Starting phenix.real_space_refine on Sun Aug 24 05:13:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hxc_35076/08_2025/8hxc_35076.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hxc_35076/08_2025/8hxc_35076.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8hxc_35076/08_2025/8hxc_35076.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hxc_35076/08_2025/8hxc_35076.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hxc_35076/08_2025/8hxc_35076.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hxc_35076/08_2025/8hxc_35076.map" } resolution = 3.12 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= 0.001 sd= 0.037 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 10941 2.51 5 N 2933 2.21 5 O 3360 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 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: 17374 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1610 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 6, 'TRANS': 194} Chain: "H" Number of atoms: 872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 872 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 2, 'TRANS': 103} Restraints were copied for chains: B, C, D, E, F, G, I, J, K, L, M, N Time building chain proxies: 2.38, per 1000 atoms: 0.14 Number of scatterers: 17374 At special positions: 0 Unit cell: (185.25, 183.35, 67.45, 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 3360 8.00 N 2933 7.00 C 10941 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=28, symmetry=0 Simple disulfide: pdb=" SG CYS A 25 " - pdb=" SG CYS B 130 " distance=2.03 Simple disulfide: pdb=" SG CYS A 56 " - pdb=" SG CYS A 217 " distance=2.03 Simple disulfide: pdb=" SG CYS A 125 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 130 " - pdb=" SG CYS G 25 " distance=2.04 Simple disulfide: pdb=" SG CYS A 160 " - pdb=" SG CYS A 205 " distance=2.02 Simple disulfide: pdb=" SG CYS B 25 " - pdb=" SG CYS C 130 " distance=1.99 Simple disulfide: pdb=" SG CYS C 25 " - pdb=" SG CYS D 130 " distance=2.05 Simple disulfide: pdb=" SG CYS D 25 " - pdb=" SG CYS E 130 " distance=2.07 Simple disulfide: pdb=" SG CYS E 25 " - pdb=" SG CYS F 130 " distance=2.01 Simple disulfide: pdb=" SG CYS F 25 " - pdb=" SG CYS G 130 " distance=2.02 Simple disulfide: pdb=" SG CYS B 56 " - pdb=" SG CYS B 217 " distance=2.03 Simple disulfide: pdb=" SG CYS C 56 " - pdb=" SG CYS C 217 " distance=2.03 Simple disulfide: pdb=" SG CYS D 56 " - pdb=" SG CYS D 217 " distance=2.03 Simple disulfide: pdb=" SG CYS E 56 " - pdb=" SG CYS E 217 " distance=2.03 Simple disulfide: pdb=" SG CYS F 56 " - pdb=" SG CYS F 217 " distance=2.03 Simple disulfide: pdb=" SG CYS G 56 " - pdb=" SG CYS G 217 " distance=2.03 Simple disulfide: pdb=" SG CYS B 125 " - pdb=" SG CYS B 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 125 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS D 125 " - pdb=" SG CYS D 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 125 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS F 125 " - pdb=" SG CYS F 157 " distance=2.03 Simple disulfide: pdb=" SG CYS G 125 " - pdb=" SG CYS G 157 " distance=2.03 Simple disulfide: pdb=" SG CYS B 160 " - pdb=" SG CYS B 205 " distance=2.02 Simple disulfide: pdb=" SG CYS C 160 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS D 160 " - pdb=" SG CYS D 205 " distance=2.02 Simple disulfide: pdb=" SG CYS E 160 " - pdb=" SG CYS E 205 " distance=2.02 Simple disulfide: pdb=" SG CYS F 160 " - pdb=" SG CYS F 205 " distance=2.02 Simple disulfide: pdb=" SG CYS G 160 " - pdb=" SG CYS G 205 " distance=2.02 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: 1.53 Conformation dependent library (CDL) restraints added in 898.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4102 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 28 sheets defined 4.9% alpha, 34.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'A' and resid 187 through 191 removed outlier: 3.649A pdb=" N MET A 190 " --> pdb=" O GLU A 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 191 removed outlier: 3.648A pdb=" N MET B 190 " --> pdb=" O GLU B 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 191 removed outlier: 3.649A pdb=" N MET C 190 " --> pdb=" O GLU C 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 191 removed outlier: 3.649A pdb=" N MET D 190 " --> pdb=" O GLU D 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 191 removed outlier: 3.649A pdb=" N MET E 190 " --> pdb=" O GLU E 187 " (cutoff:3.500A) Processing helix chain 'F' and resid 187 through 191 removed outlier: 3.647A pdb=" N MET F 190 " --> pdb=" O GLU F 187 " (cutoff:3.500A) Processing helix chain 'G' and resid 187 through 191 removed outlier: 3.648A pdb=" N MET G 190 " --> pdb=" O GLU G 187 " (cutoff:3.500A) Processing helix chain 'H' and resid 49 through 53 removed outlier: 3.710A pdb=" N GLU H 52 " --> pdb=" O SER H 49 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU H 53 " --> pdb=" O LEU H 50 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 49 through 53' Processing helix chain 'H' and resid 79 through 83 Processing helix chain 'I' and resid 49 through 53 removed outlier: 3.710A pdb=" N GLU I 52 " --> pdb=" O SER I 49 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU I 53 " --> pdb=" O LEU I 50 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 49 through 53' Processing helix chain 'I' and resid 79 through 83 Processing helix chain 'J' and resid 49 through 53 removed outlier: 3.711A pdb=" N GLU J 52 " --> pdb=" O SER J 49 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU J 53 " --> pdb=" O LEU J 50 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 49 through 53' Processing helix chain 'J' and resid 79 through 83 Processing helix chain 'K' and resid 49 through 53 removed outlier: 3.710A pdb=" N GLU K 52 " --> pdb=" O SER K 49 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU K 53 " --> pdb=" O LEU K 50 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 49 through 53' Processing helix chain 'K' and resid 79 through 83 Processing helix chain 'L' and resid 49 through 53 removed outlier: 3.710A pdb=" N GLU L 52 " --> pdb=" O SER L 49 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU L 53 " --> pdb=" O LEU L 50 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 49 through 53' Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'M' and resid 49 through 53 removed outlier: 3.710A pdb=" N GLU M 52 " --> pdb=" O SER M 49 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU M 53 " --> pdb=" O LEU M 50 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 49 through 53' Processing helix chain 'M' and resid 79 through 83 Processing helix chain 'N' and resid 49 through 53 removed outlier: 3.710A pdb=" N GLU N 52 " --> pdb=" O SER N 49 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU N 53 " --> pdb=" O LEU N 50 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 49 through 53' Processing helix chain 'N' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 181 through 184 removed outlier: 5.531A pdb=" N PHE A 36 " --> pdb=" O THR A 108 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N THR A 108 " --> pdb=" O PHE A 36 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA A 38 " --> pdb=" O LEU A 106 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N LYS A 101 " --> pdb=" O VAL A 96 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N VAL A 96 " --> pdb=" O LYS A 101 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N SER A 103 " --> pdb=" O GLU A 94 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N GLU A 94 " --> pdb=" O SER A 103 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N LEU A 105 " --> pdb=" O ALA A 92 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ALA A 92 " --> pdb=" O LEU A 105 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N PHE A 107 " --> pdb=" O VAL A 90 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 57 through 62 Processing sheet with id=AA3, first strand: chain 'A' and resid 160 through 165 removed outlier: 9.443A pdb=" N SER A 193 " --> pdb=" O HIS H 124 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N HIS H 124 " --> pdb=" O SER A 193 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N GLY A 195 " --> pdb=" O ARG H 122 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ILE H 112 " --> pdb=" O ILE H 123 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N GLN H 125 " --> pdb=" O CYS H 110 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N CYS H 110 " --> pdb=" O GLN H 125 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N ASN H 127 " --> pdb=" O TYR H 108 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N TYR H 108 " --> pdb=" O ASN H 127 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N VAL H 55 " --> pdb=" O GLU H 67 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N GLU H 67 " --> pdb=" O VAL H 55 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N TRP H 57 " --> pdb=" O LEU H 65 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 181 through 184 removed outlier: 5.530A pdb=" N PHE B 36 " --> pdb=" O THR B 108 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N THR B 108 " --> pdb=" O PHE B 36 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA B 38 " --> pdb=" O LEU B 106 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N LYS B 101 " --> pdb=" O VAL B 96 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N VAL B 96 " --> pdb=" O LYS B 101 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N SER B 103 " --> pdb=" O GLU B 94 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N GLU B 94 " --> pdb=" O SER B 103 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LEU B 105 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ALA B 92 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N PHE B 107 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 57 through 62 Processing sheet with id=AA6, first strand: chain 'B' and resid 160 through 165 removed outlier: 9.397A pdb=" N SER B 193 " --> pdb=" O HIS I 124 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N HIS I 124 " --> pdb=" O SER B 193 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N GLY B 195 " --> pdb=" O ARG I 122 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ILE I 112 " --> pdb=" O ILE I 123 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N GLN I 125 " --> pdb=" O CYS I 110 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N CYS I 110 " --> pdb=" O GLN I 125 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N ASN I 127 " --> pdb=" O TYR I 108 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N TYR I 108 " --> pdb=" O ASN I 127 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N VAL I 55 " --> pdb=" O GLU I 67 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N GLU I 67 " --> pdb=" O VAL I 55 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N TRP I 57 " --> pdb=" O LEU I 65 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 181 through 184 removed outlier: 5.530A pdb=" N PHE C 36 " --> pdb=" O THR C 108 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N THR C 108 " --> pdb=" O PHE C 36 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA C 38 " --> pdb=" O LEU C 106 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N LYS C 101 " --> pdb=" O VAL C 96 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N VAL C 96 " --> pdb=" O LYS C 101 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N SER C 103 " --> pdb=" O GLU C 94 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N GLU C 94 " --> pdb=" O SER C 103 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N LEU C 105 " --> pdb=" O ALA C 92 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ALA C 92 " --> pdb=" O LEU C 105 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N PHE C 107 " --> pdb=" O VAL C 90 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 57 through 62 Processing sheet with id=AA9, first strand: chain 'C' and resid 160 through 165 removed outlier: 9.444A pdb=" N SER C 193 " --> pdb=" O HIS J 124 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N HIS J 124 " --> pdb=" O SER C 193 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N GLY C 195 " --> pdb=" O ARG J 122 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ILE J 112 " --> pdb=" O ILE J 123 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N GLN J 125 " --> pdb=" O CYS J 110 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N CYS J 110 " --> pdb=" O GLN J 125 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N ASN J 127 " --> pdb=" O TYR J 108 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N TYR J 108 " --> pdb=" O ASN J 127 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N VAL J 55 " --> pdb=" O GLU J 67 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N GLU J 67 " --> pdb=" O VAL J 55 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N TRP J 57 " --> pdb=" O LEU J 65 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 181 through 184 removed outlier: 5.530A pdb=" N PHE D 36 " --> pdb=" O THR D 108 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N THR D 108 " --> pdb=" O PHE D 36 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA D 38 " --> pdb=" O LEU D 106 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N LYS D 101 " --> pdb=" O VAL D 96 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N VAL D 96 " --> pdb=" O LYS D 101 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N SER D 103 " --> pdb=" O GLU D 94 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N GLU D 94 " --> pdb=" O SER D 103 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LEU D 105 " --> pdb=" O ALA D 92 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ALA D 92 " --> pdb=" O LEU D 105 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N PHE D 107 " --> pdb=" O VAL D 90 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 57 through 62 Processing sheet with id=AB3, first strand: chain 'D' and resid 160 through 165 removed outlier: 9.240A pdb=" N SER D 193 " --> pdb=" O HIS K 124 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N HIS K 124 " --> pdb=" O SER D 193 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N GLY D 195 " --> pdb=" O ARG K 122 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ILE K 112 " --> pdb=" O ILE K 123 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N GLN K 125 " --> pdb=" O CYS K 110 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N CYS K 110 " --> pdb=" O GLN K 125 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N ASN K 127 " --> pdb=" O TYR K 108 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N TYR K 108 " --> pdb=" O ASN K 127 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N VAL K 55 " --> pdb=" O GLU K 67 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N GLU K 67 " --> pdb=" O VAL K 55 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N TRP K 57 " --> pdb=" O LEU K 65 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 181 through 184 removed outlier: 5.531A pdb=" N PHE E 36 " --> pdb=" O THR E 108 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N THR E 108 " --> pdb=" O PHE E 36 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA E 38 " --> pdb=" O LEU E 106 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N LYS E 101 " --> pdb=" O VAL E 96 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N VAL E 96 " --> pdb=" O LYS E 101 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N SER E 103 " --> pdb=" O GLU E 94 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N GLU E 94 " --> pdb=" O SER E 103 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N LEU E 105 " --> pdb=" O ALA E 92 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ALA E 92 " --> pdb=" O LEU E 105 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N PHE E 107 " --> pdb=" O VAL E 90 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 57 through 62 Processing sheet with id=AB6, first strand: chain 'E' and resid 160 through 165 removed outlier: 9.501A pdb=" N SER E 193 " --> pdb=" O HIS L 124 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N HIS L 124 " --> pdb=" O SER E 193 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N GLY E 195 " --> pdb=" O ARG L 122 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ILE L 112 " --> pdb=" O ILE L 123 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N GLN L 125 " --> pdb=" O CYS L 110 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N CYS L 110 " --> pdb=" O GLN L 125 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N ASN L 127 " --> pdb=" O TYR L 108 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N TYR L 108 " --> pdb=" O ASN L 127 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N VAL L 55 " --> pdb=" O GLU L 67 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N GLU L 67 " --> pdb=" O VAL L 55 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N TRP L 57 " --> pdb=" O LEU L 65 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 181 through 184 removed outlier: 5.531A pdb=" N PHE F 36 " --> pdb=" O THR F 108 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N THR F 108 " --> pdb=" O PHE F 36 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA F 38 " --> pdb=" O LEU F 106 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N LYS F 101 " --> pdb=" O VAL F 96 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N VAL F 96 " --> pdb=" O LYS F 101 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N SER F 103 " --> pdb=" O GLU F 94 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N GLU F 94 " --> pdb=" O SER F 103 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N LEU F 105 " --> pdb=" O ALA F 92 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ALA F 92 " --> pdb=" O LEU F 105 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N PHE F 107 " --> pdb=" O VAL F 90 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 57 through 62 Processing sheet with id=AB9, first strand: chain 'F' and resid 160 through 165 removed outlier: 9.487A pdb=" N SER F 193 " --> pdb=" O HIS M 124 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N HIS M 124 " --> pdb=" O SER F 193 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N GLY F 195 " --> pdb=" O ARG M 122 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ILE M 112 " --> pdb=" O ILE M 123 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N GLN M 125 " --> pdb=" O CYS M 110 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N CYS M 110 " --> pdb=" O GLN M 125 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N ASN M 127 " --> pdb=" O TYR M 108 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N TYR M 108 " --> pdb=" O ASN M 127 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N VAL M 55 " --> pdb=" O GLU M 67 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N GLU M 67 " --> pdb=" O VAL M 55 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N TRP M 57 " --> pdb=" O LEU M 65 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 181 through 184 removed outlier: 5.531A pdb=" N PHE G 36 " --> pdb=" O THR G 108 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N THR G 108 " --> pdb=" O PHE G 36 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA G 38 " --> pdb=" O LEU G 106 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N LYS G 101 " --> pdb=" O VAL G 96 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N VAL G 96 " --> pdb=" O LYS G 101 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N SER G 103 " --> pdb=" O GLU G 94 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N GLU G 94 " --> pdb=" O SER G 103 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N LEU G 105 " --> pdb=" O ALA G 92 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ALA G 92 " --> pdb=" O LEU G 105 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N PHE G 107 " --> pdb=" O VAL G 90 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 57 through 62 Processing sheet with id=AC3, first strand: chain 'G' and resid 160 through 165 removed outlier: 9.503A pdb=" N SER G 193 " --> pdb=" O HIS N 124 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N HIS N 124 " --> pdb=" O SER G 193 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N GLY G 195 " --> pdb=" O ARG N 122 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ILE N 112 " --> pdb=" O ILE N 123 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N GLN N 125 " --> pdb=" O CYS N 110 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N CYS N 110 " --> pdb=" O GLN N 125 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N ASN N 127 " --> pdb=" O TYR N 108 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N TYR N 108 " --> pdb=" O ASN N 127 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N VAL N 55 " --> pdb=" O GLU N 67 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N GLU N 67 " --> pdb=" O VAL N 55 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N TRP N 57 " --> pdb=" O LEU N 65 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 35 through 39 Processing sheet with id=AC5, first strand: chain 'I' and resid 35 through 39 Processing sheet with id=AC6, first strand: chain 'J' and resid 35 through 39 Processing sheet with id=AC7, first strand: chain 'K' and resid 35 through 39 Processing sheet with id=AC8, first strand: chain 'L' and resid 35 through 39 Processing sheet with id=AC9, first strand: chain 'M' and resid 35 through 39 Processing sheet with id=AD1, first strand: chain 'N' and resid 35 through 39 504 hydrogen bonds defined for protein. 1260 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: 2.94 Time building geometry restraints manager: 2.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5545 1.34 - 1.46: 4049 1.46 - 1.58: 7934 1.58 - 1.70: 7 1.70 - 1.83: 203 Bond restraints: 17738 Sorted by residual: bond pdb=" CA GLU L 52 " pdb=" CB GLU L 52 " ideal model delta sigma weight residual 1.527 1.630 -0.103 2.48e-02 1.63e+03 1.73e+01 bond pdb=" CA GLU M 52 " pdb=" CB GLU M 52 " ideal model delta sigma weight residual 1.527 1.630 -0.103 2.48e-02 1.63e+03 1.72e+01 bond pdb=" CA GLU J 52 " pdb=" CB GLU J 52 " ideal model delta sigma weight residual 1.527 1.630 -0.103 2.48e-02 1.63e+03 1.72e+01 bond pdb=" CA GLU H 52 " pdb=" CB GLU H 52 " ideal model delta sigma weight residual 1.527 1.630 -0.103 2.48e-02 1.63e+03 1.71e+01 bond pdb=" CA GLU N 52 " pdb=" CB GLU N 52 " ideal model delta sigma weight residual 1.527 1.630 -0.102 2.48e-02 1.63e+03 1.70e+01 ... (remaining 17733 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.08: 23417 3.08 - 6.17: 453 6.17 - 9.25: 91 9.25 - 12.34: 30 12.34 - 15.42: 19 Bond angle restraints: 24010 Sorted by residual: angle pdb=" C ASN F 203 " pdb=" N GLN F 204 " pdb=" CA GLN F 204 " ideal model delta sigma weight residual 124.31 134.19 -9.88 1.67e+00 3.59e-01 3.50e+01 angle pdb=" C ASN E 203 " pdb=" N GLN E 204 " pdb=" CA GLN E 204 " ideal model delta sigma weight residual 124.31 134.18 -9.87 1.67e+00 3.59e-01 3.49e+01 angle pdb=" C ASN A 203 " pdb=" N GLN A 204 " pdb=" CA GLN A 204 " ideal model delta sigma weight residual 124.31 134.16 -9.85 1.67e+00 3.59e-01 3.48e+01 angle pdb=" C ASN C 203 " pdb=" N GLN C 204 " pdb=" CA GLN C 204 " ideal model delta sigma weight residual 124.31 134.16 -9.85 1.67e+00 3.59e-01 3.48e+01 angle pdb=" CA GLU I 52 " pdb=" CB GLU I 52 " pdb=" CG GLU I 52 " ideal model delta sigma weight residual 114.10 125.85 -11.75 2.00e+00 2.50e-01 3.45e+01 ... (remaining 24005 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.67: 8930 15.67 - 31.34: 1326 31.34 - 47.00: 342 47.00 - 62.67: 112 62.67 - 78.34: 21 Dihedral angle restraints: 10731 sinusoidal: 4361 harmonic: 6370 Sorted by residual: dihedral pdb=" CB CYS B 160 " pdb=" SG CYS B 160 " pdb=" SG CYS B 205 " pdb=" CB CYS B 205 " ideal model delta sinusoidal sigma weight residual 93.00 165.16 -72.16 1 1.00e+01 1.00e-02 6.66e+01 dihedral pdb=" CB CYS G 160 " pdb=" SG CYS G 160 " pdb=" SG CYS G 205 " pdb=" CB CYS G 205 " ideal model delta sinusoidal sigma weight residual 93.00 165.16 -72.16 1 1.00e+01 1.00e-02 6.66e+01 dihedral pdb=" CB CYS A 160 " pdb=" SG CYS A 160 " pdb=" SG CYS A 205 " pdb=" CB CYS A 205 " ideal model delta sinusoidal sigma weight residual 93.00 165.15 -72.15 1 1.00e+01 1.00e-02 6.66e+01 ... (remaining 10728 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1747 0.058 - 0.116: 714 0.116 - 0.175: 150 0.175 - 0.233: 35 0.233 - 0.291: 21 Chirality restraints: 2667 Sorted by residual: chirality pdb=" CG LEU L 63 " pdb=" CB LEU L 63 " pdb=" CD1 LEU L 63 " pdb=" CD2 LEU L 63 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.12e+00 chirality pdb=" CG LEU N 63 " pdb=" CB LEU N 63 " pdb=" CD1 LEU N 63 " pdb=" CD2 LEU N 63 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" CG LEU M 63 " pdb=" CB LEU M 63 " pdb=" CD1 LEU M 63 " pdb=" CD2 LEU M 63 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.06e+00 ... (remaining 2664 not shown) Planarity restraints: 3066 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS M 124 " 0.015 2.00e-02 2.50e+03 2.11e-02 6.71e+00 pdb=" CG HIS M 124 " -0.045 2.00e-02 2.50e+03 pdb=" ND1 HIS M 124 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 HIS M 124 " 0.016 2.00e-02 2.50e+03 pdb=" CE1 HIS M 124 " -0.001 2.00e-02 2.50e+03 pdb=" NE2 HIS M 124 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS K 124 " 0.015 2.00e-02 2.50e+03 2.11e-02 6.67e+00 pdb=" CG HIS K 124 " -0.045 2.00e-02 2.50e+03 pdb=" ND1 HIS K 124 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 HIS K 124 " 0.016 2.00e-02 2.50e+03 pdb=" CE1 HIS K 124 " -0.001 2.00e-02 2.50e+03 pdb=" NE2 HIS K 124 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS L 124 " 0.015 2.00e-02 2.50e+03 2.10e-02 6.63e+00 pdb=" CG HIS L 124 " -0.044 2.00e-02 2.50e+03 pdb=" ND1 HIS L 124 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 HIS L 124 " 0.016 2.00e-02 2.50e+03 pdb=" CE1 HIS L 124 " -0.001 2.00e-02 2.50e+03 pdb=" NE2 HIS L 124 " 0.000 2.00e-02 2.50e+03 ... (remaining 3063 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 186 2.61 - 3.18: 13326 3.18 - 3.75: 25835 3.75 - 4.33: 36457 4.33 - 4.90: 62624 Nonbonded interactions: 138428 Sorted by model distance: nonbonded pdb=" SG CYS K 40 " pdb=" SG CYS K 110 " model vdw 2.032 3.760 nonbonded pdb=" SG CYS I 40 " pdb=" SG CYS I 110 " model vdw 2.032 3.760 nonbonded pdb=" SG CYS L 40 " pdb=" SG CYS L 110 " model vdw 2.032 3.760 nonbonded pdb=" SG CYS N 40 " pdb=" SG CYS N 110 " model vdw 2.032 3.760 nonbonded pdb=" SG CYS H 40 " pdb=" SG CYS H 110 " model vdw 2.032 3.760 ... (remaining 138423 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } 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=0.00 max=1.00 mean=0.93 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 15.330 Find NCS groups from input model: 0.160 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: 0.010 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7211 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.103 17766 Z= 0.295 Angle : 1.205 15.424 24066 Z= 0.608 Chirality : 0.068 0.291 2667 Planarity : 0.006 0.039 3066 Dihedral : 16.375 78.339 6545 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 1.05 % Allowed : 27.02 % Favored : 71.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.46 (0.17), residues: 2121 helix: None (None), residues: 0 sheet: -0.35 (0.16), residues: 903 loop : -1.48 (0.16), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG N 85 TYR 0.025 0.003 TYR G 74 PHE 0.030 0.003 PHE N 56 TRP 0.030 0.005 TRP D 34 HIS 0.027 0.003 HIS M 124 Details of bonding type rmsd covalent geometry : bond 0.00689 (17738) covalent geometry : angle 1.20383 (24010) SS BOND : bond 0.01307 ( 28) SS BOND : angle 1.53520 ( 56) hydrogen bonds : bond 0.14434 ( 504) hydrogen bonds : angle 7.95237 ( 1260) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 392 time to evaluate : 0.709 Fit side-chains REVERT: B 83 MET cc_start: 0.8012 (mmt) cc_final: 0.7597 (mpp) REVERT: B 88 ARG cc_start: 0.8734 (ptp-170) cc_final: 0.8494 (ptp90) REVERT: B 173 HIS cc_start: 0.8316 (m-70) cc_final: 0.7925 (m90) REVERT: D 83 MET cc_start: 0.8013 (mmt) cc_final: 0.7559 (mpp) REVERT: E 83 MET cc_start: 0.7906 (mmt) cc_final: 0.7433 (mpp) REVERT: F 83 MET cc_start: 0.7980 (mmt) cc_final: 0.7531 (mpp) REVERT: F 126 MET cc_start: 0.8532 (mmp) cc_final: 0.8316 (mmm) REVERT: F 213 SER cc_start: 0.8648 (p) cc_final: 0.8434 (m) REVERT: G 83 MET cc_start: 0.7999 (mmt) cc_final: 0.7610 (mpp) REVERT: H 50 LEU cc_start: 0.7873 (tt) cc_final: 0.7496 (tt) REVERT: H 74 LYS cc_start: 0.6836 (mtpp) cc_final: 0.6322 (mmtp) REVERT: I 50 LEU cc_start: 0.8022 (tt) cc_final: 0.7815 (tt) REVERT: L 50 LEU cc_start: 0.7414 (tt) cc_final: 0.7139 (tt) REVERT: L 63 LEU cc_start: 0.8093 (mm) cc_final: 0.7593 (mp) REVERT: N 50 LEU cc_start: 0.7929 (tt) cc_final: 0.7638 (tt) REVERT: N 63 LEU cc_start: 0.8531 (mm) cc_final: 0.8030 (mp) outliers start: 21 outliers final: 7 residues processed: 406 average time/residue: 0.1548 time to fit residues: 91.3222 Evaluate side-chains 274 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 267 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain D residue 143 ILE Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain F residue 143 ILE Chi-restraints excluded: chain G residue 143 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 98 optimal weight: 0.3980 chunk 194 optimal weight: 0.8980 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 30.0000 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN A 162 ASN A 173 HIS B 79 ASN B 162 ASN B 179 ASN C 79 ASN C 162 ASN ** C 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 79 ASN D 162 ASN ** D 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 204 GLN E 162 ASN E 204 GLN F 79 ASN F 162 ASN ** F 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 204 GLN G 79 ASN G 162 ASN ** G 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 179 ASN G 204 GLN H 124 HIS I 124 HIS J 124 HIS K 41 GLN K 124 HIS ** L 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 124 HIS M 124 HIS ** N 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 124 HIS N 127 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.197428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.146399 restraints weight = 19558.159| |-----------------------------------------------------------------------------| r_work (start): 0.3693 rms_B_bonded: 2.75 r_work: 0.3353 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3361 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3361 r_free = 0.3361 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1015 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3342 r_free = 0.3342 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1030 | |-----------------------------------------------------------------------------| r_final: 0.3342 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 17766 Z= 0.166 Angle : 0.669 8.437 24066 Z= 0.346 Chirality : 0.048 0.172 2667 Planarity : 0.004 0.034 3066 Dihedral : 5.099 25.624 2352 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 5.71 % Allowed : 22.71 % Favored : 71.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.44 (0.17), residues: 2121 helix: None (None), residues: 0 sheet: -0.61 (0.16), residues: 973 loop : -1.22 (0.17), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG N 85 TYR 0.013 0.001 TYR D 46 PHE 0.016 0.001 PHE H 56 TRP 0.012 0.002 TRP B 34 HIS 0.009 0.001 HIS L 124 Details of bonding type rmsd covalent geometry : bond 0.00387 (17738) covalent geometry : angle 0.66875 (24010) SS BOND : bond 0.00187 ( 28) SS BOND : angle 0.70412 ( 56) hydrogen bonds : bond 0.04047 ( 504) hydrogen bonds : angle 6.68782 ( 1260) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 262 time to evaluate : 0.508 Fit side-chains REVERT: A 113 ASP cc_start: 0.8207 (p0) cc_final: 0.7909 (p0) REVERT: B 83 MET cc_start: 0.8233 (mmt) cc_final: 0.7716 (mpp) REVERT: C 113 ASP cc_start: 0.8055 (p0) cc_final: 0.7846 (p0) REVERT: E 28 ARG cc_start: 0.8367 (OUTLIER) cc_final: 0.7870 (ptm160) REVERT: E 185 ASN cc_start: 0.8653 (t0) cc_final: 0.8275 (t0) REVERT: E 190 MET cc_start: 0.8416 (tpp) cc_final: 0.8044 (ttm) REVERT: F 113 ASP cc_start: 0.8216 (p0) cc_final: 0.7974 (p0) REVERT: H 50 LEU cc_start: 0.7927 (OUTLIER) cc_final: 0.7345 (tt) REVERT: I 50 LEU cc_start: 0.8113 (OUTLIER) cc_final: 0.7863 (tt) REVERT: I 83 MET cc_start: 0.7977 (mtt) cc_final: 0.7771 (mmm) REVERT: J 65 LEU cc_start: 0.8201 (OUTLIER) cc_final: 0.7742 (mp) REVERT: J 83 MET cc_start: 0.7928 (mtt) cc_final: 0.7682 (mmm) REVERT: J 126 MET cc_start: 0.7494 (ttt) cc_final: 0.7286 (ptm) REVERT: K 63 LEU cc_start: 0.7933 (mm) cc_final: 0.7718 (mm) REVERT: K 126 MET cc_start: 0.6970 (ptm) cc_final: 0.6709 (ptm) REVERT: L 50 LEU cc_start: 0.7438 (OUTLIER) cc_final: 0.6959 (tt) REVERT: N 50 LEU cc_start: 0.7749 (OUTLIER) cc_final: 0.7324 (tt) outliers start: 114 outliers final: 56 residues processed: 337 average time/residue: 0.1228 time to fit residues: 62.1042 Evaluate side-chains 301 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 239 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 28 ARG Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 138 ASP Chi-restraints excluded: chain D residue 143 ILE Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 159 THR Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 28 ARG Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 28 ARG Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 143 ILE Chi-restraints excluded: chain F residue 152 THR Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 42 ILE Chi-restraints excluded: chain G residue 48 ILE Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 120 SER Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain G residue 152 THR Chi-restraints excluded: chain H residue 50 LEU Chi-restraints excluded: chain I residue 50 LEU Chi-restraints excluded: chain I residue 107 LEU Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain L residue 50 LEU Chi-restraints excluded: chain L residue 107 LEU Chi-restraints excluded: chain N residue 50 LEU Chi-restraints excluded: chain N residue 107 LEU Chi-restraints excluded: chain N residue 126 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 31 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 143 optimal weight: 0.9990 chunk 142 optimal weight: 5.9990 chunk 136 optimal weight: 4.9990 chunk 26 optimal weight: 0.0980 chunk 7 optimal weight: 0.9990 chunk 138 optimal weight: 8.9990 chunk 69 optimal weight: 3.9990 chunk 161 optimal weight: 7.9990 overall best weight: 1.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 HIS A 204 GLN B 79 ASN ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 79 ASN ** C 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 79 ASN D 173 HIS ** D 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 79 ASN ** F 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 173 HIS H 41 GLN I 41 GLN ** I 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 41 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.188778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.134410 restraints weight = 20032.403| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 3.05 r_work: 0.3253 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3133 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3133 r_free = 0.3133 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1030 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3133 r_free = 0.3133 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1024 | |-----------------------------------------------------------------------------| r_final: 0.3133 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.2600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 17766 Z= 0.206 Angle : 0.658 7.848 24066 Z= 0.338 Chirality : 0.048 0.182 2667 Planarity : 0.003 0.028 3066 Dihedral : 4.976 29.532 2352 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 5.41 % Allowed : 21.60 % Favored : 72.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.49 (0.17), residues: 2121 helix: None (None), residues: 0 sheet: -0.75 (0.16), residues: 980 loop : -1.13 (0.17), residues: 1141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG J 85 TYR 0.015 0.001 TYR D 46 PHE 0.013 0.001 PHE K 56 TRP 0.009 0.002 TRP L 57 HIS 0.003 0.001 HIS E 184 Details of bonding type rmsd covalent geometry : bond 0.00485 (17738) covalent geometry : angle 0.65778 (24010) SS BOND : bond 0.00294 ( 28) SS BOND : angle 0.70219 ( 56) hydrogen bonds : bond 0.03771 ( 504) hydrogen bonds : angle 6.23520 ( 1260) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 304 time to evaluate : 0.696 Fit side-chains REVERT: A 113 ASP cc_start: 0.8324 (p0) cc_final: 0.7955 (p0) REVERT: B 84 ASP cc_start: 0.8849 (t70) cc_final: 0.8538 (t0) REVERT: B 187 GLU cc_start: 0.9063 (pt0) cc_final: 0.8849 (pt0) REVERT: C 113 ASP cc_start: 0.8281 (p0) cc_final: 0.7974 (p0) REVERT: D 85 THR cc_start: 0.9095 (p) cc_final: 0.8719 (p) REVERT: D 134 LYS cc_start: 0.8501 (tttt) cc_final: 0.8252 (ttpt) REVERT: E 28 ARG cc_start: 0.8632 (OUTLIER) cc_final: 0.8120 (ptm160) REVERT: E 30 ASP cc_start: 0.7476 (p0) cc_final: 0.7249 (p0) REVERT: E 134 LYS cc_start: 0.8359 (tttt) cc_final: 0.8029 (ttpt) REVERT: F 28 ARG cc_start: 0.8626 (OUTLIER) cc_final: 0.8181 (ptm160) REVERT: F 113 ASP cc_start: 0.8383 (p0) cc_final: 0.8092 (p0) REVERT: F 190 MET cc_start: 0.8533 (tpp) cc_final: 0.8076 (ttm) REVERT: I 50 LEU cc_start: 0.8246 (OUTLIER) cc_final: 0.8019 (tt) REVERT: I 83 MET cc_start: 0.8111 (mtt) cc_final: 0.7830 (mmm) REVERT: J 50 LEU cc_start: 0.7918 (tt) cc_final: 0.7634 (tt) REVERT: J 65 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.7993 (mt) REVERT: J 83 MET cc_start: 0.8140 (mtt) cc_final: 0.7706 (mmm) REVERT: K 126 MET cc_start: 0.7162 (ptm) cc_final: 0.6854 (ptm) REVERT: L 50 LEU cc_start: 0.7655 (OUTLIER) cc_final: 0.7304 (tt) REVERT: L 83 MET cc_start: 0.7712 (mmt) cc_final: 0.7408 (mmt) REVERT: M 50 LEU cc_start: 0.7777 (tt) cc_final: 0.7518 (tt) REVERT: N 50 LEU cc_start: 0.7966 (OUTLIER) cc_final: 0.7613 (tt) outliers start: 108 outliers final: 76 residues processed: 371 average time/residue: 0.1158 time to fit residues: 65.3129 Evaluate side-chains 358 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 276 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 28 ARG Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 28 ARG Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 28 ARG Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 24 ILE Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 114 LYS Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 143 ILE Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 159 THR Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 28 ARG Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 120 SER Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 159 THR Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 28 ARG Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 133 THR Chi-restraints excluded: chain F residue 143 ILE Chi-restraints excluded: chain F residue 152 THR Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 42 ILE Chi-restraints excluded: chain G residue 48 ILE Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 120 SER Chi-restraints excluded: chain G residue 138 ASP Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain G residue 152 THR Chi-restraints excluded: chain G residue 165 THR Chi-restraints excluded: chain G residue 215 ASP Chi-restraints excluded: chain I residue 50 LEU Chi-restraints excluded: chain I residue 65 LEU Chi-restraints excluded: chain I residue 107 LEU Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain J residue 107 LEU Chi-restraints excluded: chain K residue 65 LEU Chi-restraints excluded: chain K residue 107 LEU Chi-restraints excluded: chain L residue 50 LEU Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain L residue 107 LEU Chi-restraints excluded: chain N residue 50 LEU Chi-restraints excluded: chain N residue 107 LEU Chi-restraints excluded: chain N residue 126 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 143 optimal weight: 8.9990 chunk 160 optimal weight: 20.0000 chunk 63 optimal weight: 0.9980 chunk 152 optimal weight: 0.3980 chunk 129 optimal weight: 4.9990 chunk 191 optimal weight: 10.0000 chunk 138 optimal weight: 1.9990 chunk 98 optimal weight: 0.4980 chunk 28 optimal weight: 0.8980 chunk 109 optimal weight: 0.0870 chunk 186 optimal weight: 4.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 185 ASN F 79 ASN G 173 HIS ** I 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 41 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.190952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.136001 restraints weight = 19956.425| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 2.99 r_work: 0.3288 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3172 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3172 r_free = 0.3172 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1024 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3172 r_free = 0.3172 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1028 | |-----------------------------------------------------------------------------| r_final: 0.3172 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.2745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17766 Z= 0.125 Angle : 0.606 7.518 24066 Z= 0.306 Chirality : 0.046 0.157 2667 Planarity : 0.003 0.028 3066 Dihedral : 4.743 26.823 2352 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 4.16 % Allowed : 22.66 % Favored : 73.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.47 (0.17), residues: 2121 helix: None (None), residues: 0 sheet: -0.78 (0.16), residues: 980 loop : -1.08 (0.18), residues: 1141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J 85 TYR 0.011 0.001 TYR D 46 PHE 0.011 0.001 PHE K 56 TRP 0.008 0.002 TRP L 57 HIS 0.003 0.000 HIS N 79 Details of bonding type rmsd covalent geometry : bond 0.00288 (17738) covalent geometry : angle 0.60560 (24010) SS BOND : bond 0.00162 ( 28) SS BOND : angle 0.73345 ( 56) hydrogen bonds : bond 0.03249 ( 504) hydrogen bonds : angle 6.04125 ( 1260) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 275 time to evaluate : 0.636 Fit side-chains REVERT: A 113 ASP cc_start: 0.8309 (p0) cc_final: 0.7917 (p0) REVERT: A 190 MET cc_start: 0.8441 (tpp) cc_final: 0.7945 (ttm) REVERT: C 28 ARG cc_start: 0.8721 (OUTLIER) cc_final: 0.7899 (ptm160) REVERT: C 64 ASP cc_start: 0.8264 (t0) cc_final: 0.8032 (t0) REVERT: C 113 ASP cc_start: 0.8253 (p0) cc_final: 0.7940 (p0) REVERT: D 134 LYS cc_start: 0.8413 (tttt) cc_final: 0.8125 (ttpt) REVERT: E 190 MET cc_start: 0.8525 (tpp) cc_final: 0.8051 (ttm) REVERT: F 113 ASP cc_start: 0.8358 (p0) cc_final: 0.8007 (p0) REVERT: F 190 MET cc_start: 0.8492 (tpp) cc_final: 0.8061 (ttm) REVERT: G 114 LYS cc_start: 0.8661 (OUTLIER) cc_final: 0.8298 (tppt) REVERT: I 50 LEU cc_start: 0.7988 (OUTLIER) cc_final: 0.7722 (tt) REVERT: I 83 MET cc_start: 0.8173 (mtt) cc_final: 0.7820 (mmm) REVERT: J 65 LEU cc_start: 0.8190 (OUTLIER) cc_final: 0.7970 (mt) REVERT: J 83 MET cc_start: 0.8178 (mtt) cc_final: 0.7690 (mmm) REVERT: K 83 MET cc_start: 0.7955 (tpp) cc_final: 0.7684 (tpp) REVERT: K 126 MET cc_start: 0.7198 (ptm) cc_final: 0.6812 (ptm) REVERT: L 50 LEU cc_start: 0.7588 (OUTLIER) cc_final: 0.7265 (tt) REVERT: L 83 MET cc_start: 0.7698 (mmt) cc_final: 0.7395 (mmt) REVERT: M 130 LEU cc_start: 0.7236 (tp) cc_final: 0.6921 (tp) REVERT: N 50 LEU cc_start: 0.7832 (OUTLIER) cc_final: 0.7506 (tt) REVERT: N 97 LEU cc_start: 0.6954 (mm) cc_final: 0.6736 (mm) outliers start: 83 outliers final: 70 residues processed: 321 average time/residue: 0.1356 time to fit residues: 65.6133 Evaluate side-chains 338 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 262 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 28 ARG Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 28 ARG Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 28 ARG Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain D residue 21 LYS Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 143 ILE Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 159 THR Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 143 ILE Chi-restraints excluded: chain F residue 152 THR Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 42 ILE Chi-restraints excluded: chain G residue 48 ILE Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 114 LYS Chi-restraints excluded: chain G residue 138 ASP Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain G residue 152 THR Chi-restraints excluded: chain G residue 215 ASP Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain I residue 50 LEU Chi-restraints excluded: chain I residue 53 LEU Chi-restraints excluded: chain I residue 65 LEU Chi-restraints excluded: chain I residue 107 LEU Chi-restraints excluded: chain J residue 53 LEU Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain J residue 107 LEU Chi-restraints excluded: chain K residue 65 LEU Chi-restraints excluded: chain K residue 107 LEU Chi-restraints excluded: chain L residue 50 LEU Chi-restraints excluded: chain L residue 65 LEU Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain L residue 107 LEU Chi-restraints excluded: chain M residue 97 LEU Chi-restraints excluded: chain M residue 107 LEU Chi-restraints excluded: chain M residue 118 THR Chi-restraints excluded: chain N residue 50 LEU Chi-restraints excluded: chain N residue 107 LEU Chi-restraints excluded: chain N residue 126 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 59 optimal weight: 1.9990 chunk 159 optimal weight: 0.8980 chunk 98 optimal weight: 6.9990 chunk 84 optimal weight: 4.9990 chunk 181 optimal weight: 7.9990 chunk 90 optimal weight: 2.9990 chunk 18 optimal weight: 0.0980 chunk 195 optimal weight: 20.0000 chunk 21 optimal weight: 1.9990 chunk 104 optimal weight: 4.9990 chunk 26 optimal weight: 0.5980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 79 ASN ** F 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 116 HIS G 173 HIS ** G 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 41 GLN L 101 GLN ** L 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.188551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.133738 restraints weight = 19753.746| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 3.04 r_work: 0.3243 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3254 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3254 r_free = 0.3254 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1028 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3253 r_free = 0.3253 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1026 | |-----------------------------------------------------------------------------| r_final: 0.3253 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.3056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 17766 Z= 0.172 Angle : 0.614 7.465 24066 Z= 0.310 Chirality : 0.047 0.158 2667 Planarity : 0.003 0.027 3066 Dihedral : 4.749 28.855 2352 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 5.21 % Allowed : 22.46 % Favored : 72.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.48 (0.18), residues: 2121 helix: None (None), residues: 0 sheet: -0.83 (0.16), residues: 980 loop : -1.05 (0.18), residues: 1141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG K 85 TYR 0.015 0.001 TYR D 46 PHE 0.011 0.001 PHE K 56 TRP 0.008 0.001 TRP J 93 HIS 0.003 0.001 HIS N 79 Details of bonding type rmsd covalent geometry : bond 0.00408 (17738) covalent geometry : angle 0.61326 (24010) SS BOND : bond 0.00276 ( 28) SS BOND : angle 0.79478 ( 56) hydrogen bonds : bond 0.03239 ( 504) hydrogen bonds : angle 5.86253 ( 1260) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 279 time to evaluate : 0.531 Fit side-chains REVERT: A 113 ASP cc_start: 0.8137 (p0) cc_final: 0.7756 (p0) REVERT: C 64 ASP cc_start: 0.8183 (t0) cc_final: 0.7980 (t0) REVERT: C 113 ASP cc_start: 0.8082 (p0) cc_final: 0.7753 (p0) REVERT: E 28 ARG cc_start: 0.8568 (OUTLIER) cc_final: 0.8060 (ptm160) REVERT: E 134 LYS cc_start: 0.8358 (tttt) cc_final: 0.8041 (ttpt) REVERT: F 28 ARG cc_start: 0.8555 (OUTLIER) cc_final: 0.8114 (ptm160) REVERT: F 113 ASP cc_start: 0.8260 (p0) cc_final: 0.7893 (p0) REVERT: I 50 LEU cc_start: 0.8053 (OUTLIER) cc_final: 0.7830 (tt) REVERT: I 83 MET cc_start: 0.8111 (mtt) cc_final: 0.7775 (mmm) REVERT: I 126 MET cc_start: 0.7285 (ptm) cc_final: 0.6994 (ptm) REVERT: J 83 MET cc_start: 0.8115 (mtt) cc_final: 0.7658 (mmm) REVERT: K 65 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.7917 (mp) REVERT: K 126 MET cc_start: 0.7084 (ptm) cc_final: 0.6696 (ptm) REVERT: L 83 MET cc_start: 0.7651 (mmt) cc_final: 0.7313 (mmt) outliers start: 104 outliers final: 80 residues processed: 351 average time/residue: 0.1240 time to fit residues: 65.4414 Evaluate side-chains 346 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 262 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 28 ARG Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 28 ARG Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 28 ARG Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 24 ILE Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 143 ILE Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 159 THR Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 28 ARG Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 159 THR Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 28 ARG Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 143 ILE Chi-restraints excluded: chain F residue 152 THR Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 42 ILE Chi-restraints excluded: chain G residue 48 ILE Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 138 ASP Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain G residue 152 THR Chi-restraints excluded: chain G residue 165 THR Chi-restraints excluded: chain G residue 207 LEU Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain I residue 38 LEU Chi-restraints excluded: chain I residue 50 LEU Chi-restraints excluded: chain I residue 53 LEU Chi-restraints excluded: chain I residue 107 LEU Chi-restraints excluded: chain J residue 53 LEU Chi-restraints excluded: chain K residue 65 LEU Chi-restraints excluded: chain L residue 65 LEU Chi-restraints excluded: chain M residue 97 LEU Chi-restraints excluded: chain M residue 107 LEU Chi-restraints excluded: chain M residue 118 THR Chi-restraints excluded: chain N residue 107 LEU Chi-restraints excluded: chain N residue 126 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 104 optimal weight: 4.9990 chunk 125 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 85 optimal weight: 0.7980 chunk 75 optimal weight: 3.9990 chunk 177 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 138 optimal weight: 0.2980 chunk 92 optimal weight: 3.9990 chunk 129 optimal weight: 3.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 173 HIS ** I 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 41 GLN ** J 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 66 ASN ** 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 = 0.4147 r_free = 0.4147 target = 0.188739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.135568 restraints weight = 19788.316| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 2.86 r_work: 0.3271 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3146 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3146 r_free = 0.3146 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1026 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3145 r_free = 0.3145 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1025 | |-----------------------------------------------------------------------------| r_final: 0.3145 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.3221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 17766 Z= 0.150 Angle : 0.600 8.134 24066 Z= 0.301 Chirality : 0.046 0.153 2667 Planarity : 0.003 0.027 3066 Dihedral : 4.664 28.121 2352 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 4.71 % Allowed : 23.31 % Favored : 71.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.49 (0.18), residues: 2121 helix: None (None), residues: 0 sheet: -0.77 (0.16), residues: 952 loop : -1.12 (0.18), residues: 1169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG L 85 TYR 0.013 0.001 TYR D 46 PHE 0.010 0.001 PHE K 56 TRP 0.008 0.001 TRP I 57 HIS 0.004 0.001 HIS N 79 Details of bonding type rmsd covalent geometry : bond 0.00357 (17738) covalent geometry : angle 0.59938 (24010) SS BOND : bond 0.00225 ( 28) SS BOND : angle 0.67217 ( 56) hydrogen bonds : bond 0.03011 ( 504) hydrogen bonds : angle 5.79882 ( 1260) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 268 time to evaluate : 0.515 Fit side-chains REVERT: A 113 ASP cc_start: 0.8277 (p0) cc_final: 0.7886 (p0) REVERT: C 64 ASP cc_start: 0.8273 (t0) cc_final: 0.8030 (t0) REVERT: C 113 ASP cc_start: 0.8219 (p0) cc_final: 0.7882 (p0) REVERT: E 134 LYS cc_start: 0.8421 (tttt) cc_final: 0.8084 (ttpt) REVERT: E 190 MET cc_start: 0.8561 (tpp) cc_final: 0.8131 (ttm) REVERT: F 28 ARG cc_start: 0.8670 (OUTLIER) cc_final: 0.7544 (ptm160) REVERT: F 113 ASP cc_start: 0.8361 (p0) cc_final: 0.8000 (p0) REVERT: F 190 MET cc_start: 0.8542 (tpp) cc_final: 0.8161 (ttm) REVERT: I 50 LEU cc_start: 0.8016 (OUTLIER) cc_final: 0.7805 (tt) REVERT: I 83 MET cc_start: 0.8169 (mtt) cc_final: 0.7804 (mmm) REVERT: I 126 MET cc_start: 0.7420 (ptm) cc_final: 0.7163 (ptm) REVERT: J 83 MET cc_start: 0.8244 (mtt) cc_final: 0.7752 (mmm) REVERT: K 65 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.7950 (mp) REVERT: K 126 MET cc_start: 0.7304 (ptm) cc_final: 0.7013 (ptm) REVERT: L 83 MET cc_start: 0.7800 (mmt) cc_final: 0.7443 (mmt) REVERT: L 130 LEU cc_start: 0.7282 (tp) cc_final: 0.6977 (tt) REVERT: N 97 LEU cc_start: 0.7135 (mm) cc_final: 0.6923 (mm) REVERT: N 130 LEU cc_start: 0.7148 (OUTLIER) cc_final: 0.6765 (tt) outliers start: 94 outliers final: 75 residues processed: 330 average time/residue: 0.1327 time to fit residues: 65.7604 Evaluate side-chains 355 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 276 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 28 ARG Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 28 ARG Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 28 ARG Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 24 ILE Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 114 LYS Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 143 ILE Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 159 THR Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 28 ARG Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 143 ILE Chi-restraints excluded: chain F residue 152 THR Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 42 ILE Chi-restraints excluded: chain G residue 48 ILE Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 138 ASP Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain G residue 152 THR Chi-restraints excluded: chain G residue 165 THR Chi-restraints excluded: chain G residue 207 LEU Chi-restraints excluded: chain I residue 38 LEU Chi-restraints excluded: chain I residue 50 LEU Chi-restraints excluded: chain I residue 97 LEU Chi-restraints excluded: chain I residue 107 LEU Chi-restraints excluded: chain J residue 53 LEU Chi-restraints excluded: chain J residue 107 LEU Chi-restraints excluded: chain K residue 65 LEU Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain M residue 97 LEU Chi-restraints excluded: chain M residue 107 LEU Chi-restraints excluded: chain M residue 118 THR Chi-restraints excluded: chain N residue 107 LEU Chi-restraints excluded: chain N residue 126 MET Chi-restraints excluded: chain N residue 130 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 181 optimal weight: 4.9990 chunk 185 optimal weight: 0.9990 chunk 111 optimal weight: 1.9990 chunk 169 optimal weight: 4.9990 chunk 179 optimal weight: 8.9990 chunk 100 optimal weight: 3.9990 chunk 98 optimal weight: 0.0060 chunk 30 optimal weight: 1.9990 chunk 128 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 132 optimal weight: 0.0060 overall best weight: 1.0018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.187894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.134284 restraints weight = 19753.455| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 2.91 r_work: 0.3263 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3140 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3140 r_free = 0.3140 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1025 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3140 r_free = 0.3140 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1025 | |-----------------------------------------------------------------------------| r_final: 0.3140 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.3388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 17766 Z= 0.154 Angle : 0.598 8.526 24066 Z= 0.300 Chirality : 0.046 0.152 2667 Planarity : 0.003 0.028 3066 Dihedral : 4.599 29.232 2352 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 4.76 % Allowed : 23.31 % Favored : 71.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.50 (0.18), residues: 2121 helix: None (None), residues: 0 sheet: -0.78 (0.16), residues: 952 loop : -1.12 (0.18), residues: 1169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG L 85 TYR 0.014 0.001 TYR D 46 PHE 0.010 0.001 PHE K 56 TRP 0.008 0.001 TRP I 57 HIS 0.003 0.001 HIS N 79 Details of bonding type rmsd covalent geometry : bond 0.00367 (17738) covalent geometry : angle 0.59757 (24010) SS BOND : bond 0.00240 ( 28) SS BOND : angle 0.67851 ( 56) hydrogen bonds : bond 0.02998 ( 504) hydrogen bonds : angle 5.73103 ( 1260) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 269 time to evaluate : 0.684 Fit side-chains REVERT: C 64 ASP cc_start: 0.8269 (t0) cc_final: 0.8016 (t0) REVERT: C 215 ASP cc_start: 0.8336 (t0) cc_final: 0.8121 (t0) REVERT: E 134 LYS cc_start: 0.8463 (tttt) cc_final: 0.8101 (ttpt) REVERT: F 28 ARG cc_start: 0.8689 (OUTLIER) cc_final: 0.7757 (ptm160) REVERT: F 64 ASP cc_start: 0.8037 (t0) cc_final: 0.7811 (t0) REVERT: F 113 ASP cc_start: 0.8370 (p0) cc_final: 0.7998 (p0) REVERT: I 83 MET cc_start: 0.8150 (mtt) cc_final: 0.7819 (mmm) REVERT: I 126 MET cc_start: 0.7494 (ptm) cc_final: 0.7222 (ptm) REVERT: J 83 MET cc_start: 0.8277 (mtt) cc_final: 0.7759 (mmm) REVERT: K 65 LEU cc_start: 0.8322 (OUTLIER) cc_final: 0.7978 (mp) REVERT: K 126 MET cc_start: 0.7347 (ptm) cc_final: 0.7045 (ptm) REVERT: L 83 MET cc_start: 0.7765 (mmt) cc_final: 0.7438 (mmt) REVERT: N 130 LEU cc_start: 0.7097 (OUTLIER) cc_final: 0.6778 (tt) outliers start: 95 outliers final: 81 residues processed: 340 average time/residue: 0.1391 time to fit residues: 70.8968 Evaluate side-chains 346 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 262 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 28 ARG Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 28 ARG Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 28 ARG Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 138 ASP Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 24 ILE Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 114 LYS Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 143 ILE Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 159 THR Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 28 ARG Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 28 ARG Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 133 THR Chi-restraints excluded: chain F residue 143 ILE Chi-restraints excluded: chain F residue 152 THR Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 42 ILE Chi-restraints excluded: chain G residue 48 ILE Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 138 ASP Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain G residue 152 THR Chi-restraints excluded: chain G residue 165 THR Chi-restraints excluded: chain G residue 207 LEU Chi-restraints excluded: chain H residue 53 LEU Chi-restraints excluded: chain I residue 38 LEU Chi-restraints excluded: chain J residue 53 LEU Chi-restraints excluded: chain K residue 65 LEU Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain L residue 65 LEU Chi-restraints excluded: chain M residue 97 LEU Chi-restraints excluded: chain M residue 107 LEU Chi-restraints excluded: chain M residue 118 THR Chi-restraints excluded: chain N residue 107 LEU Chi-restraints excluded: chain N residue 126 MET Chi-restraints excluded: chain N residue 130 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 142 optimal weight: 1.9990 chunk 192 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 11 optimal weight: 6.9990 chunk 183 optimal weight: 0.6980 chunk 84 optimal weight: 4.9990 chunk 138 optimal weight: 5.9990 chunk 54 optimal weight: 4.9990 chunk 174 optimal weight: 4.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 HIS B 116 HIS ** B 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 79 ASN C 116 HIS ** C 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 116 HIS E 116 HIS F 116 HIS ** F 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 66 ASN ** 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 = 0.4105 r_free = 0.4105 target = 0.184358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.132012 restraints weight = 19946.589| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 2.90 r_work: 0.3218 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3088 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3088 r_free = 0.3088 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1025 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3088 r_free = 0.3088 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1027 | |-----------------------------------------------------------------------------| r_final: 0.3088 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.3688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.043 17766 Z= 0.272 Angle : 0.683 9.468 24066 Z= 0.343 Chirality : 0.049 0.177 2667 Planarity : 0.003 0.028 3066 Dihedral : 4.962 35.060 2352 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Rotamer: Outliers : 5.06 % Allowed : 23.51 % Favored : 71.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.73 (0.18), residues: 2121 helix: None (None), residues: 0 sheet: -1.00 (0.16), residues: 952 loop : -1.21 (0.18), residues: 1169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG L 85 TYR 0.020 0.002 TYR D 46 PHE 0.013 0.001 PHE K 56 TRP 0.008 0.001 TRP I 93 HIS 0.009 0.001 HIS I 79 Details of bonding type rmsd covalent geometry : bond 0.00653 (17738) covalent geometry : angle 0.68200 (24010) SS BOND : bond 0.00429 ( 28) SS BOND : angle 1.00797 ( 56) hydrogen bonds : bond 0.03389 ( 504) hydrogen bonds : angle 5.95539 ( 1260) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 258 time to evaluate : 0.687 Fit side-chains REVERT: A 83 MET cc_start: 0.8614 (mmm) cc_final: 0.8279 (mmm) REVERT: C 64 ASP cc_start: 0.8355 (t0) cc_final: 0.8122 (t0) REVERT: C 120 SER cc_start: 0.8992 (OUTLIER) cc_final: 0.8767 (m) REVERT: C 215 ASP cc_start: 0.8360 (t0) cc_final: 0.8129 (t0) REVERT: E 134 LYS cc_start: 0.8492 (tttt) cc_final: 0.8145 (ttpt) REVERT: F 28 ARG cc_start: 0.8781 (OUTLIER) cc_final: 0.8413 (ptm160) REVERT: F 64 ASP cc_start: 0.8098 (t0) cc_final: 0.7858 (t0) REVERT: F 113 ASP cc_start: 0.8423 (p0) cc_final: 0.8056 (p0) REVERT: I 83 MET cc_start: 0.8170 (mtt) cc_final: 0.7793 (mmm) REVERT: I 126 MET cc_start: 0.7478 (ptm) cc_final: 0.7107 (ptm) REVERT: J 83 MET cc_start: 0.8273 (mtt) cc_final: 0.7776 (mmm) REVERT: K 65 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.7997 (mp) REVERT: K 126 MET cc_start: 0.7299 (ptm) cc_final: 0.6975 (ptm) REVERT: L 83 MET cc_start: 0.7803 (mmt) cc_final: 0.7454 (mmt) REVERT: N 130 LEU cc_start: 0.7048 (OUTLIER) cc_final: 0.6745 (tt) outliers start: 101 outliers final: 76 residues processed: 334 average time/residue: 0.1202 time to fit residues: 61.9709 Evaluate side-chains 338 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 258 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 28 ARG Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 28 ARG Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 28 ARG Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 24 ILE Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 143 ILE Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 159 THR Chi-restraints excluded: chain D residue 189 SER Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 28 ARG Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 120 SER Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 159 THR Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 28 ARG Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 143 ILE Chi-restraints excluded: chain F residue 152 THR Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 42 ILE Chi-restraints excluded: chain G residue 48 ILE Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 138 ASP Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain G residue 152 THR Chi-restraints excluded: chain G residue 165 THR Chi-restraints excluded: chain H residue 53 LEU Chi-restraints excluded: chain I residue 38 LEU Chi-restraints excluded: chain I residue 53 LEU Chi-restraints excluded: chain J residue 53 LEU Chi-restraints excluded: chain K residue 65 LEU Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain L residue 65 LEU Chi-restraints excluded: chain M residue 95 LEU Chi-restraints excluded: chain M residue 97 LEU Chi-restraints excluded: chain M residue 107 LEU Chi-restraints excluded: chain M residue 118 THR Chi-restraints excluded: chain N residue 107 LEU Chi-restraints excluded: chain N residue 126 MET Chi-restraints excluded: chain N residue 130 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 160 optimal weight: 20.0000 chunk 112 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 chunk 92 optimal weight: 0.7980 chunk 198 optimal weight: 7.9990 chunk 110 optimal weight: 1.9990 chunk 38 optimal weight: 0.0170 chunk 18 optimal weight: 1.9990 chunk 172 optimal weight: 6.9990 chunk 21 optimal weight: 0.5980 chunk 205 optimal weight: 10.0000 overall best weight: 0.8820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 127 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.187098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.133498 restraints weight = 19913.387| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 2.95 r_work: 0.3249 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3123 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3123 r_free = 0.3123 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1027 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3123 r_free = 0.3123 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1025 | |-----------------------------------------------------------------------------| r_final: 0.3123 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.3682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 17766 Z= 0.151 Angle : 0.623 10.057 24066 Z= 0.311 Chirality : 0.046 0.150 2667 Planarity : 0.003 0.029 3066 Dihedral : 4.719 31.245 2352 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 3.51 % Allowed : 25.16 % Favored : 71.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.73 (0.18), residues: 2121 helix: None (None), residues: 0 sheet: -0.99 (0.16), residues: 952 loop : -1.22 (0.18), residues: 1169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG I 85 TYR 0.012 0.001 TYR D 46 PHE 0.010 0.001 PHE K 56 TRP 0.009 0.001 TRP N 57 HIS 0.006 0.001 HIS I 79 Details of bonding type rmsd covalent geometry : bond 0.00358 (17738) covalent geometry : angle 0.62282 (24010) SS BOND : bond 0.00224 ( 28) SS BOND : angle 0.76587 ( 56) hydrogen bonds : bond 0.02968 ( 504) hydrogen bonds : angle 5.85410 ( 1260) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 256 time to evaluate : 0.796 Fit side-chains REVERT: B 190 MET cc_start: 0.8665 (tpp) cc_final: 0.8415 (tpp) REVERT: C 64 ASP cc_start: 0.8286 (t0) cc_final: 0.8058 (t0) REVERT: C 215 ASP cc_start: 0.8349 (t0) cc_final: 0.8131 (t0) REVERT: E 134 LYS cc_start: 0.8390 (tttt) cc_final: 0.8044 (ttpt) REVERT: F 28 ARG cc_start: 0.8766 (OUTLIER) cc_final: 0.7686 (ptm160) REVERT: F 64 ASP cc_start: 0.8072 (t0) cc_final: 0.7821 (t0) REVERT: F 113 ASP cc_start: 0.8378 (p0) cc_final: 0.8021 (p0) REVERT: I 83 MET cc_start: 0.8212 (mtt) cc_final: 0.7876 (mmm) REVERT: I 126 MET cc_start: 0.7543 (ptm) cc_final: 0.7271 (ptm) REVERT: J 83 MET cc_start: 0.8347 (mtt) cc_final: 0.7805 (mmm) REVERT: K 65 LEU cc_start: 0.8316 (OUTLIER) cc_final: 0.7988 (mp) REVERT: K 83 MET cc_start: 0.7719 (tpp) cc_final: 0.7393 (mmm) REVERT: K 126 MET cc_start: 0.7374 (ptm) cc_final: 0.7027 (ptm) REVERT: L 83 MET cc_start: 0.7783 (mmt) cc_final: 0.7461 (mmt) REVERT: N 130 LEU cc_start: 0.7102 (OUTLIER) cc_final: 0.6797 (tt) outliers start: 70 outliers final: 65 residues processed: 310 average time/residue: 0.1323 time to fit residues: 62.1107 Evaluate side-chains 315 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 247 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 28 ARG Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 28 ARG Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 28 ARG Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 24 ILE Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 143 ILE Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 189 SER Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 28 ARG Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 159 THR Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 28 ARG Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 143 ILE Chi-restraints excluded: chain F residue 152 THR Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 42 ILE Chi-restraints excluded: chain G residue 48 ILE Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 138 ASP Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain G residue 152 THR Chi-restraints excluded: chain G residue 165 THR Chi-restraints excluded: chain G residue 207 LEU Chi-restraints excluded: chain I residue 38 LEU Chi-restraints excluded: chain I residue 107 LEU Chi-restraints excluded: chain I residue 118 THR Chi-restraints excluded: chain K residue 38 LEU Chi-restraints excluded: chain K residue 65 LEU Chi-restraints excluded: chain L residue 65 LEU Chi-restraints excluded: chain M residue 97 LEU Chi-restraints excluded: chain M residue 118 THR Chi-restraints excluded: chain N residue 107 LEU Chi-restraints excluded: chain N residue 130 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 166 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 116 optimal weight: 0.7980 chunk 69 optimal weight: 6.9990 chunk 114 optimal weight: 0.5980 chunk 93 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 49 optimal weight: 6.9990 chunk 60 optimal weight: 2.9990 chunk 191 optimal weight: 10.0000 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.185169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.127071 restraints weight = 20102.373| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 3.42 r_work: 0.3213 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3085 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3085 r_free = 0.3085 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1025 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3084 r_free = 0.3084 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1022 | |-----------------------------------------------------------------------------| r_final: 0.3084 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.3825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 17766 Z= 0.225 Angle : 0.667 10.051 24066 Z= 0.333 Chirality : 0.048 0.158 2667 Planarity : 0.003 0.040 3066 Dihedral : 4.861 33.578 2352 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 3.96 % Allowed : 24.81 % Favored : 71.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.78 (0.18), residues: 2121 helix: None (None), residues: 0 sheet: -1.07 (0.16), residues: 952 loop : -1.22 (0.18), residues: 1169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 85 TYR 0.018 0.001 TYR D 46 PHE 0.012 0.001 PHE K 56 TRP 0.008 0.001 TRP I 93 HIS 0.009 0.001 HIS I 79 Details of bonding type rmsd covalent geometry : bond 0.00540 (17738) covalent geometry : angle 0.66663 (24010) SS BOND : bond 0.00343 ( 28) SS BOND : angle 0.90349 ( 56) hydrogen bonds : bond 0.03190 ( 504) hydrogen bonds : angle 5.87346 ( 1260) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 244 time to evaluate : 0.666 Fit side-chains REVERT: A 83 MET cc_start: 0.8436 (mmm) cc_final: 0.8032 (mmm) REVERT: B 190 MET cc_start: 0.8583 (tpp) cc_final: 0.8311 (tpp) REVERT: C 64 ASP cc_start: 0.8466 (t0) cc_final: 0.8185 (t0) REVERT: C 215 ASP cc_start: 0.8454 (t70) cc_final: 0.8209 (t0) REVERT: E 134 LYS cc_start: 0.8544 (tttt) cc_final: 0.8073 (ttpt) REVERT: F 28 ARG cc_start: 0.8731 (OUTLIER) cc_final: 0.8122 (ptm160) REVERT: F 64 ASP cc_start: 0.8337 (t0) cc_final: 0.8004 (t0) REVERT: F 113 ASP cc_start: 0.8387 (p0) cc_final: 0.7936 (p0) REVERT: I 83 MET cc_start: 0.8304 (mtt) cc_final: 0.7849 (mmm) REVERT: I 126 MET cc_start: 0.7586 (ptm) cc_final: 0.7174 (ptm) REVERT: J 83 MET cc_start: 0.8378 (mtt) cc_final: 0.7799 (mmm) REVERT: K 65 LEU cc_start: 0.8193 (OUTLIER) cc_final: 0.7903 (mp) REVERT: K 83 MET cc_start: 0.7728 (tpp) cc_final: 0.7420 (mmm) REVERT: K 126 MET cc_start: 0.7259 (ptm) cc_final: 0.6866 (ptm) REVERT: L 83 MET cc_start: 0.7766 (mmt) cc_final: 0.7475 (mmt) REVERT: M 83 MET cc_start: 0.8064 (OUTLIER) cc_final: 0.7859 (tpp) REVERT: N 130 LEU cc_start: 0.7307 (OUTLIER) cc_final: 0.6864 (tt) outliers start: 79 outliers final: 70 residues processed: 307 average time/residue: 0.1151 time to fit residues: 53.6870 Evaluate side-chains 316 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 242 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 28 ARG Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 28 ARG Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 28 ARG Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 84 ASP Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 24 ILE Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 143 ILE Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 189 SER Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 28 ARG Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 120 SER Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 159 THR Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 28 ARG Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 143 ILE Chi-restraints excluded: chain F residue 152 THR Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 42 ILE Chi-restraints excluded: chain G residue 48 ILE Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 138 ASP Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain G residue 152 THR Chi-restraints excluded: chain G residue 165 THR Chi-restraints excluded: chain I residue 38 LEU Chi-restraints excluded: chain I residue 118 THR Chi-restraints excluded: chain K residue 38 LEU Chi-restraints excluded: chain K residue 65 LEU Chi-restraints excluded: chain L residue 65 LEU Chi-restraints excluded: chain M residue 83 MET Chi-restraints excluded: chain M residue 97 LEU Chi-restraints excluded: chain M residue 118 THR Chi-restraints excluded: chain N residue 95 LEU Chi-restraints excluded: chain N residue 107 LEU Chi-restraints excluded: chain N residue 130 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 202 optimal weight: 0.9980 chunk 113 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 chunk 162 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 183 optimal weight: 3.9990 chunk 117 optimal weight: 0.5980 chunk 89 optimal weight: 0.7980 chunk 180 optimal weight: 20.0000 chunk 64 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 185 ASN ** D 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 66 ASN ** 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 = 0.4147 r_free = 0.4147 target = 0.184034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.125291 restraints weight = 20044.917| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 2.74 r_work: 0.3251 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3135 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3135 r_free = 0.3135 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1022 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3135 r_free = 0.3135 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1022 | |-----------------------------------------------------------------------------| r_final: 0.3135 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.3809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17766 Z= 0.140 Angle : 0.618 10.342 24066 Z= 0.307 Chirality : 0.046 0.169 2667 Planarity : 0.003 0.033 3066 Dihedral : 4.653 29.383 2352 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 3.51 % Allowed : 25.16 % Favored : 71.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.73 (0.18), residues: 2121 helix: None (None), residues: 0 sheet: -1.00 (0.16), residues: 952 loop : -1.21 (0.18), residues: 1169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 85 TYR 0.012 0.001 TYR D 46 PHE 0.009 0.001 PHE L 56 TRP 0.010 0.001 TRP I 57 HIS 0.006 0.001 HIS I 79 Details of bonding type rmsd covalent geometry : bond 0.00332 (17738) covalent geometry : angle 0.61774 (24010) SS BOND : bond 0.00223 ( 28) SS BOND : angle 0.78085 ( 56) hydrogen bonds : bond 0.02860 ( 504) hydrogen bonds : angle 5.78129 ( 1260) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4832.03 seconds wall clock time: 83 minutes 28.81 seconds (5008.81 seconds total)