Starting phenix.real_space_refine on Sun Jun 15 10:42:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hxc_35076/06_2025/8hxc_35076.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hxc_35076/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8hxc_35076/06_2025/8hxc_35076.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hxc_35076/06_2025/8hxc_35076.map" model { file = "/net/cci-nas-00/data/ceres_data/8hxc_35076/06_2025/8hxc_35076.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hxc_35076/06_2025/8hxc_35076.cif" } resolution = 3.12 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.037 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: "I" 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: H, K, J, M, L, N, C, B, E, D, G, F Time building chain proxies: 5.33, per 1000 atoms: 0.31 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 C 25 " - pdb=" SG CYS D 130 " distance=2.05 Simple disulfide: pdb=" SG CYS B 25 " - pdb=" SG CYS C 130 " distance=1.99 Simple disulfide: pdb=" SG CYS E 25 " - pdb=" SG CYS F 130 " distance=2.01 Simple disulfide: pdb=" SG CYS D 25 " - pdb=" SG CYS E 130 " distance=2.07 Simple disulfide: pdb=" SG CYS F 25 " - pdb=" SG CYS G 130 " distance=2.02 Simple disulfide: pdb=" SG CYS C 56 " - pdb=" SG CYS C 217 " distance=2.03 Simple disulfide: pdb=" SG CYS B 56 " - pdb=" SG CYS B 217 " distance=2.03 Simple disulfide: pdb=" SG CYS E 56 " - pdb=" SG CYS E 217 " distance=2.03 Simple disulfide: pdb=" SG CYS D 56 " - pdb=" SG CYS D 217 " distance=2.03 Simple disulfide: pdb=" SG CYS G 56 " - pdb=" SG CYS G 217 " distance=2.03 Simple disulfide: pdb=" SG CYS F 56 " - pdb=" SG CYS F 217 " distance=2.03 Simple disulfide: pdb=" SG CYS C 125 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS B 125 " - pdb=" SG CYS B 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 125 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS D 125 " - pdb=" SG CYS D 157 " distance=2.03 Simple disulfide: pdb=" SG CYS G 125 " - pdb=" SG CYS G 157 " distance=2.03 Simple disulfide: pdb=" SG CYS F 125 " - pdb=" SG CYS F 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 160 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS B 160 " - pdb=" SG CYS B 205 " distance=2.02 Simple disulfide: pdb=" SG CYS E 160 " - pdb=" SG CYS E 205 " distance=2.02 Simple disulfide: pdb=" SG CYS D 160 " - pdb=" SG CYS D 205 " distance=2.02 Simple disulfide: pdb=" SG CYS G 160 " - pdb=" SG CYS G 205 " distance=2.02 Simple disulfide: pdb=" SG CYS F 160 " - pdb=" SG CYS F 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: 3.53 Conformation dependent library (CDL) restraints added in 2.0 seconds 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: 1.98 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: 4.56 Time building geometry restraints manager: 4.31 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: 0.13 Found NCS groups: ncs_group { reference = chain 'I' selection = chain 'H' selection = chain 'K' selection = chain 'J' selection = chain 'M' selection = chain 'L' selection = chain 'N' } ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' } 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: 1.370 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: 0.640 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 31.510 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.790 ------------------------------------------------------------------------------- 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 : 5.40 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.030 0.005 TRP D 34 HIS 0.027 0.003 HIS M 124 PHE 0.030 0.003 PHE N 56 TYR 0.025 0.003 TYR G 74 ARG 0.008 0.001 ARG N 85 Details of bonding type rmsd hydrogen bonds : bond 0.14434 ( 504) hydrogen bonds : angle 7.95237 ( 1260) SS BOND : bond 0.01307 ( 28) SS BOND : angle 1.53520 ( 56) covalent geometry : bond 0.00689 (17738) covalent geometry : angle 1.20383 (24010) *********************** 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 : 1.950 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: 0.7611 (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: 0.7637 (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: 0.3226 time to fit residues: 189.6313 Evaluate side-chains 273 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 266 time to evaluate : 1.908 ------------------------------------------------------------------------------- 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 177 optimal weight: 9.9990 chunk 159 optimal weight: 0.9990 chunk 88 optimal weight: 0.8980 chunk 54 optimal weight: 0.7980 chunk 107 optimal weight: 0.5980 chunk 85 optimal weight: 0.9980 chunk 164 optimal weight: 10.0000 chunk 63 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 190 optimal weight: 20.0000 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.4233 r_free = 0.4233 target = 0.198067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.151101 restraints weight = 19482.615| |-----------------------------------------------------------------------------| r_work (start): 0.3745 rms_B_bonded: 2.41 r_work: 0.3385 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3393 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3393 r_free = 0.3393 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1015 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3375 r_free = 0.3375 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1035 | |-----------------------------------------------------------------------------| r_final: 0.3375 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 17766 Z= 0.159 Angle : 0.663 8.311 24066 Z= 0.342 Chirality : 0.048 0.176 2667 Planarity : 0.004 0.028 3066 Dihedral : 5.063 25.106 2352 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 5.91 % Allowed : 22.46 % Favored : 71.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.17), residues: 2121 helix: None (None), residues: 0 sheet: -0.60 (0.16), residues: 973 loop : -1.22 (0.17), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 34 HIS 0.006 0.001 HIS L 124 PHE 0.016 0.001 PHE H 56 TYR 0.013 0.001 TYR D 46 ARG 0.010 0.001 ARG N 85 Details of bonding type rmsd hydrogen bonds : bond 0.04089 ( 504) hydrogen bonds : angle 6.68895 ( 1260) SS BOND : bond 0.00231 ( 28) SS BOND : angle 0.70278 ( 56) covalent geometry : bond 0.00368 (17738) covalent geometry : angle 0.66247 (24010) *********************** 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 382 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 264 time to evaluate : 2.081 Fit side-chains REVERT: A 41 THR cc_start: 0.8703 (p) cc_final: 0.8483 (m) REVERT: A 113 ASP cc_start: 0.8186 (p0) cc_final: 0.7878 (p0) REVERT: B 83 MET cc_start: 0.8209 (mmt) cc_final: 0.7683 (mpp) REVERT: B 113 ASP cc_start: 0.8070 (p0) cc_final: 0.7743 (p0) REVERT: C 113 ASP cc_start: 0.8061 (p0) cc_final: 0.7856 (p0) REVERT: E 28 ARG cc_start: 0.8351 (OUTLIER) cc_final: 0.7852 (ptm160) REVERT: E 113 ASP cc_start: 0.8096 (p0) cc_final: 0.7799 (p0) REVERT: E 185 ASN cc_start: 0.8640 (t0) cc_final: 0.8233 (t0) REVERT: F 113 ASP cc_start: 0.8188 (p0) cc_final: 0.7960 (p0) REVERT: G 83 MET cc_start: 0.8187 (mmt) cc_final: 0.7738 (mpp) REVERT: H 50 LEU cc_start: 0.7945 (OUTLIER) cc_final: 0.7380 (tt) REVERT: I 50 LEU cc_start: 0.8095 (OUTLIER) cc_final: 0.7843 (tt) REVERT: J 65 LEU cc_start: 0.8218 (OUTLIER) cc_final: 0.7733 (mp) REVERT: J 83 MET cc_start: 0.7900 (mtt) cc_final: 0.7672 (mmm) REVERT: K 126 MET cc_start: 0.6801 (ptm) cc_final: 0.6550 (ptm) REVERT: L 50 LEU cc_start: 0.7419 (OUTLIER) cc_final: 0.6945 (tt) REVERT: N 50 LEU cc_start: 0.7728 (OUTLIER) cc_final: 0.7312 (tt) outliers start: 118 outliers final: 57 residues processed: 343 average time/residue: 0.3189 time to fit residues: 165.4007 Evaluate side-chains 306 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 243 time to evaluate : 2.848 ------------------------------------------------------------------------------- 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 120 SER 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 208 optimal weight: 4.9990 chunk 179 optimal weight: 0.0970 chunk 36 optimal weight: 3.9990 chunk 205 optimal weight: 3.9990 chunk 209 optimal weight: 0.7980 chunk 29 optimal weight: 3.9990 chunk 127 optimal weight: 0.9980 chunk 63 optimal weight: 5.9990 chunk 103 optimal weight: 5.9990 chunk 129 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 overall best weight: 1.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 79 ASN ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 79 ASN ** C 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 G 116 HIS 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** M 41 GLN M 127 ASN N 41 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.187866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.134212 restraints weight = 19773.006| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 3.20 r_work: 0.3248 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3134 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3134 r_free = 0.3134 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1035 | |-----------------------------------------------------------------------------| |-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: 1026 | |-----------------------------------------------------------------------------| r_final: 0.3133 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 17766 Z= 0.225 Angle : 0.675 7.800 24066 Z= 0.346 Chirality : 0.049 0.185 2667 Planarity : 0.003 0.028 3066 Dihedral : 5.033 30.681 2352 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 5.16 % Allowed : 21.75 % Favored : 73.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.17), residues: 2121 helix: None (None), residues: 0 sheet: -0.76 (0.16), residues: 980 loop : -1.13 (0.17), residues: 1141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP L 57 HIS 0.003 0.001 HIS E 184 PHE 0.012 0.001 PHE K 56 TYR 0.016 0.002 TYR D 46 ARG 0.008 0.001 ARG J 85 Details of bonding type rmsd hydrogen bonds : bond 0.03815 ( 504) hydrogen bonds : angle 6.27075 ( 1260) SS BOND : bond 0.00360 ( 28) SS BOND : angle 0.73969 ( 56) covalent geometry : bond 0.00533 (17738) covalent geometry : angle 0.67481 (24010) *********************** 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 396 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 293 time to evaluate : 3.753 Fit side-chains REVERT: A 113 ASP cc_start: 0.8299 (p0) cc_final: 0.7908 (p0) REVERT: B 187 GLU cc_start: 0.9045 (pt0) cc_final: 0.8820 (pt0) REVERT: C 113 ASP cc_start: 0.8279 (p0) cc_final: 0.7941 (p0) REVERT: D 85 THR cc_start: 0.9122 (p) cc_final: 0.8775 (p) REVERT: D 134 LYS cc_start: 0.8516 (tttt) cc_final: 0.8234 (ttpt) REVERT: E 28 ARG cc_start: 0.8640 (OUTLIER) cc_final: 0.8036 (ptm160) REVERT: E 30 ASP cc_start: 0.7446 (p0) cc_final: 0.7156 (p0) REVERT: E 84 ASP cc_start: 0.8861 (t70) cc_final: 0.8241 (t70) REVERT: E 113 ASP cc_start: 0.8344 (p0) cc_final: 0.7980 (p0) REVERT: E 134 LYS cc_start: 0.8410 (tttt) cc_final: 0.8179 (ttpt) REVERT: E 190 MET cc_start: 0.8571 (tpp) cc_final: 0.8051 (ttm) REVERT: F 113 ASP cc_start: 0.8421 (p0) cc_final: 0.8109 (p0) REVERT: F 190 MET cc_start: 0.8543 (tpp) cc_final: 0.8069 (ttm) REVERT: J 65 LEU cc_start: 0.8218 (OUTLIER) cc_final: 0.7945 (mt) REVERT: J 83 MET cc_start: 0.8141 (mtt) cc_final: 0.7698 (mmm) REVERT: J 126 MET cc_start: 0.7434 (ptm) cc_final: 0.6974 (ptm) REVERT: K 126 MET cc_start: 0.7084 (ptm) cc_final: 0.6750 (ptm) REVERT: L 50 LEU cc_start: 0.7635 (OUTLIER) cc_final: 0.7309 (tt) REVERT: L 83 MET cc_start: 0.7827 (tpp) cc_final: 0.7311 (tpp) REVERT: M 50 LEU cc_start: 0.7765 (tt) cc_final: 0.7523 (tt) REVERT: N 50 LEU cc_start: 0.7991 (OUTLIER) cc_final: 0.7510 (tt) outliers start: 103 outliers final: 76 residues processed: 364 average time/residue: 0.3111 time to fit residues: 173.0205 Evaluate side-chains 346 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 266 time to evaluate : 1.910 ------------------------------------------------------------------------------- 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 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 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 120 SER 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 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 117 optimal weight: 0.9980 chunk 126 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 178 optimal weight: 9.9990 chunk 23 optimal weight: 0.5980 chunk 132 optimal weight: 2.9990 chunk 157 optimal weight: 6.9990 chunk 187 optimal weight: 20.0000 chunk 24 optimal weight: 3.9990 chunk 167 optimal weight: 8.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 ASN G 173 HIS ** I 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 41 GLN L 41 GLN ** L 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.187437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.132762 restraints weight = 19810.012| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 3.02 r_work: 0.3225 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3234 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3234 r_free = 0.3234 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1026 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3234 r_free = 0.3234 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1023 | |-----------------------------------------------------------------------------| r_final: 0.3234 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.3033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 17766 Z= 0.212 Angle : 0.646 7.776 24066 Z= 0.329 Chirality : 0.048 0.179 2667 Planarity : 0.003 0.029 3066 Dihedral : 5.001 32.919 2352 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 4.81 % Allowed : 22.46 % Favored : 72.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.17), residues: 2121 helix: None (None), residues: 0 sheet: -0.88 (0.16), residues: 980 loop : -1.11 (0.18), residues: 1141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP J 93 HIS 0.004 0.001 HIS N 79 PHE 0.012 0.001 PHE K 56 TYR 0.016 0.001 TYR D 46 ARG 0.007 0.001 ARG H 85 Details of bonding type rmsd hydrogen bonds : bond 0.03472 ( 504) hydrogen bonds : angle 6.17715 ( 1260) SS BOND : bond 0.00381 ( 28) SS BOND : angle 0.92932 ( 56) covalent geometry : bond 0.00506 (17738) covalent geometry : angle 0.64483 (24010) *********************** 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 375 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 279 time to evaluate : 1.983 Fit side-chains REVERT: A 83 MET cc_start: 0.8508 (mmm) cc_final: 0.8196 (mmm) REVERT: A 113 ASP cc_start: 0.8163 (p0) cc_final: 0.7766 (p0) REVERT: C 113 ASP cc_start: 0.8063 (p0) cc_final: 0.7703 (p0) REVERT: E 28 ARG cc_start: 0.8560 (OUTLIER) cc_final: 0.8151 (ptm160) REVERT: E 113 ASP cc_start: 0.8249 (p0) cc_final: 0.7856 (p0) REVERT: E 134 LYS cc_start: 0.8341 (tttt) cc_final: 0.8005 (ttpt) REVERT: F 28 ARG cc_start: 0.8622 (OUTLIER) cc_final: 0.8096 (ptm160) REVERT: F 113 ASP cc_start: 0.8271 (p0) cc_final: 0.7948 (p0) REVERT: G 114 LYS cc_start: 0.8592 (OUTLIER) cc_final: 0.8176 (tppt) REVERT: J 83 MET cc_start: 0.8035 (mtt) cc_final: 0.7633 (mmm) REVERT: J 126 MET cc_start: 0.7417 (ptm) cc_final: 0.7010 (ptm) REVERT: K 65 LEU cc_start: 0.8281 (OUTLIER) cc_final: 0.7913 (mp) REVERT: K 83 MET cc_start: 0.7814 (tpp) cc_final: 0.7580 (tpp) REVERT: K 126 MET cc_start: 0.7004 (ptm) cc_final: 0.6670 (ptm) REVERT: L 83 MET cc_start: 0.7645 (tpp) cc_final: 0.7122 (tpp) outliers start: 96 outliers final: 78 residues processed: 348 average time/residue: 0.3032 time to fit residues: 157.1411 Evaluate side-chains 348 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 266 time to evaluate : 2.065 ------------------------------------------------------------------------------- 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 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 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 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 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 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 114 LYS 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 H residue 107 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 53 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 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 201 optimal weight: 10.0000 chunk 76 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 2 optimal weight: 0.0980 chunk 135 optimal weight: 0.0060 chunk 23 optimal weight: 5.9990 chunk 173 optimal weight: 3.9990 chunk 152 optimal weight: 0.0050 chunk 108 optimal weight: 1.9990 chunk 101 optimal weight: 0.5980 chunk 86 optimal weight: 0.8980 overall best weight: 0.3210 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 179 ASN ** 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** ** M 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 127 ASN ** N 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 127 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.190618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.135582 restraints weight = 19839.376| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 2.99 r_work: 0.3288 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3171 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3171 r_free = 0.3171 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1023 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3171 r_free = 0.3171 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1027 | |-----------------------------------------------------------------------------| r_final: 0.3171 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.3064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 17766 Z= 0.106 Angle : 0.592 7.806 24066 Z= 0.298 Chirality : 0.045 0.158 2667 Planarity : 0.003 0.028 3066 Dihedral : 4.658 27.307 2352 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 2.56 % Allowed : 24.46 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.17), residues: 2121 helix: None (None), residues: 0 sheet: -0.87 (0.16), residues: 980 loop : -1.05 (0.18), residues: 1141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 57 HIS 0.003 0.000 HIS N 79 PHE 0.010 0.001 PHE H 56 TYR 0.009 0.001 TYR D 46 ARG 0.010 0.001 ARG L 85 Details of bonding type rmsd hydrogen bonds : bond 0.02980 ( 504) hydrogen bonds : angle 5.92933 ( 1260) SS BOND : bond 0.00194 ( 28) SS BOND : angle 0.64154 ( 56) covalent geometry : bond 0.00244 (17738) covalent geometry : angle 0.59142 (24010) *********************** 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 335 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 284 time to evaluate : 1.981 Fit side-chains REVERT: A 28 ARG cc_start: 0.8598 (OUTLIER) cc_final: 0.7838 (ptm160) REVERT: A 30 ASP cc_start: 0.7279 (p0) cc_final: 0.7036 (p0) REVERT: A 113 ASP cc_start: 0.8263 (p0) cc_final: 0.7895 (p0) REVERT: C 28 ARG cc_start: 0.8770 (OUTLIER) cc_final: 0.8008 (ptm160) REVERT: C 113 ASP cc_start: 0.8257 (p0) cc_final: 0.7941 (p0) REVERT: E 113 ASP cc_start: 0.8367 (p0) cc_final: 0.7961 (p0) REVERT: E 134 LYS cc_start: 0.8390 (tttt) cc_final: 0.8083 (ttpt) REVERT: E 190 MET cc_start: 0.8560 (tpp) cc_final: 0.8122 (ttm) REVERT: F 113 ASP cc_start: 0.8404 (p0) cc_final: 0.8052 (p0) REVERT: F 190 MET cc_start: 0.8561 (tpp) cc_final: 0.8148 (ttm) REVERT: I 126 MET cc_start: 0.7478 (ptm) cc_final: 0.7135 (ptm) REVERT: J 83 MET cc_start: 0.8222 (mtt) cc_final: 0.7732 (mmm) REVERT: J 126 MET cc_start: 0.7542 (ptm) cc_final: 0.7050 (ptm) REVERT: K 83 MET cc_start: 0.7955 (tpp) cc_final: 0.7639 (tpp) REVERT: K 126 MET cc_start: 0.7305 (ptm) cc_final: 0.6931 (ptm) REVERT: L 83 MET cc_start: 0.7823 (tpp) cc_final: 0.7265 (tpp) REVERT: L 130 LEU cc_start: 0.7385 (OUTLIER) cc_final: 0.6992 (tt) REVERT: N 130 LEU cc_start: 0.7408 (OUTLIER) cc_final: 0.6956 (tt) outliers start: 51 outliers final: 40 residues processed: 316 average time/residue: 0.3154 time to fit residues: 147.0567 Evaluate side-chains 309 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 265 time to evaluate : 1.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ARG Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 28 ARG Chi-restraints excluded: chain B residue 42 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 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 143 ILE Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 143 ILE Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 42 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 E residue 207 LEU Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 143 ILE Chi-restraints excluded: chain G residue 23 THR 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 H residue 107 LEU Chi-restraints excluded: chain I residue 38 LEU Chi-restraints excluded: chain I residue 107 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 107 LEU Chi-restraints excluded: chain L residue 130 LEU Chi-restraints excluded: chain M residue 97 LEU Chi-restraints excluded: chain M residue 107 LEU Chi-restraints excluded: chain N residue 107 LEU Chi-restraints excluded: chain N residue 130 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 4 optimal weight: 4.9990 chunk 30 optimal weight: 0.8980 chunk 160 optimal weight: 20.0000 chunk 39 optimal weight: 1.9990 chunk 177 optimal weight: 0.9990 chunk 61 optimal weight: 0.8980 chunk 70 optimal weight: 3.9990 chunk 81 optimal weight: 0.5980 chunk 25 optimal weight: 0.5980 chunk 29 optimal weight: 2.9990 chunk 155 optimal weight: 5.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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** ** I 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 41 GLN ** J 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 101 GLN ** L 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 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 = 0.4149 r_free = 0.4149 target = 0.189066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.134588 restraints weight = 19914.405| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 2.98 r_work: 0.3265 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3272 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3272 r_free = 0.3272 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1027 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3271 r_free = 0.3271 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1027 | |-----------------------------------------------------------------------------| r_final: 0.3271 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.3226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17766 Z= 0.139 Angle : 0.592 8.318 24066 Z= 0.298 Chirality : 0.045 0.148 2667 Planarity : 0.003 0.027 3066 Dihedral : 4.593 27.279 2352 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 4.31 % Allowed : 23.41 % Favored : 72.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.18), residues: 2121 helix: None (None), residues: 0 sheet: -0.74 (0.16), residues: 952 loop : -1.08 (0.18), residues: 1169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 57 HIS 0.003 0.001 HIS N 79 PHE 0.010 0.001 PHE H 56 TYR 0.013 0.001 TYR D 46 ARG 0.005 0.001 ARG L 85 Details of bonding type rmsd hydrogen bonds : bond 0.02984 ( 504) hydrogen bonds : angle 5.71120 ( 1260) SS BOND : bond 0.00229 ( 28) SS BOND : angle 0.64946 ( 56) covalent geometry : bond 0.00325 (17738) covalent geometry : angle 0.59143 (24010) *********************** 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 349 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 263 time to evaluate : 1.851 Fit side-chains REVERT: A 113 ASP cc_start: 0.8088 (p0) cc_final: 0.7706 (p0) REVERT: C 113 ASP cc_start: 0.8156 (p0) cc_final: 0.7815 (p0) REVERT: E 113 ASP cc_start: 0.8213 (p0) cc_final: 0.7823 (p0) REVERT: E 134 LYS cc_start: 0.8269 (tttt) cc_final: 0.8038 (ttpt) REVERT: E 190 MET cc_start: 0.8448 (tpp) cc_final: 0.8117 (ttm) REVERT: F 113 ASP cc_start: 0.8259 (p0) cc_final: 0.7926 (p0) REVERT: F 190 MET cc_start: 0.8378 (tpp) cc_final: 0.8106 (ttm) REVERT: I 126 MET cc_start: 0.7272 (ptm) cc_final: 0.7024 (ptm) REVERT: J 83 MET cc_start: 0.8155 (mtt) cc_final: 0.7705 (mmm) REVERT: J 126 MET cc_start: 0.7450 (ptm) cc_final: 0.6991 (ptm) REVERT: K 65 LEU cc_start: 0.8298 (OUTLIER) cc_final: 0.7938 (mp) REVERT: K 126 MET cc_start: 0.7193 (ptm) cc_final: 0.6838 (ptm) REVERT: L 83 MET cc_start: 0.7638 (tpp) cc_final: 0.7107 (tpp) REVERT: L 130 LEU cc_start: 0.7305 (OUTLIER) cc_final: 0.7033 (tt) REVERT: N 130 LEU cc_start: 0.7065 (OUTLIER) cc_final: 0.6763 (tt) outliers start: 86 outliers final: 66 residues processed: 322 average time/residue: 0.2960 time to fit residues: 142.7301 Evaluate side-chains 328 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 259 time to evaluate : 1.811 ------------------------------------------------------------------------------- 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 81 THR 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 152 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 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 42 ILE Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 114 LYS 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 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 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 207 LEU Chi-restraints excluded: chain I residue 38 LEU Chi-restraints excluded: chain I residue 107 LEU Chi-restraints excluded: chain K residue 65 LEU Chi-restraints excluded: chain L residue 65 LEU Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain L residue 130 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 130 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 35 optimal weight: 0.6980 chunk 1 optimal weight: 0.9990 chunk 124 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 119 optimal weight: 0.8980 chunk 90 optimal weight: 2.9990 chunk 81 optimal weight: 0.6980 chunk 130 optimal weight: 4.9990 chunk 143 optimal weight: 0.8980 chunk 209 optimal weight: 0.9980 chunk 167 optimal weight: 5.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 79 ASN B 179 ASN C 185 ASN ** F 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 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.189096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.136485 restraints weight = 19832.815| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 2.77 r_work: 0.3282 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3156 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3156 r_free = 0.3156 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1027 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3156 r_free = 0.3156 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1027 | |-----------------------------------------------------------------------------| r_final: 0.3156 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.3369 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= 0.138 Angle : 0.586 8.776 24066 Z= 0.295 Chirality : 0.045 0.148 2667 Planarity : 0.003 0.028 3066 Dihedral : 4.536 26.606 2352 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 4.06 % Allowed : 24.16 % Favored : 71.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.18), residues: 2121 helix: None (None), residues: 0 sheet: -0.71 (0.16), residues: 952 loop : -1.09 (0.18), residues: 1169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 57 HIS 0.003 0.001 HIS N 79 PHE 0.009 0.001 PHE H 56 TYR 0.013 0.001 TYR D 46 ARG 0.004 0.001 ARG L 85 Details of bonding type rmsd hydrogen bonds : bond 0.02912 ( 504) hydrogen bonds : angle 5.65560 ( 1260) SS BOND : bond 0.00205 ( 28) SS BOND : angle 0.60923 ( 56) covalent geometry : bond 0.00326 (17738) covalent geometry : angle 0.58630 (24010) *********************** 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 346 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 265 time to evaluate : 1.978 Fit side-chains REVERT: A 113 ASP cc_start: 0.8220 (p0) cc_final: 0.7834 (p0) REVERT: C 113 ASP cc_start: 0.8244 (p0) cc_final: 0.7875 (p0) REVERT: C 185 ASN cc_start: 0.8829 (t0) cc_final: 0.8560 (t0) REVERT: E 134 LYS cc_start: 0.8376 (tttt) cc_final: 0.8032 (ttpt) REVERT: E 190 MET cc_start: 0.8560 (tpp) cc_final: 0.8151 (ttm) REVERT: F 113 ASP cc_start: 0.8366 (p0) cc_final: 0.8019 (p0) REVERT: I 65 LEU cc_start: 0.8004 (OUTLIER) cc_final: 0.7274 (mp) REVERT: I 83 MET cc_start: 0.7389 (mmm) cc_final: 0.7146 (mmm) REVERT: I 126 MET cc_start: 0.7499 (ptm) cc_final: 0.7214 (ptm) REVERT: J 83 MET cc_start: 0.8245 (mtt) cc_final: 0.7745 (mmm) REVERT: J 126 MET cc_start: 0.7590 (ptm) cc_final: 0.7088 (ptm) REVERT: K 65 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.7993 (mp) REVERT: K 126 MET cc_start: 0.7367 (ptm) cc_final: 0.7059 (ptm) REVERT: L 83 MET cc_start: 0.7783 (tpp) cc_final: 0.7221 (tpp) REVERT: L 130 LEU cc_start: 0.7273 (OUTLIER) cc_final: 0.6976 (tt) REVERT: N 130 LEU cc_start: 0.7035 (OUTLIER) cc_final: 0.6752 (tt) outliers start: 81 outliers final: 64 residues processed: 322 average time/residue: 0.3020 time to fit residues: 145.1918 Evaluate side-chains 328 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 260 time to evaluate : 1.845 ------------------------------------------------------------------------------- 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 81 THR 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 152 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 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 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 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 42 ILE Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 82 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 138 ASP Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain G residue 152 THR Chi-restraints excluded: chain G residue 207 LEU Chi-restraints excluded: chain I residue 38 LEU Chi-restraints excluded: chain I residue 65 LEU Chi-restraints excluded: chain K residue 65 LEU Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain L residue 130 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 130 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 84 optimal weight: 0.9980 chunk 38 optimal weight: 0.6980 chunk 94 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 180 optimal weight: 0.0570 chunk 81 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 overall best weight: 0.6898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 179 ASN ** F 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 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 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 = 0.4157 r_free = 0.4157 target = 0.189762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.134878 restraints weight = 19820.311| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 3.08 r_work: 0.3269 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3277 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3277 r_free = 0.3277 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1027 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3277 r_free = 0.3277 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1028 | |-----------------------------------------------------------------------------| r_final: 0.3277 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.3442 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= 0.127 Angle : 0.596 9.495 24066 Z= 0.296 Chirality : 0.045 0.156 2667 Planarity : 0.003 0.028 3066 Dihedral : 4.469 25.985 2352 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 4.16 % Allowed : 24.01 % Favored : 71.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.18), residues: 2121 helix: None (None), residues: 0 sheet: -0.64 (0.17), residues: 882 loop : -1.15 (0.17), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 57 HIS 0.007 0.001 HIS I 79 PHE 0.009 0.001 PHE L 56 TYR 0.012 0.001 TYR D 46 ARG 0.005 0.001 ARG L 85 Details of bonding type rmsd hydrogen bonds : bond 0.02815 ( 504) hydrogen bonds : angle 5.59035 ( 1260) SS BOND : bond 0.00213 ( 28) SS BOND : angle 0.69747 ( 56) covalent geometry : bond 0.00299 (17738) covalent geometry : angle 0.59525 (24010) *********************** 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 346 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 263 time to evaluate : 1.965 Fit side-chains REVERT: C 28 ARG cc_start: 0.8707 (OUTLIER) cc_final: 0.7670 (ptm160) REVERT: C 113 ASP cc_start: 0.8100 (p0) cc_final: 0.7701 (p0) REVERT: C 185 ASN cc_start: 0.8748 (t0) cc_final: 0.8502 (t0) REVERT: E 134 LYS cc_start: 0.8224 (tttt) cc_final: 0.7958 (ttpt) REVERT: F 28 ARG cc_start: 0.8582 (OUTLIER) cc_final: 0.7250 (ptm160) REVERT: F 113 ASP cc_start: 0.8249 (p0) cc_final: 0.7892 (p0) REVERT: I 65 LEU cc_start: 0.7965 (OUTLIER) cc_final: 0.7262 (mp) REVERT: I 83 MET cc_start: 0.7494 (mmm) cc_final: 0.7291 (mmm) REVERT: I 126 MET cc_start: 0.7340 (ptm) cc_final: 0.7055 (ptm) REVERT: J 83 MET cc_start: 0.8188 (mtt) cc_final: 0.7716 (mmm) REVERT: J 126 MET cc_start: 0.7490 (ptm) cc_final: 0.7040 (ptm) REVERT: K 65 LEU cc_start: 0.8274 (OUTLIER) cc_final: 0.7942 (mp) REVERT: K 126 MET cc_start: 0.7220 (ptm) cc_final: 0.6901 (ptm) REVERT: L 83 MET cc_start: 0.7629 (tpp) cc_final: 0.7099 (tpp) REVERT: L 130 LEU cc_start: 0.7251 (OUTLIER) cc_final: 0.6988 (tt) REVERT: N 130 LEU cc_start: 0.7095 (OUTLIER) cc_final: 0.6806 (tt) outliers start: 83 outliers final: 66 residues processed: 322 average time/residue: 0.3145 time to fit residues: 151.0451 Evaluate side-chains 330 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 258 time to evaluate : 2.179 ------------------------------------------------------------------------------- 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 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 143 ILE Chi-restraints excluded: chain B residue 152 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 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 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 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 82 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 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 65 LEU Chi-restraints excluded: chain K residue 65 LEU Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain L residue 130 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 130 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 24 optimal weight: 4.9990 chunk 95 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 136 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 chunk 125 optimal weight: 1.9990 chunk 147 optimal weight: 6.9990 chunk 18 optimal weight: 0.9980 chunk 208 optimal weight: 0.9990 chunk 154 optimal weight: 7.9990 chunk 181 optimal weight: 6.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- 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 C 79 ASN D 116 HIS ** F 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 79 ASN ** 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 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 66 ASN ** 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 = 0.4295 r_free = 0.4295 target = 0.197530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.141952 restraints weight = 20524.233| |-----------------------------------------------------------------------------| r_work (start): 0.3706 rms_B_bonded: 3.14 r_work: 0.3400 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.3261 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3214 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3214 r_free = 0.3214 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1028 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3212 r_free = 0.3212 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1024 | |-----------------------------------------------------------------------------| r_final: 0.3212 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.3561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 17766 Z= 0.167 Angle : 0.622 10.177 24066 Z= 0.309 Chirality : 0.046 0.161 2667 Planarity : 0.003 0.041 3066 Dihedral : 4.562 28.102 2352 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 3.96 % Allowed : 24.56 % Favored : 71.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.18), residues: 2121 helix: None (None), residues: 0 sheet: -0.70 (0.17), residues: 882 loop : -1.16 (0.17), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 57 HIS 0.008 0.001 HIS I 79 PHE 0.010 0.001 PHE J 56 TYR 0.015 0.001 TYR D 46 ARG 0.005 0.001 ARG H 85 Details of bonding type rmsd hydrogen bonds : bond 0.02957 ( 504) hydrogen bonds : angle 5.63357 ( 1260) SS BOND : bond 0.00262 ( 28) SS BOND : angle 0.73261 ( 56) covalent geometry : bond 0.00400 (17738) covalent geometry : angle 0.62139 (24010) *********************** 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 337 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 258 time to evaluate : 1.872 Fit side-chains REVERT: A 64 ASP cc_start: 0.8329 (t0) cc_final: 0.8108 (t0) REVERT: A 220 GLU cc_start: 0.7181 (mp0) cc_final: 0.6927 (mp0) REVERT: B 190 MET cc_start: 0.8569 (tpp) cc_final: 0.8312 (tpp) REVERT: E 134 LYS cc_start: 0.8465 (tttt) cc_final: 0.8026 (ttpt) REVERT: E 190 MET cc_start: 0.8481 (tpp) cc_final: 0.7953 (ttm) REVERT: F 28 ARG cc_start: 0.8751 (OUTLIER) cc_final: 0.7408 (ptm160) REVERT: F 113 ASP cc_start: 0.8405 (p0) cc_final: 0.8016 (p0) REVERT: I 65 LEU cc_start: 0.7938 (OUTLIER) cc_final: 0.7232 (mp) REVERT: I 83 MET cc_start: 0.7676 (mmm) cc_final: 0.7422 (mmm) REVERT: I 126 MET cc_start: 0.7536 (ptm) cc_final: 0.7203 (ptm) REVERT: J 83 MET cc_start: 0.8300 (mtt) cc_final: 0.7752 (mmm) REVERT: J 126 MET cc_start: 0.7530 (ptm) cc_final: 0.6980 (ptm) REVERT: K 65 LEU cc_start: 0.8253 (OUTLIER) cc_final: 0.7938 (mp) REVERT: K 126 MET cc_start: 0.7299 (ptm) cc_final: 0.6905 (ptm) REVERT: L 83 MET cc_start: 0.7874 (tpp) cc_final: 0.7370 (tpp) REVERT: L 130 LEU cc_start: 0.7333 (OUTLIER) cc_final: 0.6967 (tt) REVERT: N 130 LEU cc_start: 0.7269 (OUTLIER) cc_final: 0.6873 (tt) outliers start: 79 outliers final: 69 residues processed: 316 average time/residue: 0.3076 time to fit residues: 146.1007 Evaluate side-chains 327 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 253 time to evaluate : 1.921 ------------------------------------------------------------------------------- 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 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 143 ILE Chi-restraints excluded: chain B residue 152 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 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 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 82 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 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 I residue 38 LEU Chi-restraints excluded: chain I residue 65 LEU Chi-restraints excluded: chain I residue 107 LEU Chi-restraints excluded: chain I residue 118 THR Chi-restraints excluded: chain J residue 53 LEU 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 L residue 86 THR Chi-restraints excluded: chain L residue 130 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 130 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 201 optimal weight: 10.0000 chunk 25 optimal weight: 1.9990 chunk 119 optimal weight: 0.2980 chunk 123 optimal weight: 0.3980 chunk 209 optimal weight: 0.9990 chunk 52 optimal weight: 4.9990 chunk 24 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 153 optimal weight: 9.9990 chunk 146 optimal weight: 2.9990 chunk 167 optimal weight: 2.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 179 ASN C 116 HIS ** F 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 66 ASN ** 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 98 HIS ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.189324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.136850 restraints weight = 19775.649| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 2.95 r_work: 0.3276 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3279 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3279 r_free = 0.3279 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1024 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3278 r_free = 0.3278 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1025 | |-----------------------------------------------------------------------------| r_final: 0.3278 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.3611 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= 0.130 Angle : 0.614 11.627 24066 Z= 0.302 Chirality : 0.046 0.163 2667 Planarity : 0.003 0.030 3066 Dihedral : 4.471 26.105 2352 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 3.61 % Allowed : 24.96 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.18), residues: 2121 helix: None (None), residues: 0 sheet: -0.69 (0.17), residues: 882 loop : -1.13 (0.17), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP J 57 HIS 0.005 0.001 HIS I 79 PHE 0.009 0.001 PHE L 56 TYR 0.012 0.001 TYR D 46 ARG 0.007 0.001 ARG H 85 Details of bonding type rmsd hydrogen bonds : bond 0.02789 ( 504) hydrogen bonds : angle 5.57581 ( 1260) SS BOND : bond 0.00168 ( 28) SS BOND : angle 0.67552 ( 56) covalent geometry : bond 0.00309 (17738) covalent geometry : angle 0.61429 (24010) ********************** 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 340 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 268 time to evaluate : 1.903 Fit side-chains REVERT: B 190 MET cc_start: 0.8546 (tpp) cc_final: 0.8325 (tpp) REVERT: B 219 ARG cc_start: 0.7528 (mtm110) cc_final: 0.7214 (mtp180) REVERT: C 28 ARG cc_start: 0.8742 (OUTLIER) cc_final: 0.7696 (ptm160) REVERT: E 134 LYS cc_start: 0.8229 (tttt) cc_final: 0.7953 (ttpt) REVERT: F 28 ARG cc_start: 0.8621 (OUTLIER) cc_final: 0.7298 (ptm160) REVERT: F 113 ASP cc_start: 0.8225 (p0) cc_final: 0.7879 (p0) REVERT: I 83 MET cc_start: 0.7494 (mmm) cc_final: 0.6694 (mmm) REVERT: I 126 MET cc_start: 0.7324 (ptm) cc_final: 0.7063 (ptm) REVERT: J 83 MET cc_start: 0.8199 (mtt) cc_final: 0.7728 (mmm) REVERT: J 126 MET cc_start: 0.7491 (ptm) cc_final: 0.7057 (ptm) REVERT: K 65 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.7972 (mp) REVERT: K 83 MET cc_start: 0.7593 (tpp) cc_final: 0.7226 (mmm) REVERT: K 126 MET cc_start: 0.7208 (ptm) cc_final: 0.6905 (ptm) REVERT: L 83 MET cc_start: 0.7658 (tpp) cc_final: 0.7169 (tpp) REVERT: N 130 LEU cc_start: 0.7033 (OUTLIER) cc_final: 0.6792 (tt) outliers start: 72 outliers final: 62 residues processed: 316 average time/residue: 0.2975 time to fit residues: 139.3885 Evaluate side-chains 328 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 262 time to evaluate : 1.822 ------------------------------------------------------------------------------- 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 81 THR Chi-restraints excluded: chain A residue 124 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 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 152 THR Chi-restraints excluded: chain B residue 179 ASN 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 81 THR 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 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 143 ILE Chi-restraints excluded: chain D residue 152 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 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 82 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 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 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 86 THR 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 130 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 20 optimal weight: 3.9990 chunk 152 optimal weight: 0.5980 chunk 201 optimal weight: 9.9990 chunk 31 optimal weight: 0.9980 chunk 83 optimal weight: 0.0040 chunk 208 optimal weight: 6.9990 chunk 189 optimal weight: 0.8980 chunk 37 optimal weight: 0.6980 chunk 122 optimal weight: 1.9990 chunk 103 optimal weight: 5.9990 chunk 185 optimal weight: 4.9990 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 79 ASN ** F 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 66 ASN ** 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 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 = 0.4201 r_free = 0.4201 target = 0.188930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.131239 restraints weight = 20186.670| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 3.32 r_work: 0.3263 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3278 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3278 r_free = 0.3278 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1025 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3276 r_free = 0.3276 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1027 | |-----------------------------------------------------------------------------| r_final: 0.3276 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.3650 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= 0.125 Angle : 0.607 10.641 24066 Z= 0.300 Chirality : 0.046 0.156 2667 Planarity : 0.003 0.029 3066 Dihedral : 4.430 25.876 2352 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 3.66 % Allowed : 24.56 % Favored : 71.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.18), residues: 2121 helix: None (None), residues: 0 sheet: -0.66 (0.17), residues: 882 loop : -1.12 (0.17), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP M 57 HIS 0.003 0.001 HIS I 79 PHE 0.009 0.001 PHE M 56 TYR 0.014 0.001 TYR B 181 ARG 0.007 0.001 ARG H 85 Details of bonding type rmsd hydrogen bonds : bond 0.02754 ( 504) hydrogen bonds : angle 5.51778 ( 1260) SS BOND : bond 0.00159 ( 28) SS BOND : angle 0.62135 ( 56) covalent geometry : bond 0.00296 (17738) covalent geometry : angle 0.60714 (24010) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10304.35 seconds wall clock time: 180 minutes 11.00 seconds (10811.00 seconds total)