Starting phenix.real_space_refine on Wed Mar 4 16:00:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hxb_35075/03_2026/8hxb_35075.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hxb_35075/03_2026/8hxb_35075.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8hxb_35075/03_2026/8hxb_35075.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hxb_35075/03_2026/8hxb_35075.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hxb_35075/03_2026/8hxb_35075.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hxb_35075/03_2026/8hxb_35075.map" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.061 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 120 5.16 5 C 9378 2.51 5 N 2514 2.21 5 O 2880 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14892 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: "G" Number of atoms: 872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 872 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 2, 'TRANS': 103} Restraints were copied for chains: B, C, D, E, F, H, I, J, K, L Time building chain proxies: 1.89, per 1000 atoms: 0.13 Number of scatterers: 14892 At special positions: 0 Unit cell: (160.55, 175.75, 65.55, 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 120 16.00 O 2880 8.00 N 2514 7.00 C 9378 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS A 25 " - pdb=" SG CYS B 130 " distance=1.99 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 F 25 " distance=2.06 Simple disulfide: pdb=" SG CYS A 160 " - pdb=" SG CYS A 205 " distance=2.02 Simple disulfide: pdb=" SG CYS B 25 " - pdb=" SG CYS C 130 " distance=2.01 Simple disulfide: pdb=" SG CYS C 25 " - pdb=" SG CYS D 130 " distance=1.97 Simple disulfide: pdb=" SG CYS D 25 " - pdb=" SG CYS E 130 " distance=2.09 Simple disulfide: pdb=" SG CYS E 25 " - pdb=" SG CYS F 130 " distance=2.11 Simple disulfide: pdb=" SG CYS B 56 " - pdb=" SG CYS B 217 " distance=2.03 Simple disulfide: pdb=" SG CYS C 56 " - pdb=" SG CYS C 217 " distance=2.03 Simple disulfide: pdb=" SG CYS D 56 " - pdb=" SG CYS D 217 " distance=2.03 Simple disulfide: pdb=" SG CYS E 56 " - pdb=" SG CYS E 217 " distance=2.03 Simple disulfide: pdb=" SG CYS F 56 " - pdb=" SG CYS F 217 " distance=2.03 Simple disulfide: pdb=" SG CYS B 125 " - pdb=" SG CYS B 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 125 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS D 125 " - pdb=" SG CYS D 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 125 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS F 125 " - pdb=" SG CYS F 157 " distance=2.03 Simple disulfide: pdb=" SG CYS B 160 " - pdb=" SG CYS B 205 " distance=2.02 Simple disulfide: pdb=" SG CYS C 160 " - pdb=" SG CYS C 205 " distance=2.02 Simple disulfide: pdb=" SG CYS D 160 " - pdb=" SG CYS D 205 " distance=2.02 Simple disulfide: pdb=" SG CYS E 160 " - pdb=" SG CYS E 205 " distance=2.02 Simple disulfide: pdb=" SG CYS F 160 " - pdb=" SG CYS F 205 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.29 Conformation dependent library (CDL) restraints added in 778.6 milliseconds 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3516 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 29 sheets defined 4.9% alpha, 42.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 187 through 191 Processing helix chain 'B' and resid 187 through 191 Processing helix chain 'C' and resid 187 through 191 Processing helix chain 'D' and resid 187 through 191 Processing helix chain 'E' and resid 187 through 191 Processing helix chain 'F' and resid 187 through 191 Processing helix chain 'G' and resid 49 through 53 removed outlier: 3.845A pdb=" N GLU G 52 " --> pdb=" O SER G 49 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU G 53 " --> pdb=" O LEU G 50 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 49 through 53' Processing helix chain 'G' and resid 79 through 83 Processing helix chain 'H' and resid 49 through 53 removed outlier: 3.845A pdb=" N GLU H 52 " --> pdb=" O SER H 49 " (cutoff:3.500A) removed outlier: 3.714A 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: 3.845A pdb=" N GLU I 52 " --> pdb=" O SER I 49 " (cutoff:3.500A) removed outlier: 3.715A 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: 3.845A pdb=" N GLU J 52 " --> pdb=" O SER J 49 " (cutoff:3.500A) removed outlier: 3.715A 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: 3.846A pdb=" N GLU K 52 " --> pdb=" O SER K 49 " (cutoff:3.500A) removed outlier: 3.715A 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: 3.845A pdb=" N GLU L 52 " --> pdb=" O SER L 49 " (cutoff:3.500A) removed outlier: 3.715A 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 sheet with id=AA1, first strand: chain 'A' and resid 22 through 23 removed outlier: 4.350A pdb=" N CYS B 130 " --> pdb=" O THR A 23 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 181 through 184 removed outlier: 5.575A pdb=" N PHE A 36 " --> pdb=" O THR A 108 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N THR A 108 " --> pdb=" O PHE A 36 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA A 38 " --> pdb=" O LEU A 106 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LYS A 101 " --> pdb=" O VAL A 96 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N VAL A 96 " --> pdb=" O LYS A 101 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N SER A 103 " --> pdb=" O GLU A 94 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N GLU A 94 " --> pdb=" O SER A 103 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N LEU A 105 " --> pdb=" O ALA A 92 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ALA A 92 " --> pdb=" O LEU A 105 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N PHE A 107 " --> pdb=" O VAL A 90 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 181 through 184 removed outlier: 9.387A pdb=" N SER A 193 " --> pdb=" O HIS G 124 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N HIS G 124 " --> pdb=" O SER A 193 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N GLY A 195 " --> pdb=" O ARG G 122 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ILE G 112 " --> pdb=" O ILE G 123 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N GLN G 125 " --> pdb=" O CYS G 110 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N CYS G 110 " --> pdb=" O GLN G 125 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N ASN G 127 " --> pdb=" O TYR G 108 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N TYR G 108 " --> pdb=" O ASN G 127 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N TRP G 57 " --> pdb=" O ASN G 66 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ASN G 66 " --> pdb=" O TRP G 57 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 57 through 63 Processing sheet with id=AA5, first strand: chain 'A' and resid 130 through 131 removed outlier: 4.388A pdb=" N CYS A 130 " --> pdb=" O THR F 23 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 22 through 23 removed outlier: 4.337A pdb=" N CYS C 130 " --> pdb=" O THR B 23 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 181 through 184 removed outlier: 5.576A pdb=" N PHE B 36 " --> pdb=" O THR B 108 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N THR B 108 " --> pdb=" O PHE B 36 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA B 38 " --> pdb=" O LEU B 106 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LYS B 101 " --> pdb=" O VAL B 96 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N VAL B 96 " --> pdb=" O LYS B 101 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N SER B 103 " --> pdb=" O GLU B 94 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N GLU B 94 " --> pdb=" O SER B 103 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N LEU B 105 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ALA B 92 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N PHE B 107 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 181 through 184 removed outlier: 9.372A pdb=" N SER B 193 " --> pdb=" O HIS H 124 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N HIS H 124 " --> pdb=" O SER B 193 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N GLY B 195 " --> pdb=" O ARG H 122 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ILE H 112 " --> pdb=" O ILE H 123 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N GLN H 125 " --> pdb=" O CYS H 110 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N CYS H 110 " --> pdb=" O GLN H 125 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N ASN H 127 " --> pdb=" O TYR H 108 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N TYR H 108 " --> pdb=" O ASN H 127 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N TRP H 57 " --> pdb=" O ASN H 66 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ASN H 66 " --> pdb=" O TRP H 57 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 57 through 63 Processing sheet with id=AB1, first strand: chain 'C' and resid 22 through 23 removed outlier: 4.362A pdb=" N CYS D 130 " --> pdb=" O THR C 23 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 181 through 184 removed outlier: 5.576A pdb=" N PHE C 36 " --> pdb=" O THR C 108 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N THR C 108 " --> pdb=" O PHE C 36 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA C 38 " --> pdb=" O LEU C 106 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N LYS C 101 " --> pdb=" O VAL C 96 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N VAL C 96 " --> pdb=" O LYS C 101 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N SER C 103 " --> pdb=" O GLU C 94 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N GLU C 94 " --> pdb=" O SER C 103 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N LEU C 105 " --> pdb=" O ALA C 92 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ALA C 92 " --> pdb=" O LEU C 105 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N PHE C 107 " --> pdb=" O VAL C 90 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 181 through 184 removed outlier: 9.416A pdb=" N SER C 193 " --> pdb=" O HIS I 124 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N HIS I 124 " --> pdb=" O SER C 193 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N GLY C 195 " --> pdb=" O ARG I 122 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ILE I 112 " --> pdb=" O ILE I 123 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N GLN I 125 " --> pdb=" O CYS I 110 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N CYS I 110 " --> pdb=" O GLN I 125 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N ASN I 127 " --> pdb=" O TYR I 108 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N TYR I 108 " --> pdb=" O ASN I 127 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N TRP I 57 " --> pdb=" O ASN I 66 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ASN I 66 " --> pdb=" O TRP I 57 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 57 through 63 Processing sheet with id=AB5, first strand: chain 'D' and resid 181 through 184 removed outlier: 5.576A pdb=" N PHE D 36 " --> pdb=" O THR D 108 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N THR D 108 " --> pdb=" O PHE D 36 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA D 38 " --> pdb=" O LEU D 106 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LYS D 101 " --> pdb=" O VAL D 96 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N VAL D 96 " --> pdb=" O LYS D 101 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N SER D 103 " --> pdb=" O GLU D 94 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N GLU D 94 " --> pdb=" O SER D 103 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N LEU D 105 " --> pdb=" O ALA D 92 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ALA D 92 " --> pdb=" O LEU D 105 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N PHE D 107 " --> pdb=" O VAL D 90 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 181 through 184 removed outlier: 9.355A pdb=" N SER D 193 " --> pdb=" O HIS J 124 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N HIS J 124 " --> pdb=" O SER D 193 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N GLY D 195 " --> pdb=" O ARG J 122 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ILE J 112 " --> pdb=" O ILE J 123 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N GLN J 125 " --> pdb=" O CYS J 110 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N CYS J 110 " --> pdb=" O GLN J 125 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N ASN J 127 " --> pdb=" O TYR J 108 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N TYR J 108 " --> pdb=" O ASN J 127 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TRP J 57 " --> pdb=" O ASN J 66 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ASN J 66 " --> pdb=" O TRP J 57 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 57 through 63 Processing sheet with id=AB8, first strand: chain 'E' and resid 22 through 23 removed outlier: 4.399A pdb=" N CYS F 130 " --> pdb=" O THR E 23 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 181 through 184 removed outlier: 5.576A pdb=" N PHE E 36 " --> pdb=" O THR E 108 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N THR E 108 " --> pdb=" O PHE E 36 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA E 38 " --> pdb=" O LEU E 106 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LYS E 101 " --> pdb=" O VAL E 96 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N VAL E 96 " --> pdb=" O LYS E 101 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N SER E 103 " --> pdb=" O GLU E 94 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N GLU E 94 " --> pdb=" O SER E 103 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N LEU E 105 " --> pdb=" O ALA E 92 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ALA E 92 " --> pdb=" O LEU E 105 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N PHE E 107 " --> pdb=" O VAL E 90 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 181 through 184 removed outlier: 9.183A pdb=" N SER E 193 " --> pdb=" O HIS K 124 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N HIS K 124 " --> pdb=" O SER E 193 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N GLY E 195 " --> pdb=" O ARG K 122 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ILE K 112 " --> pdb=" O ILE K 123 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N GLN K 125 " --> pdb=" O CYS K 110 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N CYS K 110 " --> pdb=" O GLN K 125 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N ASN K 127 " --> pdb=" O TYR K 108 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N TYR K 108 " --> pdb=" O ASN K 127 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N TRP K 57 " --> pdb=" O ASN K 66 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ASN K 66 " --> pdb=" O TRP K 57 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 57 through 63 Processing sheet with id=AC3, first strand: chain 'F' and resid 181 through 184 removed outlier: 5.575A pdb=" N PHE F 36 " --> pdb=" O THR F 108 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N THR F 108 " --> pdb=" O PHE F 36 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA F 38 " --> pdb=" O LEU F 106 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LYS F 101 " --> pdb=" O VAL F 96 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N VAL F 96 " --> pdb=" O LYS F 101 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N SER F 103 " --> pdb=" O GLU F 94 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N GLU F 94 " --> pdb=" O SER F 103 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N LEU F 105 " --> pdb=" O ALA F 92 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ALA F 92 " --> pdb=" O LEU F 105 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N PHE F 107 " --> pdb=" O VAL F 90 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 181 through 184 removed outlier: 9.417A pdb=" N SER F 193 " --> pdb=" O HIS L 124 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N HIS L 124 " --> pdb=" O SER F 193 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N GLY F 195 " --> pdb=" O ARG L 122 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ILE L 112 " --> pdb=" O ILE L 123 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N GLN L 125 " --> pdb=" O CYS L 110 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N CYS L 110 " --> pdb=" O GLN L 125 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N ASN L 127 " --> pdb=" O TYR L 108 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N TYR L 108 " --> pdb=" O ASN L 127 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TRP L 57 " --> pdb=" O ASN L 66 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ASN L 66 " --> pdb=" O TRP L 57 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 57 through 63 Processing sheet with id=AC6, first strand: chain 'G' and resid 35 through 39 Processing sheet with id=AC7, first strand: chain 'H' and resid 35 through 39 Processing sheet with id=AC8, first strand: chain 'I' and resid 35 through 39 Processing sheet with id=AC9, first strand: chain 'J' and resid 35 through 39 Processing sheet with id=AD1, first strand: chain 'K' and resid 35 through 39 Processing sheet with id=AD2, first strand: chain 'L' and resid 35 through 39 527 hydrogen bonds defined for protein. 1365 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.44 Time building geometry restraints manager: 1.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4602 1.33 - 1.46: 3122 1.46 - 1.58: 7300 1.58 - 1.70: 6 1.70 - 1.82: 174 Bond restraints: 15204 Sorted by residual: bond pdb=" CA GLU I 52 " pdb=" CB GLU I 52 " ideal model delta sigma weight residual 1.539 1.665 -0.125 4.88e-02 4.20e+02 6.60e+00 bond pdb=" CA GLU H 52 " pdb=" CB GLU H 52 " ideal model delta sigma weight residual 1.539 1.665 -0.125 4.88e-02 4.20e+02 6.58e+00 bond pdb=" CA GLU K 52 " pdb=" CB GLU K 52 " ideal model delta sigma weight residual 1.539 1.665 -0.125 4.88e-02 4.20e+02 6.58e+00 bond pdb=" CA GLU G 52 " pdb=" CB GLU G 52 " ideal model delta sigma weight residual 1.539 1.664 -0.125 4.88e-02 4.20e+02 6.54e+00 bond pdb=" CA GLU L 52 " pdb=" CB GLU L 52 " ideal model delta sigma weight residual 1.539 1.664 -0.125 4.88e-02 4.20e+02 6.51e+00 ... (remaining 15199 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.01: 20027 3.01 - 6.03: 446 6.03 - 9.04: 71 9.04 - 12.05: 24 12.05 - 15.07: 12 Bond angle restraints: 20580 Sorted by residual: angle pdb=" CA LEU K 50 " pdb=" CB LEU K 50 " pdb=" CG LEU K 50 " ideal model delta sigma weight residual 116.30 131.37 -15.07 3.50e+00 8.16e-02 1.85e+01 angle pdb=" CA LEU H 50 " pdb=" CB LEU H 50 " pdb=" CG LEU H 50 " ideal model delta sigma weight residual 116.30 131.36 -15.06 3.50e+00 8.16e-02 1.85e+01 angle pdb=" CA LEU J 50 " pdb=" CB LEU J 50 " pdb=" CG LEU J 50 " ideal model delta sigma weight residual 116.30 131.36 -15.06 3.50e+00 8.16e-02 1.85e+01 angle pdb=" CA LEU G 50 " pdb=" CB LEU G 50 " pdb=" CG LEU G 50 " ideal model delta sigma weight residual 116.30 131.36 -15.06 3.50e+00 8.16e-02 1.85e+01 angle pdb=" CA LEU L 50 " pdb=" CB LEU L 50 " pdb=" CG LEU L 50 " ideal model delta sigma weight residual 116.30 131.35 -15.05 3.50e+00 8.16e-02 1.85e+01 ... (remaining 20575 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.42: 7423 13.42 - 26.84: 1205 26.84 - 40.26: 372 40.26 - 53.68: 134 53.68 - 67.10: 64 Dihedral angle restraints: 9198 sinusoidal: 3738 harmonic: 5460 Sorted by residual: dihedral pdb=" CA LEU F 40 " pdb=" C LEU F 40 " pdb=" N THR F 41 " pdb=" CA THR F 41 " ideal model delta harmonic sigma weight residual -180.00 -158.91 -21.09 0 5.00e+00 4.00e-02 1.78e+01 dihedral pdb=" CA LEU E 40 " pdb=" C LEU E 40 " pdb=" N THR E 41 " pdb=" CA THR E 41 " ideal model delta harmonic sigma weight residual -180.00 -158.93 -21.07 0 5.00e+00 4.00e-02 1.78e+01 dihedral pdb=" CA LEU D 40 " pdb=" C LEU D 40 " pdb=" N THR D 41 " pdb=" CA THR D 41 " ideal model delta harmonic sigma weight residual 180.00 -158.95 -21.05 0 5.00e+00 4.00e-02 1.77e+01 ... (remaining 9195 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 1651 0.073 - 0.146: 545 0.146 - 0.219: 66 0.219 - 0.292: 12 0.292 - 0.365: 12 Chirality restraints: 2286 Sorted by residual: chirality pdb=" CB ILE E 209 " pdb=" CA ILE E 209 " pdb=" CG1 ILE E 209 " pdb=" CG2 ILE E 209 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.36 2.00e-01 2.50e+01 3.33e+00 chirality pdb=" CB ILE F 209 " pdb=" CA ILE F 209 " pdb=" CG1 ILE F 209 " pdb=" CG2 ILE F 209 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.36 2.00e-01 2.50e+01 3.31e+00 chirality pdb=" CB ILE C 209 " pdb=" CA ILE C 209 " pdb=" CG1 ILE C 209 " pdb=" CG2 ILE C 209 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.36 2.00e-01 2.50e+01 3.31e+00 ... (remaining 2283 not shown) Planarity restraints: 2628 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE F 209 " 0.018 2.00e-02 2.50e+03 3.60e-02 1.29e+01 pdb=" C ILE F 209 " -0.062 2.00e-02 2.50e+03 pdb=" O ILE F 209 " 0.024 2.00e-02 2.50e+03 pdb=" N LYS F 210 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE C 209 " -0.018 2.00e-02 2.50e+03 3.59e-02 1.29e+01 pdb=" C ILE C 209 " 0.062 2.00e-02 2.50e+03 pdb=" O ILE C 209 " -0.024 2.00e-02 2.50e+03 pdb=" N LYS C 210 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE E 209 " -0.018 2.00e-02 2.50e+03 3.59e-02 1.29e+01 pdb=" C ILE E 209 " 0.062 2.00e-02 2.50e+03 pdb=" O ILE E 209 " -0.024 2.00e-02 2.50e+03 pdb=" N LYS E 210 " -0.021 2.00e-02 2.50e+03 ... (remaining 2625 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 119 2.61 - 3.18: 11407 3.18 - 3.75: 22478 3.75 - 4.33: 32184 4.33 - 4.90: 54721 Nonbonded interactions: 120909 Sorted by model distance: nonbonded pdb=" SG CYS I 40 " pdb=" SG CYS I 110 " model vdw 2.032 3.760 nonbonded pdb=" SG CYS H 40 " pdb=" SG CYS H 110 " model vdw 2.032 3.760 nonbonded pdb=" SG CYS J 40 " pdb=" SG CYS J 110 " model vdw 2.032 3.760 nonbonded pdb=" SG CYS K 40 " pdb=" SG CYS K 110 " model vdw 2.032 3.760 nonbonded pdb=" SG CYS G 40 " pdb=" SG CYS G 110 " model vdw 2.033 3.760 ... (remaining 120904 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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: 0.010 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.080 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: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.860 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6682 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 0.125 15228 Z= 0.297 Angle : 1.151 15.068 20628 Z= 0.581 Chirality : 0.072 0.365 2286 Planarity : 0.006 0.039 2628 Dihedral : 16.218 67.096 5610 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 1.64 % Allowed : 26.78 % Favored : 71.58 % Cbeta Deviations : 0.34 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.43 (0.18), residues: 1818 helix: None (None), residues: 0 sheet: -0.55 (0.17), residues: 834 loop : -1.29 (0.18), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG L 122 TYR 0.045 0.003 TYR G 82 PHE 0.023 0.003 PHE G 88 TRP 0.015 0.002 TRP G 57 HIS 0.023 0.002 HIS G 124 Details of bonding type rmsd covalent geometry : bond 0.00712 (15204) covalent geometry : angle 1.15047 (20580) SS BOND : bond 0.02690 ( 24) SS BOND : angle 1.52119 ( 48) hydrogen bonds : bond 0.17704 ( 509) hydrogen bonds : angle 8.40269 ( 1365) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 333 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 THR cc_start: 0.7854 (m) cc_final: 0.7559 (m) REVERT: A 187 GLU cc_start: 0.7754 (mt-10) cc_final: 0.7443 (mt-10) REVERT: B 47 ASP cc_start: 0.8224 (m-30) cc_final: 0.7898 (m-30) REVERT: B 58 MET cc_start: 0.8593 (ptm) cc_final: 0.8392 (ptm) REVERT: B 101 LYS cc_start: 0.8649 (tppt) cc_final: 0.8444 (tppt) REVERT: C 39 GLU cc_start: 0.7429 (tm-30) cc_final: 0.7133 (tt0) REVERT: C 47 ASP cc_start: 0.8380 (m-30) cc_final: 0.8054 (m-30) REVERT: C 85 THR cc_start: 0.8157 (p) cc_final: 0.7123 (t) REVERT: C 101 LYS cc_start: 0.8660 (tppt) cc_final: 0.8331 (mmtp) REVERT: C 187 GLU cc_start: 0.7776 (mt-10) cc_final: 0.7416 (mt-10) REVERT: D 47 ASP cc_start: 0.8202 (m-30) cc_final: 0.7886 (m-30) REVERT: D 85 THR cc_start: 0.8493 (p) cc_final: 0.7355 (t) REVERT: D 86 ASP cc_start: 0.8021 (m-30) cc_final: 0.7419 (m-30) REVERT: D 136 ASN cc_start: 0.8478 (t0) cc_final: 0.8100 (t0) REVERT: D 164 GLU cc_start: 0.7314 (mm-30) cc_final: 0.7087 (mm-30) REVERT: D 165 THR cc_start: 0.7772 (m) cc_final: 0.7447 (m) REVERT: D 173 HIS cc_start: 0.8216 (m-70) cc_final: 0.7929 (m-70) REVERT: D 184 HIS cc_start: 0.8313 (p90) cc_final: 0.7971 (p-80) REVERT: E 47 ASP cc_start: 0.7697 (m-30) cc_final: 0.7407 (m-30) REVERT: E 85 THR cc_start: 0.8464 (p) cc_final: 0.7137 (t) REVERT: E 101 LYS cc_start: 0.8637 (tppt) cc_final: 0.8284 (tppp) REVERT: E 126 MET cc_start: 0.8460 (mmp) cc_final: 0.8177 (mmm) REVERT: E 143 ILE cc_start: 0.6706 (OUTLIER) cc_final: 0.6402 (pt) REVERT: E 175 LEU cc_start: 0.7542 (pp) cc_final: 0.7327 (mm) REVERT: F 39 GLU cc_start: 0.7153 (tm-30) cc_final: 0.6815 (tm-30) REVERT: F 47 ASP cc_start: 0.8388 (m-30) cc_final: 0.8097 (m-30) REVERT: F 55 GLU cc_start: 0.7930 (tp30) cc_final: 0.7728 (tp30) REVERT: F 101 LYS cc_start: 0.8634 (tppt) cc_final: 0.8405 (tppt) REVERT: F 187 GLU cc_start: 0.7965 (mt-10) cc_final: 0.7605 (mt-10) REVERT: G 120 MET cc_start: 0.8069 (ttp) cc_final: 0.7806 (ttt) outliers start: 28 outliers final: 8 residues processed: 351 average time/residue: 0.4772 time to fit residues: 186.3022 Evaluate side-chains 234 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 225 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain D residue 209 ILE Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 209 ILE Chi-restraints excluded: chain F residue 143 ILE Chi-restraints excluded: chain F residue 209 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 ASN A 129 ASN A 162 ASN ** A 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 68 ASN ** B 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 162 ASN ** B 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 68 ASN ** C 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 162 ASN C 173 HIS ** C 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 68 ASN ** D 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 162 ASN ** D 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 162 ASN ** E 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 68 ASN F 129 ASN F 162 ASN ** F 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.206087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.173306 restraints weight = 12798.064| |-----------------------------------------------------------------------------| r_work (start): 0.3869 rms_B_bonded: 0.95 r_work: 0.3452 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.3236 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3184 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3184 r_free = 0.3184 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 786 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3147 r_free = 0.3147 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 787 | |-----------------------------------------------------------------------------| r_final: 0.3147 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 15228 Z= 0.169 Angle : 0.640 9.750 20628 Z= 0.331 Chirality : 0.048 0.171 2286 Planarity : 0.004 0.039 2628 Dihedral : 5.254 30.706 2022 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 5.20 % Allowed : 20.47 % Favored : 74.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.19), residues: 1818 helix: None (None), residues: 0 sheet: -0.49 (0.17), residues: 852 loop : -0.73 (0.20), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 219 TYR 0.009 0.001 TYR D 74 PHE 0.020 0.002 PHE H 56 TRP 0.008 0.002 TRP H 57 HIS 0.011 0.001 HIS I 124 Details of bonding type rmsd covalent geometry : bond 0.00408 (15204) covalent geometry : angle 0.64014 (20580) SS BOND : bond 0.00304 ( 24) SS BOND : angle 0.67517 ( 48) hydrogen bonds : bond 0.04398 ( 509) hydrogen bonds : angle 6.45453 ( 1365) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 230 time to evaluate : 0.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 THR cc_start: 0.8364 (m) cc_final: 0.8050 (m) REVERT: B 47 ASP cc_start: 0.8608 (m-30) cc_final: 0.8315 (m-30) REVERT: B 84 ASP cc_start: 0.8312 (OUTLIER) cc_final: 0.8047 (t70) REVERT: B 101 LYS cc_start: 0.8593 (tppt) cc_final: 0.8377 (mmtp) REVERT: C 85 THR cc_start: 0.8628 (p) cc_final: 0.7192 (t) REVERT: C 119 ILE cc_start: 0.8800 (OUTLIER) cc_final: 0.8257 (mm) REVERT: C 186 SER cc_start: 0.8183 (m) cc_final: 0.7980 (p) REVERT: C 187 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.8178 (mt-10) REVERT: D 47 ASP cc_start: 0.8713 (m-30) cc_final: 0.8496 (m-30) REVERT: D 85 THR cc_start: 0.8657 (p) cc_final: 0.7378 (t) REVERT: E 65 ARG cc_start: 0.8666 (mtp180) cc_final: 0.8422 (mtp180) REVERT: E 85 THR cc_start: 0.8750 (p) cc_final: 0.7266 (t) REVERT: E 101 LYS cc_start: 0.8543 (tppt) cc_final: 0.8292 (mmtp) REVERT: F 47 ASP cc_start: 0.8743 (m-30) cc_final: 0.8447 (m-30) REVERT: F 119 ILE cc_start: 0.8832 (OUTLIER) cc_final: 0.8096 (mm) REVERT: F 141 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.8064 (tm-30) REVERT: G 100 LEU cc_start: 0.7192 (OUTLIER) cc_final: 0.6953 (mt) REVERT: H 100 LEU cc_start: 0.7280 (OUTLIER) cc_final: 0.6977 (mt) REVERT: I 100 LEU cc_start: 0.7109 (OUTLIER) cc_final: 0.6855 (mt) REVERT: J 100 LEU cc_start: 0.6877 (OUTLIER) cc_final: 0.6624 (mt) REVERT: L 100 LEU cc_start: 0.7168 (OUTLIER) cc_final: 0.6927 (mt) outliers start: 89 outliers final: 49 residues processed: 293 average time/residue: 0.4548 time to fit residues: 149.1344 Evaluate side-chains 273 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 214 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 85 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 A residue 193 SER Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 60 GLU Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 193 SER Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 59 SER Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 193 SER Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain D residue 101 LYS 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 165 THR Chi-restraints excluded: chain E residue 59 SER Chi-restraints excluded: chain E residue 60 GLU Chi-restraints excluded: chain E residue 64 ASP Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain E residue 138 ASP Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 165 THR Chi-restraints excluded: chain E residue 193 SER Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 59 SER Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 84 ASP Chi-restraints excluded: chain F residue 85 THR Chi-restraints excluded: chain F residue 119 ILE Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain F residue 141 GLU Chi-restraints excluded: chain F residue 143 ILE Chi-restraints excluded: chain F residue 152 THR Chi-restraints excluded: chain F residue 193 SER Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain J residue 100 LEU Chi-restraints excluded: chain L residue 100 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 151 optimal weight: 6.9990 chunk 38 optimal weight: 4.9990 chunk 156 optimal weight: 6.9990 chunk 85 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 109 optimal weight: 0.8980 chunk 93 optimal weight: 0.9980 chunk 162 optimal weight: 2.9990 chunk 179 optimal weight: 3.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 184 HIS ** B 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 116 HIS ** C 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 184 HIS ** E 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 116 HIS ** E 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 116 HIS ** F 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.196793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.129031 restraints weight = 13093.821| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 2.51 r_work: 0.3043 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2910 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2914 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2914 r_free = 0.2914 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 787 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2911 r_free = 0.2911 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 789 | |-----------------------------------------------------------------------------| r_final: 0.2911 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.2830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 15228 Z= 0.269 Angle : 0.681 8.742 20628 Z= 0.358 Chirality : 0.052 0.173 2286 Planarity : 0.004 0.039 2628 Dihedral : 5.521 39.455 2012 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 6.14 % Allowed : 20.41 % Favored : 73.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.20), residues: 1818 helix: None (None), residues: 0 sheet: -0.47 (0.17), residues: 852 loop : -0.62 (0.21), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 88 TYR 0.014 0.002 TYR B 183 PHE 0.021 0.002 PHE H 56 TRP 0.011 0.002 TRP D 34 HIS 0.008 0.001 HIS I 124 Details of bonding type rmsd covalent geometry : bond 0.00634 (15204) covalent geometry : angle 0.68011 (20580) SS BOND : bond 0.00440 ( 24) SS BOND : angle 0.85570 ( 48) hydrogen bonds : bond 0.04495 ( 509) hydrogen bonds : angle 6.41097 ( 1365) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 210 time to evaluate : 0.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 GLU cc_start: 0.8216 (tm-30) cc_final: 0.7951 (tp30) REVERT: A 83 MET cc_start: 0.8647 (mmt) cc_final: 0.8325 (mmt) REVERT: A 165 THR cc_start: 0.8540 (OUTLIER) cc_final: 0.8193 (m) REVERT: B 119 ILE cc_start: 0.8796 (OUTLIER) cc_final: 0.8194 (mm) REVERT: B 138 ASP cc_start: 0.8259 (OUTLIER) cc_final: 0.7941 (m-30) REVERT: B 187 GLU cc_start: 0.8286 (mt-10) cc_final: 0.8082 (mt-10) REVERT: C 39 GLU cc_start: 0.8070 (tm-30) cc_final: 0.7652 (tp30) REVERT: C 72 THR cc_start: 0.8809 (p) cc_final: 0.8177 (m) REVERT: C 80 MET cc_start: 0.9225 (OUTLIER) cc_final: 0.8942 (ttt) REVERT: C 141 GLU cc_start: 0.8883 (OUTLIER) cc_final: 0.8436 (tm-30) REVERT: C 186 SER cc_start: 0.8619 (m) cc_final: 0.8292 (p) REVERT: C 187 GLU cc_start: 0.8565 (OUTLIER) cc_final: 0.8278 (mt-10) REVERT: C 220 GLU cc_start: 0.6894 (OUTLIER) cc_final: 0.5724 (mp0) REVERT: D 39 GLU cc_start: 0.8228 (tm-30) cc_final: 0.7952 (tp30) REVERT: E 39 GLU cc_start: 0.8046 (tm-30) cc_final: 0.7759 (tp30) REVERT: E 58 MET cc_start: 0.8960 (ptm) cc_final: 0.8749 (ptm) REVERT: E 138 ASP cc_start: 0.8237 (OUTLIER) cc_final: 0.7902 (m-30) REVERT: E 187 GLU cc_start: 0.8329 (mt-10) cc_final: 0.8119 (mt-10) REVERT: F 39 GLU cc_start: 0.8062 (tm-30) cc_final: 0.7782 (tp30) REVERT: F 72 THR cc_start: 0.8781 (p) cc_final: 0.8161 (m) REVERT: F 141 GLU cc_start: 0.8938 (OUTLIER) cc_final: 0.8466 (tm-30) REVERT: F 190 MET cc_start: 0.8418 (mmp) cc_final: 0.8183 (mmm) REVERT: F 220 GLU cc_start: 0.7096 (OUTLIER) cc_final: 0.6648 (mm-30) REVERT: G 100 LEU cc_start: 0.7237 (OUTLIER) cc_final: 0.7037 (mt) REVERT: I 100 LEU cc_start: 0.7259 (OUTLIER) cc_final: 0.7031 (mt) REVERT: L 100 LEU cc_start: 0.7283 (OUTLIER) cc_final: 0.7066 (mt) outliers start: 105 outliers final: 52 residues processed: 286 average time/residue: 0.5025 time to fit residues: 159.3427 Evaluate side-chains 262 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 197 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 85 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 A residue 165 THR Chi-restraints excluded: chain A residue 193 SER Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 60 GLU Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 193 SER Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 59 SER Chi-restraints excluded: chain C residue 60 GLU Chi-restraints excluded: chain C residue 80 MET Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 141 GLU 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 187 GLU Chi-restraints excluded: chain C residue 193 SER Chi-restraints excluded: chain C residue 220 GLU Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain D residue 101 LYS 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 165 THR Chi-restraints excluded: chain D residue 193 SER Chi-restraints excluded: chain E residue 59 SER Chi-restraints excluded: chain E residue 60 GLU Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 138 ASP Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 165 THR Chi-restraints excluded: chain E residue 193 SER Chi-restraints excluded: chain E residue 197 THR Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 59 SER Chi-restraints excluded: chain F residue 60 GLU Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 84 ASP Chi-restraints excluded: chain F residue 85 THR Chi-restraints excluded: chain F residue 141 GLU Chi-restraints excluded: chain F residue 143 ILE Chi-restraints excluded: chain F residue 152 THR Chi-restraints excluded: chain F residue 193 SER Chi-restraints excluded: chain F residue 220 GLU Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain G residue 120 MET Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain L residue 100 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 164 optimal weight: 9.9990 chunk 48 optimal weight: 0.9980 chunk 102 optimal weight: 0.6980 chunk 106 optimal weight: 1.9990 chunk 158 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 47 optimal weight: 0.7980 chunk 33 optimal weight: 0.1980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 HIS ** A 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 184 HIS ** B 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 184 HIS E 68 ASN ** E 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 176 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 = 0.4150 r_free = 0.4150 target = 0.198527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.133017 restraints weight = 13192.494| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 3.02 r_work: 0.3142 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3007 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3007 r_free = 0.3007 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 789 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3006 r_free = 0.3006 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 789 | |-----------------------------------------------------------------------------| r_final: 0.3006 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.2878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15228 Z= 0.133 Angle : 0.558 7.491 20628 Z= 0.294 Chirality : 0.046 0.155 2286 Planarity : 0.003 0.021 2628 Dihedral : 4.986 33.528 2010 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 5.79 % Allowed : 22.87 % Favored : 71.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.20), residues: 1818 helix: None (None), residues: 0 sheet: -0.48 (0.17), residues: 846 loop : -0.47 (0.21), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 191 TYR 0.007 0.001 TYR F 74 PHE 0.020 0.001 PHE H 56 TRP 0.006 0.001 TRP H 57 HIS 0.006 0.001 HIS I 124 Details of bonding type rmsd covalent geometry : bond 0.00310 (15204) covalent geometry : angle 0.55806 (20580) SS BOND : bond 0.00209 ( 24) SS BOND : angle 0.45980 ( 48) hydrogen bonds : bond 0.03378 ( 509) hydrogen bonds : angle 5.95706 ( 1365) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 191 time to evaluate : 0.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 ASN cc_start: 0.8008 (p0) cc_final: 0.7697 (m110) REVERT: A 141 GLU cc_start: 0.8792 (OUTLIER) cc_final: 0.8521 (tm-30) REVERT: A 165 THR cc_start: 0.8340 (m) cc_final: 0.8053 (m) REVERT: B 47 ASP cc_start: 0.8738 (m-30) cc_final: 0.8388 (m-30) REVERT: B 49 ASN cc_start: 0.8111 (p0) cc_final: 0.7745 (m-40) REVERT: B 55 GLU cc_start: 0.8727 (tp30) cc_final: 0.8318 (tp30) REVERT: B 60 GLU cc_start: 0.7391 (OUTLIER) cc_final: 0.7090 (tm-30) REVERT: B 119 ILE cc_start: 0.8779 (OUTLIER) cc_final: 0.8203 (mm) REVERT: B 138 ASP cc_start: 0.8101 (OUTLIER) cc_final: 0.7822 (m-30) REVERT: C 101 LYS cc_start: 0.8742 (OUTLIER) cc_final: 0.7928 (mppt) REVERT: C 141 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.8073 (tm-30) REVERT: C 186 SER cc_start: 0.8475 (m) cc_final: 0.8171 (p) REVERT: C 187 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.8134 (mt-10) REVERT: D 39 GLU cc_start: 0.8177 (tm-30) cc_final: 0.7962 (tp30) REVERT: D 165 THR cc_start: 0.8416 (m) cc_final: 0.8079 (m) REVERT: D 169 LYS cc_start: 0.8726 (OUTLIER) cc_final: 0.8147 (pmtt) REVERT: E 39 GLU cc_start: 0.7993 (tm-30) cc_final: 0.7754 (tp30) REVERT: E 49 ASN cc_start: 0.8067 (p0) cc_final: 0.7710 (m-40) REVERT: E 58 MET cc_start: 0.8927 (ptm) cc_final: 0.8649 (ptm) REVERT: E 60 GLU cc_start: 0.7258 (OUTLIER) cc_final: 0.6953 (tm-30) REVERT: E 80 MET cc_start: 0.8999 (ttm) cc_final: 0.8791 (ttt) REVERT: E 138 ASP cc_start: 0.8089 (OUTLIER) cc_final: 0.7805 (m-30) REVERT: E 187 GLU cc_start: 0.8251 (mt-10) cc_final: 0.8031 (mt-10) REVERT: F 47 ASP cc_start: 0.8829 (m-30) cc_final: 0.8551 (m-30) REVERT: F 60 GLU cc_start: 0.7429 (OUTLIER) cc_final: 0.6993 (tm-30) REVERT: F 110 GLN cc_start: 0.8393 (tt0) cc_final: 0.8139 (tt0) REVERT: F 141 GLU cc_start: 0.8618 (OUTLIER) cc_final: 0.8081 (tm-30) REVERT: F 220 GLU cc_start: 0.6833 (OUTLIER) cc_final: 0.6389 (mm-30) REVERT: I 100 LEU cc_start: 0.7119 (OUTLIER) cc_final: 0.6888 (mt) REVERT: J 63 LEU cc_start: 0.7217 (OUTLIER) cc_final: 0.6991 (mt) REVERT: L 100 LEU cc_start: 0.7160 (OUTLIER) cc_final: 0.6930 (mt) outliers start: 99 outliers final: 39 residues processed: 264 average time/residue: 0.5132 time to fit residues: 149.8019 Evaluate side-chains 237 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 182 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 193 SER Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 60 GLU Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 127 GLU 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 193 SER Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 101 LYS Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 141 GLU Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 193 SER Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 159 THR Chi-restraints excluded: chain D residue 169 LYS Chi-restraints excluded: chain D residue 193 SER Chi-restraints excluded: chain E residue 59 SER Chi-restraints excluded: chain E residue 60 GLU Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 138 ASP Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 193 SER Chi-restraints excluded: chain F residue 60 GLU Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 85 THR Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain F residue 141 GLU Chi-restraints excluded: chain F residue 143 ILE Chi-restraints excluded: chain F residue 152 THR Chi-restraints excluded: chain F residue 220 GLU Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain J residue 63 LEU Chi-restraints excluded: chain L residue 100 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 62 optimal weight: 2.9990 chunk 152 optimal weight: 0.3980 chunk 143 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 12 optimal weight: 0.0980 chunk 110 optimal weight: 1.9990 chunk 122 optimal weight: 6.9990 chunk 164 optimal weight: 10.0000 chunk 84 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 153 optimal weight: 4.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 184 HIS B 116 HIS ** B 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 116 HIS ** D 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 184 HIS ** E 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 176 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 = 0.4103 r_free = 0.4103 target = 0.193411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.129669 restraints weight = 13262.966| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 2.84 r_work: 0.3059 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2933 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2902 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2902 r_free = 0.2902 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 789 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2901 r_free = 0.2901 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 788 | |-----------------------------------------------------------------------------| r_final: 0.2901 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.3261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 15228 Z= 0.256 Angle : 0.647 7.529 20628 Z= 0.342 Chirality : 0.051 0.165 2286 Planarity : 0.003 0.022 2628 Dihedral : 5.348 37.882 2010 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 7.43 % Allowed : 20.94 % Favored : 71.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.20), residues: 1818 helix: None (None), residues: 0 sheet: -0.40 (0.18), residues: 834 loop : -0.55 (0.21), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 65 TYR 0.013 0.002 TYR B 183 PHE 0.020 0.002 PHE G 56 TRP 0.008 0.001 TRP D 34 HIS 0.007 0.001 HIS I 124 Details of bonding type rmsd covalent geometry : bond 0.00603 (15204) covalent geometry : angle 0.64634 (20580) SS BOND : bond 0.00447 ( 24) SS BOND : angle 0.76193 ( 48) hydrogen bonds : bond 0.03886 ( 509) hydrogen bonds : angle 5.99774 ( 1365) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 177 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 GLU cc_start: 0.8251 (tm-30) cc_final: 0.8043 (tp30) REVERT: A 49 ASN cc_start: 0.8163 (OUTLIER) cc_final: 0.7802 (m110) REVERT: A 141 GLU cc_start: 0.8910 (OUTLIER) cc_final: 0.8435 (tm-30) REVERT: A 165 THR cc_start: 0.8514 (m) cc_final: 0.8192 (m) REVERT: B 49 ASN cc_start: 0.8256 (p0) cc_final: 0.7844 (m-40) REVERT: B 119 ILE cc_start: 0.8877 (OUTLIER) cc_final: 0.8293 (mm) REVERT: B 138 ASP cc_start: 0.8258 (OUTLIER) cc_final: 0.7950 (m-30) REVERT: B 187 GLU cc_start: 0.8378 (mt-10) cc_final: 0.8175 (mt-10) REVERT: C 72 THR cc_start: 0.8876 (p) cc_final: 0.8311 (m) REVERT: C 101 LYS cc_start: 0.8799 (OUTLIER) cc_final: 0.8002 (mppt) REVERT: C 141 GLU cc_start: 0.8758 (OUTLIER) cc_final: 0.8292 (tm-30) REVERT: C 165 THR cc_start: 0.8557 (m) cc_final: 0.8353 (m) REVERT: C 186 SER cc_start: 0.8642 (m) cc_final: 0.8396 (p) REVERT: C 220 GLU cc_start: 0.7101 (OUTLIER) cc_final: 0.5999 (mp0) REVERT: D 49 ASN cc_start: 0.8240 (OUTLIER) cc_final: 0.7848 (m110) REVERT: D 141 GLU cc_start: 0.8948 (OUTLIER) cc_final: 0.8544 (tm-30) REVERT: D 165 THR cc_start: 0.8496 (m) cc_final: 0.8141 (m) REVERT: D 169 LYS cc_start: 0.8602 (OUTLIER) cc_final: 0.8013 (pmtt) REVERT: E 49 ASN cc_start: 0.8231 (p0) cc_final: 0.7853 (m-40) REVERT: E 55 GLU cc_start: 0.8793 (tp30) cc_final: 0.8401 (tp30) REVERT: E 58 MET cc_start: 0.9055 (ptm) cc_final: 0.8821 (ptm) REVERT: E 119 ILE cc_start: 0.8803 (OUTLIER) cc_final: 0.8154 (mm) REVERT: E 138 ASP cc_start: 0.8249 (OUTLIER) cc_final: 0.7937 (m-30) REVERT: F 72 THR cc_start: 0.8884 (p) cc_final: 0.8301 (m) REVERT: F 141 GLU cc_start: 0.8835 (OUTLIER) cc_final: 0.8347 (tm-30) REVERT: F 220 GLU cc_start: 0.7086 (OUTLIER) cc_final: 0.6586 (mm-30) REVERT: G 63 LEU cc_start: 0.7266 (OUTLIER) cc_final: 0.7064 (mt) REVERT: I 100 LEU cc_start: 0.7295 (OUTLIER) cc_final: 0.7007 (mt) REVERT: J 63 LEU cc_start: 0.7371 (OUTLIER) cc_final: 0.7155 (mt) REVERT: L 100 LEU cc_start: 0.7276 (OUTLIER) cc_final: 0.7007 (mt) outliers start: 127 outliers final: 62 residues processed: 278 average time/residue: 0.4779 time to fit residues: 148.2349 Evaluate side-chains 254 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 174 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 49 ASN Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 101 LYS Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 193 SER Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 127 GLU 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 193 SER Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 59 SER Chi-restraints excluded: chain C residue 60 GLU Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 101 LYS Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 141 GLU Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 193 SER Chi-restraints excluded: chain C residue 220 GLU Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 49 ASN Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 141 GLU 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 169 LYS Chi-restraints excluded: chain D residue 193 SER Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 59 SER Chi-restraints excluded: chain E residue 60 GLU Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 138 ASP Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 193 SER Chi-restraints excluded: chain E residue 197 THR Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 59 SER Chi-restraints excluded: chain F residue 60 GLU Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 85 THR Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain F residue 141 GLU Chi-restraints excluded: chain F residue 143 ILE Chi-restraints excluded: chain F residue 152 THR Chi-restraints excluded: chain F residue 193 SER Chi-restraints excluded: chain F residue 220 GLU Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain J residue 63 LEU Chi-restraints excluded: chain J residue 118 THR Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain L residue 100 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 133 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 chunk 47 optimal weight: 0.9990 chunk 172 optimal weight: 0.0770 chunk 146 optimal weight: 9.9990 chunk 160 optimal weight: 0.6980 chunk 95 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 overall best weight: 0.6740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 184 HIS ** B 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 184 HIS ** E 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.196319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.152436 restraints weight = 13162.906| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 1.14 r_work: 0.3277 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3062 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3062 r_free = 0.3062 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 788 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3061 r_free = 0.3061 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 788 | |-----------------------------------------------------------------------------| r_final: 0.3061 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.3268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15228 Z= 0.141 Angle : 0.553 7.344 20628 Z= 0.296 Chirality : 0.046 0.153 2286 Planarity : 0.003 0.028 2628 Dihedral : 4.993 34.139 2010 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 6.43 % Allowed : 22.57 % Favored : 70.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.20), residues: 1818 helix: None (None), residues: 0 sheet: -0.52 (0.18), residues: 846 loop : -0.43 (0.21), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 111 TYR 0.007 0.001 TYR A 74 PHE 0.020 0.001 PHE G 56 TRP 0.005 0.001 TRP K 57 HIS 0.005 0.001 HIS I 124 Details of bonding type rmsd covalent geometry : bond 0.00324 (15204) covalent geometry : angle 0.55325 (20580) SS BOND : bond 0.00246 ( 24) SS BOND : angle 0.49988 ( 48) hydrogen bonds : bond 0.03254 ( 509) hydrogen bonds : angle 5.88867 ( 1365) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 187 time to evaluate : 0.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 GLU cc_start: 0.8630 (OUTLIER) cc_final: 0.8272 (tm-30) REVERT: A 165 THR cc_start: 0.8333 (m) cc_final: 0.7984 (m) REVERT: B 60 GLU cc_start: 0.7852 (tm-30) cc_final: 0.7558 (tm-30) REVERT: B 119 ILE cc_start: 0.8816 (OUTLIER) cc_final: 0.8220 (mm) REVERT: B 138 ASP cc_start: 0.7960 (OUTLIER) cc_final: 0.7697 (m-30) REVERT: C 101 LYS cc_start: 0.8708 (OUTLIER) cc_final: 0.7888 (mppt) REVERT: C 110 GLN cc_start: 0.8400 (tt0) cc_final: 0.8192 (tt0) REVERT: C 141 GLU cc_start: 0.8469 (OUTLIER) cc_final: 0.8077 (tm-30) REVERT: D 47 ASP cc_start: 0.8747 (m-30) cc_final: 0.8520 (m-30) REVERT: D 55 GLU cc_start: 0.8696 (tp30) cc_final: 0.8158 (tp30) REVERT: D 141 GLU cc_start: 0.8756 (OUTLIER) cc_final: 0.8554 (tm-30) REVERT: D 165 THR cc_start: 0.8283 (m) cc_final: 0.7910 (m) REVERT: D 169 LYS cc_start: 0.8590 (OUTLIER) cc_final: 0.8055 (pmtt) REVERT: D 170 ILE cc_start: 0.8901 (OUTLIER) cc_final: 0.7852 (tp) REVERT: D 220 GLU cc_start: 0.7014 (OUTLIER) cc_final: 0.5569 (mp0) REVERT: E 128 MET cc_start: 0.7314 (mmm) cc_final: 0.7049 (mmm) REVERT: E 138 ASP cc_start: 0.7978 (OUTLIER) cc_final: 0.7722 (m-30) REVERT: F 55 GLU cc_start: 0.8634 (tp30) cc_final: 0.8282 (tp30) REVERT: F 141 GLU cc_start: 0.8524 (OUTLIER) cc_final: 0.8075 (tm-30) REVERT: F 220 GLU cc_start: 0.6991 (OUTLIER) cc_final: 0.6371 (mm-30) REVERT: G 63 LEU cc_start: 0.7294 (OUTLIER) cc_final: 0.7089 (mt) REVERT: I 63 LEU cc_start: 0.7306 (OUTLIER) cc_final: 0.6977 (mt) REVERT: I 100 LEU cc_start: 0.7319 (OUTLIER) cc_final: 0.7029 (mt) REVERT: J 63 LEU cc_start: 0.7412 (OUTLIER) cc_final: 0.7181 (mt) REVERT: L 100 LEU cc_start: 0.7223 (OUTLIER) cc_final: 0.6939 (mt) outliers start: 110 outliers final: 52 residues processed: 279 average time/residue: 0.4943 time to fit residues: 153.1752 Evaluate side-chains 263 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 194 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 127 GLU 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 193 SER Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 59 SER Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 101 LYS Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 141 GLU Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 169 LYS Chi-restraints excluded: chain C residue 193 SER Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 101 LYS Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 141 GLU 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 169 LYS Chi-restraints excluded: chain D residue 170 ILE Chi-restraints excluded: chain D residue 193 SER Chi-restraints excluded: chain D residue 220 GLU Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 59 SER Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 138 ASP Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 197 THR Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 59 SER Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 85 THR Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain F residue 141 GLU Chi-restraints excluded: chain F residue 143 ILE Chi-restraints excluded: chain F residue 152 THR Chi-restraints excluded: chain F residue 193 SER Chi-restraints excluded: chain F residue 220 GLU Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain I residue 63 LEU Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain J residue 63 LEU Chi-restraints excluded: chain L residue 100 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 144 optimal weight: 7.9990 chunk 140 optimal weight: 10.0000 chunk 68 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 117 optimal weight: 0.8980 chunk 50 optimal weight: 3.9990 chunk 178 optimal weight: 5.9990 chunk 164 optimal weight: 10.0000 chunk 139 optimal weight: 4.9990 chunk 153 optimal weight: 0.7980 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 129 ASN ** A 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 184 HIS ** B 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 184 HIS E 68 ASN ** E 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 110 GLN ** F 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.191065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.124840 restraints weight = 13188.863| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 2.77 r_work: 0.2983 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2961 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2961 r_free = 0.2961 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 788 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2961 r_free = 0.2961 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 788 | |-----------------------------------------------------------------------------| r_final: 0.2961 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.3723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.078 15228 Z= 0.352 Angle : 0.722 7.694 20628 Z= 0.384 Chirality : 0.055 0.189 2286 Planarity : 0.004 0.043 2628 Dihedral : 5.651 40.188 2010 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 6.55 % Allowed : 22.46 % Favored : 70.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.20), residues: 1818 helix: None (None), residues: 0 sheet: -0.43 (0.18), residues: 834 loop : -0.68 (0.20), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 65 TYR 0.014 0.002 TYR A 20 PHE 0.026 0.002 PHE G 56 TRP 0.013 0.002 TRP D 34 HIS 0.007 0.001 HIS I 124 Details of bonding type rmsd covalent geometry : bond 0.00840 (15204) covalent geometry : angle 0.72135 (20580) SS BOND : bond 0.00600 ( 24) SS BOND : angle 0.97709 ( 48) hydrogen bonds : bond 0.04164 ( 509) hydrogen bonds : angle 6.11332 ( 1365) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 193 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 GLU cc_start: 0.8911 (OUTLIER) cc_final: 0.8594 (tm-30) REVERT: A 165 THR cc_start: 0.8468 (m) cc_final: 0.8119 (m) REVERT: A 220 GLU cc_start: 0.7022 (OUTLIER) cc_final: 0.5562 (mp0) REVERT: B 47 ASP cc_start: 0.8762 (m-30) cc_final: 0.8402 (m-30) REVERT: B 55 GLU cc_start: 0.8772 (tp30) cc_final: 0.8420 (tp30) REVERT: B 119 ILE cc_start: 0.8901 (OUTLIER) cc_final: 0.8320 (mm) REVERT: B 138 ASP cc_start: 0.8085 (OUTLIER) cc_final: 0.7824 (m-30) REVERT: B 187 GLU cc_start: 0.8400 (mt-10) cc_final: 0.8189 (mt-10) REVERT: C 72 THR cc_start: 0.8931 (p) cc_final: 0.8338 (m) REVERT: C 141 GLU cc_start: 0.8816 (OUTLIER) cc_final: 0.8454 (tm-30) REVERT: C 220 GLU cc_start: 0.7152 (OUTLIER) cc_final: 0.6120 (mp0) REVERT: D 141 GLU cc_start: 0.8902 (OUTLIER) cc_final: 0.8596 (tm-30) REVERT: D 169 LYS cc_start: 0.8538 (OUTLIER) cc_final: 0.8284 (pttt) REVERT: D 170 ILE cc_start: 0.8966 (OUTLIER) cc_final: 0.7972 (tp) REVERT: D 220 GLU cc_start: 0.7105 (OUTLIER) cc_final: 0.5635 (mp0) REVERT: E 60 GLU cc_start: 0.8038 (tm-30) cc_final: 0.7797 (tm-30) REVERT: E 119 ILE cc_start: 0.8838 (OUTLIER) cc_final: 0.8243 (mm) REVERT: E 138 ASP cc_start: 0.8083 (OUTLIER) cc_final: 0.7843 (m-30) REVERT: F 47 ASP cc_start: 0.8867 (m-30) cc_final: 0.8652 (m-30) REVERT: F 55 GLU cc_start: 0.8768 (tp30) cc_final: 0.8508 (tp30) REVERT: F 72 THR cc_start: 0.8927 (p) cc_final: 0.8321 (m) REVERT: F 141 GLU cc_start: 0.8841 (OUTLIER) cc_final: 0.8452 (tm-30) REVERT: F 220 GLU cc_start: 0.7158 (OUTLIER) cc_final: 0.6532 (mm-30) REVERT: I 63 LEU cc_start: 0.7251 (OUTLIER) cc_final: 0.6982 (mt) outliers start: 112 outliers final: 61 residues processed: 279 average time/residue: 0.4912 time to fit residues: 152.1507 Evaluate side-chains 248 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 172 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 193 SER Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 193 SER Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 49 ASN Chi-restraints excluded: chain C residue 59 SER Chi-restraints excluded: chain C residue 60 GLU Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 141 GLU Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 169 LYS Chi-restraints excluded: chain C residue 193 SER Chi-restraints excluded: chain C residue 220 GLU Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 101 LYS Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 141 GLU 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 D residue 169 LYS Chi-restraints excluded: chain D residue 170 ILE Chi-restraints excluded: chain D residue 193 SER Chi-restraints excluded: chain D residue 220 GLU Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 59 SER Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 138 ASP Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 193 SER Chi-restraints excluded: chain E residue 197 THR Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 49 ASN Chi-restraints excluded: chain F residue 59 SER Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 85 THR Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain F residue 141 GLU Chi-restraints excluded: chain F residue 143 ILE Chi-restraints excluded: chain F residue 152 THR Chi-restraints excluded: chain F residue 193 SER Chi-restraints excluded: chain F residue 220 GLU Chi-restraints excluded: chain I residue 63 LEU Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain L residue 100 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 100 optimal weight: 0.0770 chunk 150 optimal weight: 8.9990 chunk 2 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 54 optimal weight: 0.7980 chunk 72 optimal weight: 3.9990 chunk 98 optimal weight: 0.7980 chunk 105 optimal weight: 0.5980 chunk 66 optimal weight: 0.8980 chunk 101 optimal weight: 0.6980 chunk 123 optimal weight: 7.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 ASN ** E 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.197090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.134527 restraints weight = 13248.830| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 2.50 r_work: 0.3096 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2969 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2969 r_free = 0.2969 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 788 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2968 r_free = 0.2968 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 789 | |-----------------------------------------------------------------------------| r_final: 0.2968 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.3575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15228 Z= 0.137 Angle : 0.562 7.964 20628 Z= 0.301 Chirality : 0.046 0.159 2286 Planarity : 0.003 0.027 2628 Dihedral : 5.068 33.897 2010 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 5.09 % Allowed : 24.39 % Favored : 70.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.85 (0.20), residues: 1818 helix: None (None), residues: 0 sheet: -0.56 (0.18), residues: 846 loop : -0.44 (0.21), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 219 TYR 0.007 0.001 TYR D 183 PHE 0.025 0.001 PHE G 56 TRP 0.005 0.001 TRP G 57 HIS 0.005 0.001 HIS I 124 Details of bonding type rmsd covalent geometry : bond 0.00313 (15204) covalent geometry : angle 0.56244 (20580) SS BOND : bond 0.00266 ( 24) SS BOND : angle 0.46570 ( 48) hydrogen bonds : bond 0.03242 ( 509) hydrogen bonds : angle 5.94702 ( 1365) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 191 time to evaluate : 0.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 GLU cc_start: 0.8785 (OUTLIER) cc_final: 0.8354 (tm-30) REVERT: A 165 THR cc_start: 0.8451 (m) cc_final: 0.8155 (m) REVERT: A 220 GLU cc_start: 0.7050 (OUTLIER) cc_final: 0.5741 (mp0) REVERT: B 60 GLU cc_start: 0.7811 (tm-30) cc_final: 0.7560 (tm-30) REVERT: B 101 LYS cc_start: 0.8704 (OUTLIER) cc_final: 0.8422 (tppt) REVERT: B 119 ILE cc_start: 0.8844 (OUTLIER) cc_final: 0.8309 (mm) REVERT: B 138 ASP cc_start: 0.8123 (OUTLIER) cc_final: 0.7852 (m-30) REVERT: C 55 GLU cc_start: 0.8673 (tp30) cc_final: 0.8328 (tp30) REVERT: C 110 GLN cc_start: 0.8478 (tt0) cc_final: 0.8221 (tt0) REVERT: C 141 GLU cc_start: 0.8626 (OUTLIER) cc_final: 0.8173 (tm-30) REVERT: D 47 ASP cc_start: 0.8791 (m-30) cc_final: 0.8540 (m-30) REVERT: D 141 GLU cc_start: 0.8874 (OUTLIER) cc_final: 0.8668 (tm-30) REVERT: D 165 THR cc_start: 0.8378 (m) cc_final: 0.8049 (m) REVERT: D 170 ILE cc_start: 0.8949 (OUTLIER) cc_final: 0.7894 (tp) REVERT: D 220 GLU cc_start: 0.7086 (OUTLIER) cc_final: 0.5654 (mp0) REVERT: E 60 GLU cc_start: 0.7860 (tm-30) cc_final: 0.7542 (tm-30) REVERT: E 101 LYS cc_start: 0.8680 (OUTLIER) cc_final: 0.8414 (tppt) REVERT: E 119 ILE cc_start: 0.8782 (OUTLIER) cc_final: 0.8209 (mm) REVERT: E 128 MET cc_start: 0.7499 (mmm) cc_final: 0.7255 (mmm) REVERT: E 138 ASP cc_start: 0.8135 (OUTLIER) cc_final: 0.7878 (m-30) REVERT: F 55 GLU cc_start: 0.8639 (tp30) cc_final: 0.8292 (tp30) REVERT: F 141 GLU cc_start: 0.8661 (OUTLIER) cc_final: 0.8176 (tm-30) REVERT: I 63 LEU cc_start: 0.7290 (OUTLIER) cc_final: 0.7024 (mt) REVERT: I 100 LEU cc_start: 0.7297 (OUTLIER) cc_final: 0.7011 (mt) outliers start: 87 outliers final: 50 residues processed: 258 average time/residue: 0.5171 time to fit residues: 147.6133 Evaluate side-chains 260 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 195 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 101 LYS Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 193 SER Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 141 GLU Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 169 LYS Chi-restraints excluded: chain C residue 193 SER Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 141 GLU 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 170 ILE Chi-restraints excluded: chain D residue 193 SER Chi-restraints excluded: chain D residue 220 GLU Chi-restraints excluded: chain E residue 59 SER Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 101 LYS Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain E residue 138 ASP Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 193 SER Chi-restraints excluded: chain E residue 197 THR Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 85 THR Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain F residue 141 GLU Chi-restraints excluded: chain F residue 143 ILE Chi-restraints excluded: chain F residue 152 THR Chi-restraints excluded: chain F residue 193 SER Chi-restraints excluded: chain I residue 63 LEU Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain L residue 100 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 131 optimal weight: 6.9990 chunk 171 optimal weight: 7.9990 chunk 156 optimal weight: 8.9990 chunk 94 optimal weight: 0.9990 chunk 78 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 121 optimal weight: 7.9990 chunk 75 optimal weight: 7.9990 chunk 83 optimal weight: 3.9990 chunk 143 optimal weight: 0.5980 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.190155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.124567 restraints weight = 13210.386| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 2.46 r_work: 0.3038 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2901 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2901 r_free = 0.2901 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 789 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2901 r_free = 0.2901 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 788 | |-----------------------------------------------------------------------------| r_final: 0.2901 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.3874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.077 15228 Z= 0.348 Angle : 0.726 8.022 20628 Z= 0.384 Chirality : 0.054 0.181 2286 Planarity : 0.004 0.037 2628 Dihedral : 5.635 39.616 2010 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 5.09 % Allowed : 25.09 % Favored : 69.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.20), residues: 1818 helix: None (None), residues: 0 sheet: -0.47 (0.18), residues: 834 loop : -0.73 (0.20), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 65 TYR 0.013 0.002 TYR D 20 PHE 0.031 0.002 PHE G 56 TRP 0.013 0.002 TRP A 34 HIS 0.007 0.001 HIS I 124 Details of bonding type rmsd covalent geometry : bond 0.00827 (15204) covalent geometry : angle 0.72519 (20580) SS BOND : bond 0.00629 ( 24) SS BOND : angle 0.97434 ( 48) hydrogen bonds : bond 0.04139 ( 509) hydrogen bonds : angle 6.09998 ( 1365) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 178 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 ASP cc_start: 0.7986 (OUTLIER) cc_final: 0.7773 (t70) REVERT: A 141 GLU cc_start: 0.8945 (OUTLIER) cc_final: 0.8568 (tm-30) REVERT: A 165 THR cc_start: 0.8526 (OUTLIER) cc_final: 0.8193 (m) REVERT: A 220 GLU cc_start: 0.7027 (OUTLIER) cc_final: 0.5583 (mp0) REVERT: B 55 GLU cc_start: 0.8743 (tp30) cc_final: 0.8420 (tp30) REVERT: B 60 GLU cc_start: 0.7932 (tm-30) cc_final: 0.7699 (tm-30) REVERT: B 119 ILE cc_start: 0.8908 (OUTLIER) cc_final: 0.8332 (mm) REVERT: B 138 ASP cc_start: 0.8171 (OUTLIER) cc_final: 0.7911 (m-30) REVERT: B 187 GLU cc_start: 0.8392 (mt-10) cc_final: 0.8191 (mt-10) REVERT: C 72 THR cc_start: 0.8913 (p) cc_final: 0.8326 (m) REVERT: C 141 GLU cc_start: 0.8857 (OUTLIER) cc_final: 0.8447 (tm-30) REVERT: C 220 GLU cc_start: 0.7172 (OUTLIER) cc_final: 0.6153 (mp0) REVERT: D 84 ASP cc_start: 0.8029 (OUTLIER) cc_final: 0.7821 (t70) REVERT: D 141 GLU cc_start: 0.8962 (OUTLIER) cc_final: 0.8629 (tm-30) REVERT: D 165 THR cc_start: 0.8508 (OUTLIER) cc_final: 0.8150 (m) REVERT: D 170 ILE cc_start: 0.9011 (OUTLIER) cc_final: 0.8031 (tp) REVERT: D 220 GLU cc_start: 0.7077 (OUTLIER) cc_final: 0.5608 (mp0) REVERT: E 119 ILE cc_start: 0.8867 (OUTLIER) cc_final: 0.8291 (mm) REVERT: E 138 ASP cc_start: 0.8154 (OUTLIER) cc_final: 0.7892 (m-30) REVERT: F 47 ASP cc_start: 0.8889 (m-30) cc_final: 0.8658 (m-30) REVERT: F 55 GLU cc_start: 0.8798 (tp30) cc_final: 0.8584 (tp30) REVERT: F 72 THR cc_start: 0.8915 (p) cc_final: 0.8314 (m) REVERT: F 141 GLU cc_start: 0.8896 (OUTLIER) cc_final: 0.8472 (tm-30) REVERT: I 63 LEU cc_start: 0.7272 (OUTLIER) cc_final: 0.7019 (mt) outliers start: 87 outliers final: 58 residues processed: 248 average time/residue: 0.5359 time to fit residues: 146.8223 Evaluate side-chains 246 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 171 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 49 ASN Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 84 ASP Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 101 LYS Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 193 SER Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 59 SER Chi-restraints excluded: chain C residue 60 GLU Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 141 GLU Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 169 LYS Chi-restraints excluded: chain C residue 193 SER Chi-restraints excluded: chain C residue 220 GLU Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 49 ASN Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain D residue 84 ASP Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 101 LYS Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 141 GLU 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 D residue 170 ILE Chi-restraints excluded: chain D residue 193 SER Chi-restraints excluded: chain D residue 220 GLU Chi-restraints excluded: chain E residue 59 SER Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 138 ASP Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 193 SER Chi-restraints excluded: chain E residue 197 THR Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 85 THR Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain F residue 141 GLU Chi-restraints excluded: chain F residue 143 ILE Chi-restraints excluded: chain F residue 152 THR Chi-restraints excluded: chain F residue 193 SER Chi-restraints excluded: chain I residue 63 LEU Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain L residue 100 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 85 optimal weight: 0.9990 chunk 164 optimal weight: 4.9990 chunk 53 optimal weight: 0.5980 chunk 86 optimal weight: 0.9990 chunk 8 optimal weight: 0.5980 chunk 89 optimal weight: 4.9990 chunk 167 optimal weight: 8.9990 chunk 133 optimal weight: 2.9990 chunk 92 optimal weight: 0.6980 chunk 72 optimal weight: 3.9990 chunk 47 optimal weight: 0.7980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.195804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.133362 restraints weight = 13156.142| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 2.20 r_work: 0.3092 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2948 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2948 r_free = 0.2948 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 788 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2948 r_free = 0.2948 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 789 | |-----------------------------------------------------------------------------| r_final: 0.2948 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.3733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15228 Z= 0.154 Angle : 0.591 8.203 20628 Z= 0.314 Chirality : 0.047 0.162 2286 Planarity : 0.003 0.031 2628 Dihedral : 5.155 34.950 2010 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 4.27 % Allowed : 25.85 % Favored : 69.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.20), residues: 1818 helix: None (None), residues: 0 sheet: -0.59 (0.18), residues: 846 loop : -0.51 (0.21), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 219 TYR 0.008 0.001 TYR A 74 PHE 0.030 0.001 PHE G 56 TRP 0.006 0.001 TRP G 57 HIS 0.005 0.001 HIS I 124 Details of bonding type rmsd covalent geometry : bond 0.00355 (15204) covalent geometry : angle 0.59126 (20580) SS BOND : bond 0.00317 ( 24) SS BOND : angle 0.54624 ( 48) hydrogen bonds : bond 0.03369 ( 509) hydrogen bonds : angle 5.96817 ( 1365) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 181 time to evaluate : 0.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 GLU cc_start: 0.8783 (OUTLIER) cc_final: 0.8329 (tm-30) REVERT: A 165 THR cc_start: 0.8442 (m) cc_final: 0.8102 (m) REVERT: A 220 GLU cc_start: 0.7060 (OUTLIER) cc_final: 0.5720 (mp0) REVERT: B 60 GLU cc_start: 0.7848 (tm-30) cc_final: 0.7592 (tm-30) REVERT: B 119 ILE cc_start: 0.8871 (OUTLIER) cc_final: 0.8316 (mm) REVERT: B 138 ASP cc_start: 0.8154 (OUTLIER) cc_final: 0.7864 (m-30) REVERT: C 110 GLN cc_start: 0.8494 (tt0) cc_final: 0.8236 (tt0) REVERT: C 141 GLU cc_start: 0.8626 (OUTLIER) cc_final: 0.8150 (tm-30) REVERT: C 220 GLU cc_start: 0.7165 (OUTLIER) cc_final: 0.6099 (mp0) REVERT: D 47 ASP cc_start: 0.8794 (m-30) cc_final: 0.8554 (m-30) REVERT: D 141 GLU cc_start: 0.8877 (OUTLIER) cc_final: 0.8640 (tm-30) REVERT: D 165 THR cc_start: 0.8412 (m) cc_final: 0.8069 (m) REVERT: D 170 ILE cc_start: 0.8978 (OUTLIER) cc_final: 0.7916 (tp) REVERT: D 220 GLU cc_start: 0.7122 (OUTLIER) cc_final: 0.5712 (mp0) REVERT: E 60 GLU cc_start: 0.7870 (tm-30) cc_final: 0.7597 (tm-30) REVERT: E 119 ILE cc_start: 0.8789 (OUTLIER) cc_final: 0.8210 (mm) REVERT: E 138 ASP cc_start: 0.8157 (OUTLIER) cc_final: 0.7872 (m-30) REVERT: F 141 GLU cc_start: 0.8669 (OUTLIER) cc_final: 0.8144 (tm-30) REVERT: I 63 LEU cc_start: 0.7344 (OUTLIER) cc_final: 0.7099 (mt) REVERT: L 126 MET cc_start: 0.8126 (ttp) cc_final: 0.7925 (ptm) outliers start: 73 outliers final: 50 residues processed: 236 average time/residue: 0.5267 time to fit residues: 137.5044 Evaluate side-chains 242 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 179 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 101 LYS Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 193 SER Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 141 GLU Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 169 LYS Chi-restraints excluded: chain C residue 193 SER Chi-restraints excluded: chain C residue 220 GLU Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 141 GLU 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 170 ILE Chi-restraints excluded: chain D residue 193 SER Chi-restraints excluded: chain D residue 220 GLU Chi-restraints excluded: chain E residue 59 SER Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain E residue 138 ASP Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 193 SER Chi-restraints excluded: chain E residue 197 THR Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 85 THR Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain F residue 141 GLU Chi-restraints excluded: chain F residue 143 ILE Chi-restraints excluded: chain F residue 152 THR Chi-restraints excluded: chain I residue 63 LEU Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain L residue 100 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 93 optimal weight: 0.0370 chunk 176 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 91 optimal weight: 0.9990 chunk 123 optimal weight: 0.8980 chunk 133 optimal weight: 8.9990 chunk 14 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 166 optimal weight: 8.9990 chunk 118 optimal weight: 2.9990 chunk 102 optimal weight: 0.7980 overall best weight: 0.7458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.194882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.129744 restraints weight = 13231.905| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 2.67 r_work: 0.3040 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3046 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3046 r_free = 0.3046 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 789 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3045 r_free = 0.3045 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 789 | |-----------------------------------------------------------------------------| r_final: 0.3045 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.3727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15228 Z= 0.148 Angle : 0.579 7.752 20628 Z= 0.308 Chirality : 0.046 0.161 2286 Planarity : 0.003 0.026 2628 Dihedral : 5.010 34.631 2010 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 4.33 % Allowed : 25.91 % Favored : 69.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.20), residues: 1818 helix: None (None), residues: 0 sheet: -0.59 (0.18), residues: 846 loop : -0.45 (0.21), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 219 TYR 0.008 0.001 TYR A 74 PHE 0.029 0.001 PHE G 56 TRP 0.007 0.001 TRP G 57 HIS 0.005 0.001 HIS I 124 Details of bonding type rmsd covalent geometry : bond 0.00345 (15204) covalent geometry : angle 0.57958 (20580) SS BOND : bond 0.00267 ( 24) SS BOND : angle 0.49428 ( 48) hydrogen bonds : bond 0.03272 ( 509) hydrogen bonds : angle 5.88162 ( 1365) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5761.25 seconds wall clock time: 98 minutes 48.18 seconds (5928.18 seconds total)