optimal weight: 0.6980 chunk 104 optimal weight: 0.0870 chunk 177 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 187 optimal weight: 6.9990 chunk 167 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 179 optimal weight: 0.4980 overall best weight: 0.6158 ------------------------------------------------------------------------------- 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** ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 58 GLN E 15 ASN ** F 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 46 GLN ** G 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 98 HIS ** I 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.139797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.110010 restraints weight = 47354.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.114079 restraints weight = 32411.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.117117 restraints weight = 24195.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.119495 restraints weight = 19095.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.121290 restraints weight = 15699.346| |-----------------------------------------------------------------------------| r_work (final): 0.4013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6964 moved from start: 0.6859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16190 Z= 0.141 Angle : 0.921 15.779 22040 Z= 0.424 Chirality : 0.048 0.401 2610 Planarity : 0.007 0.110 2700 Dihedral : 6.066 54.329 2190 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 15.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 6.88 % Allowed : 30.98 % Favored : 62.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 9.09 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.14 (0.19), residues: 1970 helix: 0.45 (0.14), residues: 1340 sheet: 0.61 (0.50), residues: 100 loop : -1.46 (0.28), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 51 TYR 0.022 0.002 TYR F 66 PHE 0.051 0.002 PHE F 9 TRP 0.031 0.002 TRP A 78 HIS 0.008 0.001 HIS B 98 Details of bonding type rmsd covalent geometry : bond 0.00312 (16160) covalent geometry : angle 0.91600 (21980) SS BOND : bond 0.00424 ( 30) SS BOND : angle 2.01699 ( 60) hydrogen bonds : bond 0.04073 ( 950) hydrogen bonds : angle 4.33340 ( 2820) *********************** 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 569 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 450 time to evaluate : 0.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 28 LEU cc_start: 0.9434 (mm) cc_final: 0.9108 (mm) REVERT: D 34 MET cc_start: 0.8651 (mmm) cc_final: 0.8354 (mmm) REVERT: D 39 LEU cc_start: 0.9526 (mt) cc_final: 0.9061 (tp) REVERT: D 42 ARG cc_start: 0.9183 (tpt90) cc_final: 0.8704 (ttt180) REVERT: D 46 GLN cc_start: 0.9433 (tm-30) cc_final: 0.9099 (mm-40) REVERT: D 47 ASP cc_start: 0.9018 (p0) cc_final: 0.8721 (p0) REVERT: D 86 LEU cc_start: 0.9324 (mm) cc_final: 0.9079 (mm) REVERT: D 147 LEU cc_start: 0.9020 (mt) cc_final: 0.8811 (mt) REVERT: D 194 LYS cc_start: 0.8578 (OUTLIER) cc_final: 0.8207 (mmmt) REVERT: D 211 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8556 (tt) REVERT: A 23 LYS cc_start: 0.8785 (mmtt) cc_final: 0.8398 (mmtp) REVERT: A 30 MET cc_start: 0.9055 (tmm) cc_final: 0.8706 (tmm) REVERT: B 33 ARG cc_start: 0.8607 (ttt180) cc_final: 0.8216 (ttm-80) REVERT: B 55 ASN cc_start: 0.8990 (m-40) cc_final: 0.8157 (t0) REVERT: B 74 HIS cc_start: 0.8319 (p90) cc_final: 0.8069 (p90) REVERT: B 202 TRP cc_start: 0.9336 (t60) cc_final: 0.8914 (t60) REVERT: C 12 ILE cc_start: 0.9263 (OUTLIER) cc_final: 0.9011 (tp) REVERT: C 34 MET cc_start: 0.8200 (OUTLIER) cc_final: 0.7632 (pmm) REVERT: C 52 PHE cc_start: 0.6792 (t80) cc_final: 0.5579 (t80) REVERT: C 77 PHE cc_start: 0.8822 (OUTLIER) cc_final: 0.8566 (m-80) REVERT: E 20 MET cc_start: 0.4071 (OUTLIER) cc_final: 0.3466 (mtp) REVERT: E 23 LYS cc_start: 0.8890 (ptpt) cc_final: 0.8384 (pttm) REVERT: E 34 MET cc_start: 0.7651 (mmp) cc_final: 0.6635 (tmm) REVERT: E 39 LEU cc_start: 0.9683 (tp) cc_final: 0.9406 (pp) REVERT: E 51 ARG cc_start: 0.8334 (tpt170) cc_final: 0.7889 (tpt170) REVERT: E 81 GLN cc_start: 0.8991 (pt0) cc_final: 0.8747 (pt0) REVERT: E 87 LEU cc_start: 0.9313 (tt) cc_final: 0.8664 (mm) REVERT: E 98 HIS cc_start: 0.9509 (t70) cc_final: 0.9030 (t-170) REVERT: E 190 ARG cc_start: 0.8556 (ptm160) cc_final: 0.8235 (ptm160) REVERT: E 202 TRP cc_start: 0.8153 (t60) cc_final: 0.7711 (t60) REVERT: F 20 MET cc_start: 0.8545 (ppp) cc_final: 0.8307 (pmm) REVERT: F 39 LEU cc_start: 0.9559 (mt) cc_final: 0.9111 (tp) REVERT: F 42 ARG cc_start: 0.9184 (tpt90) cc_final: 0.8887 (tpt90) REVERT: F 51 ARG cc_start: 0.8425 (mmm160) cc_final: 0.8098 (mmm160) REVERT: F 147 LEU cc_start: 0.8640 (mt) cc_final: 0.8393 (mt) REVERT: G 30 MET cc_start: 0.9341 (tmm) cc_final: 0.8941 (tmm) REVERT: G 77 PHE cc_start: 0.8781 (t80) cc_final: 0.8324 (t80) REVERT: G 173 PHE cc_start: 0.7768 (OUTLIER) cc_final: 0.7158 (t80) REVERT: G 198 MET cc_start: 0.8507 (ptt) cc_final: 0.8165 (ptt) REVERT: G 224 MET cc_start: 0.4728 (OUTLIER) cc_final: 0.3732 (ptm) REVERT: H 74 HIS cc_start: 0.8552 (p-80) cc_final: 0.8147 (p90) REVERT: H 76 ARG cc_start: 0.6999 (ppt170) cc_final: 0.6754 (ptm160) REVERT: H 194 LYS cc_start: 0.9233 (mttp) cc_final: 0.8789 (mttt) REVERT: H 198 MET cc_start: 0.9195 (tmm) cc_final: 0.8631 (ppp) REVERT: H 201 LEU cc_start: 0.9654 (mp) cc_final: 0.9255 (tt) REVERT: I 33 ARG cc_start: 0.7493 (ttt180) cc_final: 0.6986 (ttt180) REVERT: I 52 PHE cc_start: 0.5392 (t80) cc_final: 0.4792 (t80) REVERT: I 77 PHE cc_start: 0.9231 (OUTLIER) cc_final: 0.8842 (t80) REVERT: I 224 MET cc_start: 0.8949 (mmm) cc_final: 0.7673 (tmm) REVERT: J 20 MET cc_start: 0.4437 (tpp) cc_final: 0.4224 (tpp) REVERT: J 23 LYS cc_start: 0.8690 (ptmt) cc_final: 0.8360 (ptmm) REVERT: J 34 MET cc_start: 0.6450 (ttt) cc_final: 0.6237 (tpt) REVERT: J 51 ARG cc_start: 0.8295 (tpt170) cc_final: 0.7710 (tpt170) REVERT: J 81 GLN cc_start: 0.9131 (pp30) cc_final: 0.8707 (pp30) REVERT: J 157 PHE cc_start: 0.9187 (m-80) cc_final: 0.8898 (t80) REVERT: J 202 TRP cc_start: 0.8092 (t60) cc_final: 0.7496 (t60) outliers start: 119 outliers final: 93 residues processed: 515 average time/residue: 0.1245 time to fit residues: 96.3198 Evaluate side-chains 534 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 432 time to evaluate : 0.627 ------------------------------------------------------------------------------- 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 145 ILE Chi-restraints excluded: chain D residue 194 LYS Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 185 ASP 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 54 CYS Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 146 HIS Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain C residue 12 ILE Chi-restraints excluded: chain C residue 34 MET Chi-restraints excluded: chain C residue 58 GLN Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 77 PHE Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 98 HIS Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 186 CYS Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 11 ILE Chi-restraints excluded: chain E residue 20 MET Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 54 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 91 VAL Chi-restraints excluded: chain E residue 180 CYS Chi-restraints excluded: chain E residue 197 LEU Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 18 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 97 LEU Chi-restraints excluded: chain F residue 187 TYR Chi-restraints excluded: chain G residue 4 VAL Chi-restraints excluded: chain G residue 14 LEU Chi-restraints excluded: chain G residue 53 VAL 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 173 PHE 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 30 MET Chi-restraints excluded: chain H residue 50 GLU Chi-restraints excluded: chain H residue 54 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 215 ASP Chi-restraints excluded: chain H residue 223 ARG Chi-restraints excluded: chain I residue 13 THR Chi-restraints excluded: chain I residue 39 LEU Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 69 PHE Chi-restraints excluded: chain I residue 77 PHE Chi-restraints excluded: chain I residue 98 HIS Chi-restraints excluded: chain I residue 134 LEU Chi-restraints excluded: chain I residue 161 HIS Chi-restraints excluded: chain I residue 186 CYS Chi-restraints excluded: chain I residue 198 MET Chi-restraints excluded: chain I residue 199 LEU Chi-restraints excluded: chain I residue 211 LEU Chi-restraints excluded: chain I residue 213 LEU Chi-restraints excluded: chain J residue 10 LEU Chi-restraints excluded: chain J residue 11 ILE Chi-restraints excluded: chain J residue 53 VAL Chi-restraints excluded: chain J residue 54 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 149 LEU Chi-restraints excluded: chain J residue 180 CYS 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 159 optimal weight: 5.9990 chunk 193 optimal weight: 3.9990 chunk 72 optimal weight: 5.9990 chunk 179 optimal weight: 0.8980 chunk 50 optimal weight: 9.9990 chunk 10 optimal weight: 20.0000 chunk 100 optimal weight: 8.9990 chunk 197 optimal weight: 0.6980 chunk 147 optimal weight: 0.0970 chunk 173 optimal weight: 0.9990 chunk 196 optimal weight: 4.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- 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 ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 46 GLN ** J 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.134119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.106148 restraints weight = 46712.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.110149 restraints weight = 31333.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.113197 restraints weight = 23077.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.115474 restraints weight = 17925.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.117223 restraints weight = 14551.253| |-----------------------------------------------------------------------------| r_work (final): 0.3977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6994 moved from start: 0.7094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 16190 Z= 0.154 Angle : 0.920 13.974 22040 Z= 0.429 Chirality : 0.048 0.450 2610 Planarity : 0.007 0.113 2700 Dihedral : 6.055 53.699 2190 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 17.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 6.82 % Allowed : 31.10 % Favored : 62.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 9.09 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.10 (0.19), residues: 1970 helix: 0.53 (0.15), residues: 1340 sheet: 0.30 (0.50), residues: 100 loop : -1.52 (0.28), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 51 TYR 0.021 0.002 TYR J 143 PHE 0.045 0.002 PHE F 9 TRP 0.024 0.002 TRP A 78 HIS 0.007 0.001 HIS D 146 Details of bonding type rmsd covalent geometry : bond 0.00340 (16160) covalent geometry : angle 0.91482 (21980) SS BOND : bond 0.00385 ( 30) SS BOND : angle 2.05903 ( 60) hydrogen bonds : bond 0.03953 ( 950) hydrogen bonds : angle 4.41522 ( 2820) *********************** 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 565 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 447 time to evaluate : 1.137 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: D 28 LEU cc_start: 0.9464 (mm) cc_final: 0.9138 (mm) REVERT: D 33 ARG cc_start: 0.8956 (ttt180) cc_final: 0.8744 (ttt180) REVERT: D 34 MET cc_start: 0.8708 (mmm) cc_final: 0.8417 (mmm) REVERT: D 39 LEU cc_start: 0.9525 (mt) cc_final: 0.9060 (tp) REVERT: D 42 ARG cc_start: 0.9241 (tpt90) cc_final: 0.8677 (ttt180) REVERT: D 46 GLN cc_start: 0.9443 (tm-30) cc_final: 0.9102 (mm-40) REVERT: D 86 LEU cc_start: 0.9353 (mm) cc_final: 0.9115 (mm) REVERT: D 211 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8593 (tt) REVERT: A 20 MET cc_start: 0.6285 (mmm) cc_final: 0.5335 (mmt) REVERT: A 23 LYS cc_start: 0.8880 (mmtt) cc_final: 0.8289 (mmtm) REVERT: A 30 MET cc_start: 0.9032 (tmm) cc_final: 0.8737 (tmm) REVERT: B 12 ILE cc_start: 0.8430 (OUTLIER) cc_final: 0.8000 (tp) REVERT: B 33 ARG cc_start: 0.8680 (ttt180) cc_final: 0.8186 (ttm-80) REVERT: B 194 LYS cc_start: 0.9411 (mttp) cc_final: 0.8607 (mttp) REVERT: B 198 MET cc_start: 0.9259 (tmm) cc_final: 0.8483 (ptt) REVERT: B 202 TRP cc_start: 0.9324 (t60) cc_final: 0.8564 (t-100) REVERT: C 12 ILE cc_start: 0.9332 (OUTLIER) cc_final: 0.9086 (tp) REVERT: C 52 PHE cc_start: 0.6958 (t80) cc_final: 0.5536 (t80) REVERT: C 77 PHE cc_start: 0.8804 (OUTLIER) cc_final: 0.8532 (m-80) REVERT: E 20 MET cc_start: 0.4184 (OUTLIER) cc_final: 0.3559 (mtp) REVERT: E 23 LYS cc_start: 0.8895 (ptpt) cc_final: 0.8381 (pttm) REVERT: E 34 MET cc_start: 0.7654 (mmp) cc_final: 0.6685 (tmm) REVERT: E 39 LEU cc_start: 0.9692 (tp) cc_final: 0.9402 (pp) REVERT: E 45 TYR cc_start: 0.8637 (m-10) cc_final: 0.8322 (m-10) REVERT: E 51 ARG cc_start: 0.8365 (tpt170) cc_final: 0.7959 (tpt170) REVERT: E 81 GLN cc_start: 0.9005 (pt0) cc_final: 0.8490 (pt0) REVERT: E 87 LEU cc_start: 0.9319 (tt) cc_final: 0.8640 (mm) REVERT: E 98 HIS cc_start: 0.9499 (t70) cc_final: 0.8997 (t-170) REVERT: E 202 TRP cc_start: 0.8131 (t60) cc_final: 0.7705 (t60) REVERT: F 20 MET cc_start: 0.8531 (ppp) cc_final: 0.8146 (pmm) REVERT: F 23 LYS cc_start: 0.9275 (mmtt) cc_final: 0.8678 (mmtp) REVERT: F 39 LEU cc_start: 0.9556 (mt) cc_final: 0.9107 (tp) REVERT: F 42 ARG cc_start: 0.9250 (tpt90) cc_final: 0.8941 (tpt90) REVERT: F 147 LEU cc_start: 0.8627 (mt) cc_final: 0.8377 (mt) REVERT: G 7 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8697 (pt) REVERT: G 77 PHE cc_start: 0.8799 (t80) cc_final: 0.8382 (t80) REVERT: G 157 PHE cc_start: 0.8845 (m-80) cc_final: 0.8453 (m-80) REVERT: G 173 PHE cc_start: 0.7483 (OUTLIER) cc_final: 0.7195 (t80) REVERT: G 198 MET cc_start: 0.8499 (ptt) cc_final: 0.8159 (ptt) REVERT: G 224 MET cc_start: 0.5130 (OUTLIER) cc_final: 0.3975 (ptm) REVERT: H 33 ARG cc_start: 0.9013 (ttt180) cc_final: 0.8220 (ttt90) REVERT: H 34 MET cc_start: 0.8676 (mmm) cc_final: 0.8067 (mmm) REVERT: H 76 ARG cc_start: 0.7006 (ppt170) cc_final: 0.6618 (ppt170) REVERT: H 194 LYS cc_start: 0.9258 (mttp) cc_final: 0.8835 (mttt) REVERT: H 198 MET cc_start: 0.9193 (tmm) cc_final: 0.8679 (ppp) REVERT: H 201 LEU cc_start: 0.9653 (mp) cc_final: 0.9248 (tt) REVERT: H 218 CYS cc_start: 0.9362 (t) cc_final: 0.8844 (p) REVERT: I 33 ARG cc_start: 0.7582 (ttt180) cc_final: 0.6781 (ttt90) REVERT: I 34 MET cc_start: 0.9090 (mmp) cc_final: 0.8642 (mmm) REVERT: I 52 PHE cc_start: 0.6482 (t80) cc_final: 0.5312 (t80) REVERT: I 77 PHE cc_start: 0.9244 (OUTLIER) cc_final: 0.8842 (t80) REVERT: I 224 MET cc_start: 0.8985 (mmm) cc_final: 0.7654 (tmm) REVERT: J 20 MET cc_start: 0.4330 (tpp) cc_final: 0.3861 (mmt) REVERT: J 23 LYS cc_start: 0.8747 (ptmt) cc_final: 0.8348 (ptmm) REVERT: J 51 ARG cc_start: 0.8332 (tpt170) cc_final: 0.8116 (tpt170) REVERT: J 81 GLN cc_start: 0.9142 (pp30) cc_final: 0.8615 (pp30) REVERT: J 157 PHE cc_start: 0.9186 (OUTLIER) cc_final: 0.8913 (t80) REVERT: J 202 TRP cc_start: 0.8092 (t60) cc_final: 0.7473 (t60) outliers start: 118 outliers final: 94 residues processed: 509 average time/residue: 0.1250 time to fit residues: 95.7655 Evaluate side-chains 539 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 435 time to evaluate : 0.557 ------------------------------------------------------------------------------- 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 145 ILE Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 185 ASP 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 54 CYS Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 146 HIS Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain C residue 12 ILE Chi-restraints excluded: chain C residue 34 MET Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 77 PHE Chi-restraints excluded: chain C residue 98 HIS Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 186 CYS Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 11 ILE Chi-restraints excluded: chain E residue 20 MET Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 54 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 91 VAL Chi-restraints excluded: chain E residue 180 CYS Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 52 PHE Chi-restraints excluded: chain F residue 54 CYS Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain F residue 74 HIS Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 4 VAL Chi-restraints excluded: chain G residue 7 LEU Chi-restraints excluded: chain G residue 14 LEU Chi-restraints excluded: chain G residue 15 ASN Chi-restraints excluded: chain G residue 53 VAL 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 173 PHE 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 30 MET Chi-restraints excluded: chain H residue 50 GLU Chi-restraints excluded: chain H residue 54 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 215 ASP Chi-restraints excluded: chain H residue 223 ARG Chi-restraints excluded: chain I residue 13 THR Chi-restraints excluded: chain I residue 39 LEU Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 69 PHE Chi-restraints excluded: chain I residue 77 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 186 CYS Chi-restraints excluded: chain I residue 198 MET Chi-restraints excluded: chain I residue 199 LEU Chi-restraints excluded: chain I residue 211 LEU Chi-restraints excluded: chain I residue 213 LEU Chi-restraints excluded: chain J residue 10 LEU Chi-restraints excluded: chain J residue 11 ILE Chi-restraints excluded: chain J residue 53 VAL Chi-restraints excluded: chain J residue 54 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 91 VAL Chi-restraints excluded: chain J residue 149 LEU Chi-restraints excluded: chain J residue 157 PHE Chi-restraints excluded: chain J residue 180 CYS Chi-restraints excluded: chain J residue 216 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 147 optimal weight: 4.9990 chunk 1 optimal weight: 0.9980 chunk 79 optimal weight: 6.9990 chunk 199 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 chunk 166 optimal weight: 0.8980 chunk 107 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 chunk 40 optimal weight: 7.9990 chunk 39 optimal weight: 3.9990 chunk 95 optimal weight: 10.0000 overall best weight: 1.3782 ------------------------------------------------------------------------------- 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 ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 17 ASN ** F 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 46 GLN ** G 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 49 GLN ** H 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 161 HIS ** I 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 46 GLN ** J 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.134073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.106372 restraints weight = 46691.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.110466 restraints weight = 30860.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.113502 restraints weight = 22381.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.115777 restraints weight = 17277.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.117531 restraints weight = 13965.835| |-----------------------------------------------------------------------------| r_work (final): 0.3973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7018 moved from start: 0.7389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16190 Z= 0.158 Angle : 0.931 14.609 22040 Z= 0.434 Chirality : 0.049 0.442 2610 Planarity : 0.007 0.114 2700 Dihedral : 6.117 53.968 2190 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 17.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 6.65 % Allowed : 31.91 % Favored : 61.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 9.09 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.07 (0.20), residues: 1970 helix: 0.63 (0.15), residues: 1320 sheet: -0.12 (0.50), residues: 100 loop : -1.18 (0.29), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 51 TYR 0.022 0.002 TYR I 66 PHE 0.044 0.002 PHE F 9 TRP 0.020 0.002 TRP E 78 HIS 0.004 0.001 HIS H 161 Details of bonding type rmsd covalent geometry : bond 0.00346 (16160) covalent geometry : angle 0.92743 (21980) SS BOND : bond 0.00402 ( 30) SS BOND : angle 1.84003 ( 60) hydrogen bonds : bond 0.04024 ( 950) hydrogen bonds : angle 4.43741 ( 2820) *********************** 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 563 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 448 time to evaluate : 0.739 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: 0.9495 (mm) cc_final: 0.9176 (mm) REVERT: D 33 ARG cc_start: 0.8909 (ttt180) cc_final: 0.8681 (ttt180) REVERT: D 34 MET cc_start: 0.8707 (mmm) cc_final: 0.8398 (mmm) REVERT: D 39 LEU cc_start: 0.9525 (mt) cc_final: 0.9051 (tp) REVERT: D 42 ARG cc_start: 0.9259 (tpt90) cc_final: 0.8798 (ttt180) REVERT: D 46 GLN cc_start: 0.9438 (tm-30) cc_final: 0.9111 (mm-40) REVERT: D 86 LEU cc_start: 0.9312 (mm) cc_final: 0.9053 (mm) REVERT: D 193 GLU cc_start: 0.8143 (mm-30) cc_final: 0.7935 (mm-30) REVERT: D 211 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8584 (tt) REVERT: A 20 MET cc_start: 0.6344 (mmm) cc_final: 0.5391 (mmt) REVERT: A 23 LYS cc_start: 0.8912 (mmtt) cc_final: 0.8278 (mmtp) REVERT: A 30 MET cc_start: 0.9001 (tmm) cc_final: 0.8598 (tmm) REVERT: A 34 MET cc_start: 0.9113 (mmm) cc_final: 0.8579 (mpp) REVERT: B 12 ILE cc_start: 0.8480 (OUTLIER) cc_final: 0.8025 (tp) REVERT: B 33 ARG cc_start: 0.8507 (ttt180) cc_final: 0.8299 (ttm-80) REVERT: B 55 ASN cc_start: 0.8979 (m-40) cc_final: 0.8189 (t0) REVERT: B 193 GLU cc_start: 0.9640 (mm-30) cc_final: 0.9297 (mm-30) REVERT: B 202 TRP cc_start: 0.9314 (t60) cc_final: 0.8573 (t-100) REVERT: C 12 ILE cc_start: 0.9329 (OUTLIER) cc_final: 0.9087 (tp) REVERT: C 34 MET cc_start: 0.8252 (OUTLIER) cc_final: 0.7638 (pmm) REVERT: C 48 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7928 (pm20) REVERT: C 52 PHE cc_start: 0.6874 (t80) cc_final: 0.5351 (t80) REVERT: C 77 PHE cc_start: 0.8796 (OUTLIER) cc_final: 0.8509 (m-80) REVERT: E 20 MET cc_start: 0.4174 (OUTLIER) cc_final: 0.3741 (ttm) REVERT: E 23 LYS cc_start: 0.8920 (ptpt) cc_final: 0.8399 (pttm) REVERT: E 34 MET cc_start: 0.7850 (mmp) cc_final: 0.6748 (tmm) REVERT: E 39 LEU cc_start: 0.9694 (tp) cc_final: 0.9417 (pp) REVERT: E 51 ARG cc_start: 0.8426 (tpt170) cc_final: 0.8025 (tpt170) REVERT: E 81 GLN cc_start: 0.8972 (pt0) cc_final: 0.8460 (pt0) REVERT: E 87 LEU cc_start: 0.9347 (tt) cc_final: 0.8699 (mt) REVERT: E 98 HIS cc_start: 0.9472 (t70) cc_final: 0.8977 (t-170) REVERT: E 202 TRP cc_start: 0.8089 (t60) cc_final: 0.7648 (t60) REVERT: F 20 MET cc_start: 0.8520 (ppp) cc_final: 0.8253 (pmm) REVERT: F 39 LEU cc_start: 0.9568 (mt) cc_final: 0.9118 (tp) REVERT: F 42 ARG cc_start: 0.9230 (tpt90) cc_final: 0.8905 (tpt90) REVERT: F 147 LEU cc_start: 0.8598 (mt) cc_final: 0.8362 (mt) REVERT: G 7 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8718 (pt) REVERT: G 20 MET cc_start: 0.5129 (mmm) cc_final: 0.4671 (mmm) REVERT: G 77 PHE cc_start: 0.8802 (t80) cc_final: 0.8412 (t80) REVERT: G 157 PHE cc_start: 0.8834 (m-80) cc_final: 0.8472 (m-80) REVERT: G 172 LYS cc_start: 0.8396 (tptm) cc_final: 0.7813 (tptp) REVERT: G 198 MET cc_start: 0.8509 (ptt) cc_final: 0.8155 (ptt) REVERT: G 224 MET cc_start: 0.5338 (OUTLIER) cc_final: 0.4118 (ptm) REVERT: G 226 ARG cc_start: 0.7861 (ptp-170) cc_final: 0.7655 (ptp-170) REVERT: H 33 ARG cc_start: 0.9018 (ttt180) cc_final: 0.8220 (ttt90) REVERT: H 34 MET cc_start: 0.8686 (mmm) cc_final: 0.8143 (mmm) REVERT: H 78 TRP cc_start: 0.9207 (m-10) cc_final: 0.8953 (m-10) REVERT: H 198 MET cc_start: 0.9172 (tmm) cc_final: 0.8874 (ppp) REVERT: H 201 LEU cc_start: 0.9637 (mp) cc_final: 0.9380 (pp) REVERT: H 218 CYS cc_start: 0.9420 (t) cc_final: 0.8948 (p) REVERT: I 33 ARG cc_start: 0.7586 (ttt180) cc_final: 0.7080 (ttt90) REVERT: I 52 PHE cc_start: 0.6581 (t80) cc_final: 0.5455 (t80) REVERT: I 77 PHE cc_start: 0.9158 (OUTLIER) cc_final: 0.8744 (t80) REVERT: I 224 MET cc_start: 0.9003 (mmm) cc_final: 0.7731 (tmm) REVERT: J 20 MET cc_start: 0.4160 (tpp) cc_final: 0.3683 (mmt) REVERT: J 23 LYS cc_start: 0.8774 (ptmt) cc_final: 0.8352 (ptmm) REVERT: J 51 ARG cc_start: 0.8311 (tpt170) cc_final: 0.8080 (tpt170) REVERT: J 81 GLN cc_start: 0.9156 (pp30) cc_final: 0.8584 (pp30) REVERT: J 157 PHE cc_start: 0.9169 (OUTLIER) cc_final: 0.8909 (t80) REVERT: J 202 TRP cc_start: 0.8050 (t60) cc_final: 0.7439 (t60) outliers start: 115 outliers final: 88 residues processed: 507 average time/residue: 0.1252 time to fit residues: 95.3667 Evaluate side-chains 539 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 440 time to evaluate : 0.650 ------------------------------------------------------------------------------- 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 145 ILE Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 185 ASP 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 54 CYS Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 146 HIS Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain C residue 12 ILE Chi-restraints excluded: chain C residue 34 MET Chi-restraints excluded: chain C residue 48 GLU Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 77 PHE Chi-restraints excluded: chain C residue 98 HIS Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 186 CYS Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 11 ILE Chi-restraints excluded: chain E residue 20 MET Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 54 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 149 LEU Chi-restraints excluded: chain E residue 180 CYS Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 18 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 97 LEU Chi-restraints excluded: chain F residue 186 CYS Chi-restraints excluded: chain G residue 4 VAL Chi-restraints excluded: chain G residue 7 LEU Chi-restraints excluded: chain G residue 14 LEU Chi-restraints excluded: chain G residue 53 VAL 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 224 MET Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 30 MET Chi-restraints excluded: chain H residue 50 GLU Chi-restraints excluded: chain H residue 54 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 215 ASP Chi-restraints excluded: chain H residue 223 ARG Chi-restraints excluded: chain I residue 13 THR Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 69 PHE Chi-restraints excluded: chain I residue 77 PHE Chi-restraints excluded: chain I residue 98 HIS Chi-restraints excluded: chain I residue 153 LEU Chi-restraints excluded: chain I residue 161 HIS Chi-restraints excluded: chain I residue 186 CYS Chi-restraints excluded: chain I residue 198 MET Chi-restraints excluded: chain I residue 199 LEU Chi-restraints excluded: chain I residue 211 LEU Chi-restraints excluded: chain I residue 213 LEU Chi-restraints excluded: chain J residue 10 LEU Chi-restraints excluded: chain J residue 11 ILE Chi-restraints excluded: chain J residue 53 VAL Chi-restraints excluded: chain J residue 54 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 91 VAL Chi-restraints excluded: chain J residue 149 LEU Chi-restraints excluded: chain J residue 157 PHE Chi-restraints excluded: chain J residue 180 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 118 optimal weight: 0.8980 chunk 113 optimal weight: 0.8980 chunk 114 optimal weight: 4.9990 chunk 164 optimal weight: 0.8980 chunk 108 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 107 optimal weight: 4.9990 chunk 168 optimal weight: 8.9990 chunk 138 optimal weight: 0.9980 chunk 94 optimal weight: 0.3980 chunk 85 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 46 GLN ** J 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.135628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.107829 restraints weight = 46084.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.111948 restraints weight = 30520.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.115013 restraints weight = 22232.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.117323 restraints weight = 17199.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.119102 restraints weight = 13898.164| |-----------------------------------------------------------------------------| r_work (final): 0.3993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6980 moved from start: 0.7476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 16190 Z= 0.144 Angle : 0.938 16.571 22040 Z= 0.431 Chirality : 0.049 0.445 2610 Planarity : 0.007 0.116 2700 Dihedral : 6.079 54.378 2190 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 15.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 5.78 % Allowed : 33.35 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.04 (0.20), residues: 1970 helix: 0.61 (0.15), residues: 1320 sheet: -0.19 (0.51), residues: 100 loop : -1.18 (0.29), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 51 TYR 0.034 0.002 TYR D 143 PHE 0.022 0.001 PHE F 209 TRP 0.020 0.002 TRP A 78 HIS 0.010 0.001 HIS H 161 Details of bonding type rmsd covalent geometry : bond 0.00324 (16160) covalent geometry : angle 0.93554 (21980) SS BOND : bond 0.00413 ( 30) SS BOND : angle 1.67960 ( 60) hydrogen bonds : bond 0.03969 ( 950) hydrogen bonds : angle 4.42463 ( 2820) ********************** 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 544 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 444 time to evaluate : 0.638 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: D 28 LEU cc_start: 0.9494 (mm) cc_final: 0.9151 (mm) REVERT: D 34 MET cc_start: 0.8644 (mmm) cc_final: 0.8324 (mmm) REVERT: D 39 LEU cc_start: 0.9514 (mt) cc_final: 0.9049 (tp) REVERT: D 42 ARG cc_start: 0.9238 (tpt90) cc_final: 0.8788 (ttt180) REVERT: D 46 GLN cc_start: 0.9448 (tm-30) cc_final: 0.9104 (mm-40) REVERT: D 51 ARG cc_start: 0.8970 (mmt180) cc_final: 0.8550 (mmt90) REVERT: D 78 TRP cc_start: 0.6904 (m-10) cc_final: 0.5535 (m-90) REVERT: D 86 LEU cc_start: 0.9282 (mm) cc_final: 0.9010 (mm) REVERT: D 193 GLU cc_start: 0.8231 (mm-30) cc_final: 0.8007 (mm-30) REVERT: D 211 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8579 (tt) REVERT: A 20 MET cc_start: 0.6437 (mmm) cc_final: 0.5589 (mmt) REVERT: A 23 LYS cc_start: 0.8894 (mmtt) cc_final: 0.8291 (mmtm) REVERT: A 30 MET cc_start: 0.8972 (tmm) cc_final: 0.8656 (tmm) REVERT: A 78 TRP cc_start: 0.9322 (m-90) cc_final: 0.8286 (m-90) REVERT: A 198 MET cc_start: 0.8094 (ptt) cc_final: 0.7197 (tpt) REVERT: B 33 ARG cc_start: 0.8626 (ttt180) cc_final: 0.8274 (ttm-80) REVERT: B 55 ASN cc_start: 0.8991 (m-40) cc_final: 0.8233 (t0) REVERT: B 154 GLU cc_start: 0.9288 (tt0) cc_final: 0.9053 (tt0) REVERT: B 193 GLU cc_start: 0.9657 (mm-30) cc_final: 0.9321 (mm-30) REVERT: B 202 TRP cc_start: 0.9318 (t60) cc_final: 0.8572 (t-100) REVERT: C 12 ILE cc_start: 0.9306 (OUTLIER) cc_final: 0.9066 (tp) REVERT: C 34 MET cc_start: 0.8267 (OUTLIER) cc_final: 0.7600 (pmm) REVERT: C 52 PHE cc_start: 0.6880 (t80) cc_final: 0.5353 (t80) REVERT: C 77 PHE cc_start: 0.8799 (OUTLIER) cc_final: 0.8501 (m-80) REVERT: E 23 LYS cc_start: 0.8802 (ptpt) cc_final: 0.8399 (pttt) REVERT: E 34 MET cc_start: 0.7705 (mmp) cc_final: 0.6826 (tmm) REVERT: E 39 LEU cc_start: 0.9696 (tp) cc_final: 0.9403 (pp) REVERT: E 51 ARG cc_start: 0.8403 (tpt170) cc_final: 0.8002 (tpt170) REVERT: E 81 GLN cc_start: 0.9012 (pt0) cc_final: 0.8725 (pt0) REVERT: E 87 LEU cc_start: 0.9288 (tt) cc_final: 0.8632 (mt) REVERT: E 98 HIS cc_start: 0.9454 (t70) cc_final: 0.8983 (t-170) REVERT: E 202 TRP cc_start: 0.8048 (t60) cc_final: 0.7608 (t60) REVERT: F 20 MET cc_start: 0.8515 (ppp) cc_final: 0.8105 (pmm) REVERT: F 23 LYS cc_start: 0.9301 (mmtt) cc_final: 0.8661 (mmtp) REVERT: F 39 LEU cc_start: 0.9554 (mt) cc_final: 0.9097 (tp) REVERT: F 42 ARG cc_start: 0.9220 (tpt90) cc_final: 0.8892 (tpt90) REVERT: F 51 ARG cc_start: 0.8656 (mmm160) cc_final: 0.8357 (mmm160) REVERT: F 147 LEU cc_start: 0.8561 (mt) cc_final: 0.8327 (mt) REVERT: G 20 MET cc_start: 0.4938 (mmm) cc_final: 0.4601 (mmm) REVERT: G 77 PHE cc_start: 0.8773 (t80) cc_final: 0.8389 (t80) REVERT: G 157 PHE cc_start: 0.8770 (m-80) cc_final: 0.8436 (m-80) REVERT: G 198 MET cc_start: 0.8513 (ptt) cc_final: 0.8177 (ptt) REVERT: G 224 MET cc_start: 0.5002 (OUTLIER) cc_final: 0.3908 (ptm) REVERT: H 33 ARG cc_start: 0.9013 (ttt180) cc_final: 0.8384 (ttm-80) REVERT: H 78 TRP cc_start: 0.9213 (m-10) cc_final: 0.8966 (m-10) REVERT: H 154 GLU cc_start: 0.9226 (tp30) cc_final: 0.8329 (tt0) REVERT: H 194 LYS cc_start: 0.9200 (mttp) cc_final: 0.8827 (mttt) REVERT: H 198 MET cc_start: 0.9166 (tmm) cc_final: 0.8879 (ppp) REVERT: H 201 LEU cc_start: 0.9627 (mp) cc_final: 0.9348 (pp) REVERT: H 218 CYS cc_start: 0.9413 (t) cc_final: 0.8944 (p) REVERT: I 33 ARG cc_start: 0.7573 (ttt180) cc_final: 0.6930 (ttt180) REVERT: I 52 PHE cc_start: 0.6687 (t80) cc_final: 0.5562 (t80) REVERT: I 77 PHE cc_start: 0.9137 (OUTLIER) cc_final: 0.8737 (t80) REVERT: I 224 MET cc_start: 0.9010 (mmm) cc_final: 0.7749 (tmm) REVERT: J 20 MET cc_start: 0.3973 (tpp) cc_final: 0.3527 (mmt) REVERT: J 23 LYS cc_start: 0.8727 (ptmt) cc_final: 0.8322 (ptmm) REVERT: J 51 ARG cc_start: 0.8276 (tpt170) cc_final: 0.8032 (tpt170) REVERT: J 81 GLN cc_start: 0.9137 (pp30) cc_final: 0.8543 (pp30) REVERT: J 157 PHE cc_start: 0.9179 (OUTLIER) cc_final: 0.8928 (t80) REVERT: J 202 TRP cc_start: 0.8030 (t60) cc_final: 0.7425 (t60) outliers start: 100 outliers final: 83 residues processed: 496 average time/residue: 0.1252 time to fit residues: 93.1651 Evaluate side-chains 526 residues out of total 1730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 436 time to evaluate : 0.613 ------------------------------------------------------------------------------- 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 11 ILE Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 185 ASP 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 54 CYS Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 146 HIS Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain C residue 12 ILE Chi-restraints excluded: chain C residue 34 MET Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 77 PHE Chi-restraints excluded: chain C residue 98 HIS Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 186 CYS Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 11 ILE Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 54 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 91 VAL Chi-restraints excluded: chain E residue 149 LEU Chi-restraints excluded: chain E residue 180 CYS Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 18 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 97 LEU Chi-restraints excluded: chain G residue 4 VAL Chi-restraints excluded: chain G residue 14 LEU Chi-restraints excluded: chain G residue 53 VAL 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 224 MET Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 30 MET Chi-restraints excluded: chain H residue 50 GLU Chi-restraints excluded: chain H residue 54 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 215 ASP Chi-restraints excluded: chain H residue 223 ARG Chi-restraints excluded: chain I residue 13 THR Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 69 PHE Chi-restraints excluded: chain I residue 77 PHE Chi-restraints excluded: chain I residue 98 HIS Chi-restraints excluded: chain I residue 153 LEU Chi-restraints excluded: chain I residue 161 HIS Chi-restraints excluded: chain I residue 186 CYS Chi-restraints excluded: chain I residue 198 MET Chi-restraints excluded: chain I residue 199 LEU Chi-restraints excluded: chain I residue 211 LEU Chi-restraints excluded: chain I residue 213 LEU Chi-restraints excluded: chain J residue 10 LEU Chi-restraints excluded: chain J residue 11 ILE Chi-restraints excluded: chain J residue 53 VAL Chi-restraints excluded: chain J residue 54 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 91 VAL Chi-restraints excluded: chain J residue 149 LEU Chi-restraints excluded: chain J residue 157 PHE Chi-restraints excluded: chain J residue 180 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 155 optimal weight: 2.9990 chunk 143 optimal weight: 2.9990 chunk 10 optimal weight: 20.0000 chunk 169 optimal weight: 2.9990 chunk 153 optimal weight: 0.7980 chunk 100 optimal weight: 7.9990 chunk 128 optimal weight: 0.0060 chunk 196 optimal weight: 0.8980 chunk 21 optimal weight: 0.4980 chunk 134 optimal weight: 9.9990 chunk 44 optimal weight: 0.9980 overall best weight: 0.6396 ------------------------------------------------------------------------------- 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** ** E 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 161 HIS ** I 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 46 GLN ** J 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.136332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.108544 restraints weight = 46380.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.112621 restraints weight = 31223.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.115621 restraints weight = 22854.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.117944 restraints weight = 17832.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.119704 restraints weight = 14424.581| |-----------------------------------------------------------------------------| r_work (final): 0.4013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6981 moved from start: 0.7622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 16190 Z= 0.142 Angle : 0.949 15.370 22040 Z= 0.431 Chirality : 0.048 0.432 2610 Planarity : 0.007 0.116 2700 Dihedral : 6.018 53.835 2190 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 15.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 5.03 % Allowed : 33.99 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.09 (0.20), residues: 1970 helix: 0.64 (0.15), residues: 1310 sheet: -0.30 (0.51), residues: 100 loop : -1.08 (0.29), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 76 TYR 0.028 0.002 TYR D 143 PHE 0.021 0.001 PHE D 173 TRP 0.019 0.002 TRP A 78 HIS 0.005 0.001 HIS A 74 Details of bonding type rmsd covalent geometry : bond 0.00321 (16160) covalent geometry : angle 0.94656 (21980) SS BOND : bond 0.00381 ( 30) SS BOND : angle 1.55303 ( 60) hydrogen bonds : bond 0.03868 ( 950) hydrogen bonds : angle 4.40326 ( 2820) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3904.61 seconds wall clock time: 67 minutes 57.72 seconds (4077.72 seconds total)