Starting phenix.real_space_refine on Fri May 16 18:03:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hxb_35075/05_2025/8hxb_35075.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hxb_35075/05_2025/8hxb_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8hxb_35075/05_2025/8hxb_35075.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hxb_35075/05_2025/8hxb_35075.map" model { file = "/net/cci-nas-00/data/ceres_data/8hxb_35075/05_2025/8hxb_35075.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hxb_35075/05_2025/8hxb_35075.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.061 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: I, H, K, J, L, C, B, E, D, F Time building chain proxies: 5.57, per 1000 atoms: 0.37 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 C 25 " - pdb=" SG CYS D 130 " distance=1.97 Simple disulfide: pdb=" SG CYS B 25 " - pdb=" SG CYS C 130 " distance=2.01 Simple disulfide: pdb=" SG CYS E 25 " - pdb=" SG CYS F 130 " distance=2.11 Simple disulfide: pdb=" SG CYS D 25 " - pdb=" SG CYS E 130 " distance=2.09 Simple disulfide: pdb=" SG CYS C 56 " - pdb=" SG CYS C 217 " distance=2.03 Simple disulfide: pdb=" SG CYS B 56 " - pdb=" SG CYS B 217 " distance=2.03 Simple disulfide: pdb=" SG CYS E 56 " - pdb=" SG CYS E 217 " distance=2.03 Simple disulfide: pdb=" SG CYS D 56 " - pdb=" SG CYS D 217 " distance=2.03 Simple disulfide: pdb=" SG CYS F 56 " - pdb=" SG CYS F 217 " distance=2.03 Simple disulfide: pdb=" SG CYS C 125 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS B 125 " - pdb=" SG CYS B 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 125 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS D 125 " - pdb=" SG CYS D 157 " distance=2.03 Simple disulfide: pdb=" SG CYS F 125 " - pdb=" SG CYS F 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 160 " - pdb=" SG CYS C 205 " distance=2.02 Simple disulfide: pdb=" SG CYS B 160 " - pdb=" SG CYS B 205 " distance=2.02 Simple disulfide: pdb=" SG CYS E 160 " - pdb=" SG CYS E 205 " distance=2.02 Simple disulfide: pdb=" SG CYS D 160 " - pdb=" SG CYS D 205 " distance=2.02 Simple disulfide: pdb=" SG CYS F 160 " - pdb=" SG CYS F 205 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.17 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 1.80 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: 4.10 Time building geometry restraints manager: 3.79 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: 0.12 Found NCS groups: ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'H' selection = chain 'K' selection = chain 'J' selection = chain 'L' } ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.93 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.050 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: 0.490 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 29.600 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.420 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.18), residues: 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 TRP 0.015 0.002 TRP G 57 HIS 0.023 0.002 HIS G 124 PHE 0.023 0.003 PHE G 88 TYR 0.045 0.003 TYR G 82 ARG 0.005 0.001 ARG L 122 Details of bonding type rmsd hydrogen bonds : bond 0.17704 ( 509) hydrogen bonds : angle 8.40269 ( 1365) SS BOND : bond 0.02690 ( 24) SS BOND : angle 1.52119 ( 48) covalent geometry : bond 0.00712 (15204) covalent geometry : angle 1.15047 (20580) *********************** 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 : 1.517 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: 0.6707 (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: 0.9943 time to fit residues: 390.4062 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 : 1.505 ------------------------------------------------------------------------------- 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 151 optimal weight: 1.9990 chunk 136 optimal weight: 9.9990 chunk 75 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 92 optimal weight: 0.7980 chunk 72 optimal weight: 0.7980 chunk 141 optimal weight: 0.0980 chunk 54 optimal weight: 1.9990 chunk 85 optimal weight: 0.6980 chunk 105 optimal weight: 0.7980 chunk 163 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 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 = 0.4248 r_free = 0.4248 target = 0.207821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.178363 restraints weight = 12798.448| |-----------------------------------------------------------------------------| r_work (start): 0.3911 rms_B_bonded: 0.89 r_work: 0.3519 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.3272 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3227 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3227 r_free = 0.3227 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 786 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3190 r_free = 0.3190 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 791 | |-----------------------------------------------------------------------------| r_final: 0.3190 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 15228 Z= 0.147 Angle : 0.621 9.575 20628 Z= 0.321 Chirality : 0.048 0.190 2286 Planarity : 0.004 0.040 2628 Dihedral : 5.160 30.050 2022 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 4.85 % Allowed : 21.05 % Favored : 74.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.19), residues: 1818 helix: None (None), residues: 0 sheet: -0.50 (0.17), residues: 852 loop : -0.74 (0.20), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 57 HIS 0.011 0.001 HIS I 124 PHE 0.019 0.002 PHE H 56 TYR 0.008 0.001 TYR F 74 ARG 0.005 0.000 ARG C 219 Details of bonding type rmsd hydrogen bonds : bond 0.04196 ( 509) hydrogen bonds : angle 6.46450 ( 1365) SS BOND : bond 0.00252 ( 24) SS BOND : angle 0.66101 ( 48) covalent geometry : bond 0.00355 (15204) covalent geometry : angle 0.62122 (20580) *********************** 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 313 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 230 time to evaluate : 1.796 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 THR cc_start: 0.8330 (m) cc_final: 0.8012 (m) REVERT: B 47 ASP cc_start: 0.8575 (m-30) cc_final: 0.8284 (m-30) REVERT: B 55 GLU cc_start: 0.8539 (tp30) cc_final: 0.7747 (tp30) REVERT: B 84 ASP cc_start: 0.8372 (OUTLIER) cc_final: 0.8104 (t70) REVERT: C 85 THR cc_start: 0.8602 (p) cc_final: 0.7108 (t) REVERT: C 119 ILE cc_start: 0.8761 (OUTLIER) cc_final: 0.8233 (mm) REVERT: D 47 ASP cc_start: 0.8620 (m-30) cc_final: 0.8411 (m-30) REVERT: D 83 MET cc_start: 0.8552 (mmm) cc_final: 0.8199 (mmt) REVERT: D 85 THR cc_start: 0.8666 (p) cc_final: 0.7288 (t) REVERT: D 164 GLU cc_start: 0.8427 (mm-30) cc_final: 0.8212 (mm-30) REVERT: E 39 GLU cc_start: 0.7869 (tm-30) cc_final: 0.7658 (tm-30) REVERT: E 85 THR cc_start: 0.8725 (p) cc_final: 0.7143 (t) REVERT: E 101 LYS cc_start: 0.8516 (tppt) cc_final: 0.8314 (tppt) REVERT: F 47 ASP cc_start: 0.8662 (m-30) cc_final: 0.8346 (m-30) REVERT: F 119 ILE cc_start: 0.8821 (OUTLIER) cc_final: 0.8049 (mm) REVERT: F 141 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.7969 (tm-30) REVERT: G 100 LEU cc_start: 0.7153 (OUTLIER) cc_final: 0.6911 (mt) REVERT: H 100 LEU cc_start: 0.7318 (OUTLIER) cc_final: 0.6963 (mt) REVERT: I 100 LEU cc_start: 0.7051 (OUTLIER) cc_final: 0.6797 (mt) REVERT: J 100 LEU cc_start: 0.6772 (OUTLIER) cc_final: 0.6505 (mt) REVERT: L 100 LEU cc_start: 0.7147 (OUTLIER) cc_final: 0.6897 (mt) outliers start: 83 outliers final: 44 residues processed: 289 average time/residue: 0.9614 time to fit residues: 314.0890 Evaluate side-chains 263 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 210 time to evaluate : 1.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP 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 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 193 SER Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 143 ILE Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 193 SER Chi-restraints excluded: chain E residue 59 SER 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 193 SER 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 152 optimal weight: 6.9990 chunk 15 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 106 optimal weight: 0.8980 chunk 9 optimal weight: 6.9990 chunk 64 optimal weight: 0.4980 chunk 139 optimal weight: 4.9990 chunk 94 optimal weight: 1.9990 chunk 96 optimal weight: 0.7980 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 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 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.195798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.120809 restraints weight = 13157.088| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 1.72 r_work: 0.3173 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3039 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3039 r_free = 0.3039 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 791 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3036 r_free = 0.3036 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 791 | |-----------------------------------------------------------------------------| r_final: 0.3036 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.2679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 15228 Z= 0.207 Angle : 0.631 8.603 20628 Z= 0.332 Chirality : 0.050 0.171 2286 Planarity : 0.004 0.038 2628 Dihedral : 5.267 34.924 2012 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.20), residues: 1818 helix: None (None), residues: 0 sheet: -0.52 (0.17), residues: 846 loop : -0.51 (0.21), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 34 HIS 0.008 0.001 HIS I 124 PHE 0.020 0.002 PHE H 56 TYR 0.012 0.001 TYR B 183 ARG 0.004 0.001 ARG A 191 Details of bonding type rmsd hydrogen bonds : bond 0.04266 ( 509) hydrogen bonds : angle 6.33689 ( 1365) SS BOND : bond 0.00352 ( 24) SS BOND : angle 0.69828 ( 48) covalent geometry : bond 0.00485 (15204) covalent geometry : angle 0.63083 (20580) *********************** 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 313 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 208 time to evaluate : 1.646 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: 0.8412 (m) cc_final: 0.8051 (m) REVERT: B 39 GLU cc_start: 0.7925 (tm-30) cc_final: 0.7699 (tp30) REVERT: B 55 GLU cc_start: 0.8686 (tp30) cc_final: 0.8312 (tp30) REVERT: B 119 ILE cc_start: 0.8767 (OUTLIER) cc_final: 0.8174 (mm) REVERT: B 138 ASP cc_start: 0.8024 (OUTLIER) cc_final: 0.7666 (m-30) REVERT: C 39 GLU cc_start: 0.7976 (tm-30) cc_final: 0.7594 (tp30) REVERT: C 72 THR cc_start: 0.8724 (p) cc_final: 0.8139 (m) REVERT: C 80 MET cc_start: 0.9194 (OUTLIER) cc_final: 0.8937 (ttt) REVERT: C 220 GLU cc_start: 0.6735 (OUTLIER) cc_final: 0.5453 (mp0) REVERT: D 85 THR cc_start: 0.8725 (p) cc_final: 0.7555 (t) REVERT: D 165 THR cc_start: 0.8441 (OUTLIER) cc_final: 0.8056 (m) REVERT: E 39 GLU cc_start: 0.7893 (tm-30) cc_final: 0.7650 (tp30) REVERT: E 58 MET cc_start: 0.8889 (ptm) cc_final: 0.8654 (ptm) REVERT: E 65 ARG cc_start: 0.8704 (mtp180) cc_final: 0.8491 (mtp180) REVERT: E 101 LYS cc_start: 0.8682 (tppt) cc_final: 0.8380 (mmtp) REVERT: E 138 ASP cc_start: 0.8082 (OUTLIER) cc_final: 0.7685 (m-30) REVERT: F 39 GLU cc_start: 0.7970 (tm-30) cc_final: 0.7650 (tp30) REVERT: F 60 GLU cc_start: 0.7607 (OUTLIER) cc_final: 0.7328 (tm-30) REVERT: F 72 THR cc_start: 0.8755 (p) cc_final: 0.8179 (m) REVERT: F 141 GLU cc_start: 0.8726 (OUTLIER) cc_final: 0.8247 (tm-30) REVERT: F 207 LEU cc_start: 0.7255 (OUTLIER) cc_final: 0.7055 (mp) REVERT: F 220 GLU cc_start: 0.6770 (OUTLIER) cc_final: 0.6507 (mm-30) REVERT: I 100 LEU cc_start: 0.7158 (OUTLIER) cc_final: 0.6935 (mt) REVERT: J 100 LEU cc_start: 0.7005 (OUTLIER) cc_final: 0.6786 (mt) REVERT: L 100 LEU cc_start: 0.7191 (OUTLIER) cc_final: 0.6981 (mt) outliers start: 105 outliers final: 49 residues processed: 286 average time/residue: 1.0335 time to fit residues: 329.9519 Evaluate side-chains 246 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 184 time to evaluate : 1.780 ------------------------------------------------------------------------------- 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 59 SER Chi-restraints excluded: chain B residue 60 GLU 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 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 124 THR 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 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 82 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 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 207 LEU Chi-restraints excluded: chain F residue 220 GLU Chi-restraints excluded: chain G residue 120 MET Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain J residue 100 LEU Chi-restraints excluded: chain J residue 120 MET 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 27 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 chunk 95 optimal weight: 0.0870 chunk 48 optimal weight: 0.6980 chunk 143 optimal weight: 5.9990 chunk 101 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 88 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 overall best weight: 0.8360 ------------------------------------------------------------------------------- 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 116 HIS ** B 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 116 HIS ** C 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 116 HIS ** 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 116 HIS ** 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.199637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.132337 restraints weight = 12982.185| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 2.09 r_work: 0.3153 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3050 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3050 r_free = 0.3050 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 791 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3049 r_free = 0.3049 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 789 | |-----------------------------------------------------------------------------| r_final: 0.3049 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.2877 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= 0.157 Angle : 0.570 7.595 20628 Z= 0.302 Chirality : 0.047 0.157 2286 Planarity : 0.003 0.037 2628 Dihedral : 5.123 33.959 2012 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 5.50 % Allowed : 22.28 % Favored : 72.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.20), residues: 1818 helix: None (None), residues: 0 sheet: -0.47 (0.17), residues: 846 loop : -0.46 (0.21), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 57 HIS 0.006 0.001 HIS I 124 PHE 0.020 0.001 PHE K 56 TYR 0.007 0.001 TYR E 183 ARG 0.004 0.000 ARG A 191 Details of bonding type rmsd hydrogen bonds : bond 0.03835 ( 509) hydrogen bonds : angle 6.29492 ( 1365) SS BOND : bond 0.00261 ( 24) SS BOND : angle 0.52627 ( 48) covalent geometry : bond 0.00364 (15204) covalent geometry : angle 0.57056 (20580) *********************** 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 282 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 188 time to evaluate : 1.541 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: 0.8060 (tm-30) cc_final: 0.7788 (tp30) REVERT: A 49 ASN cc_start: 0.7916 (p0) cc_final: 0.7571 (m110) REVERT: A 94 GLU cc_start: 0.8681 (mt-10) cc_final: 0.8328 (mt-10) REVERT: A 141 GLU cc_start: 0.8804 (OUTLIER) cc_final: 0.8500 (tm-30) REVERT: A 165 THR cc_start: 0.8371 (m) cc_final: 0.8037 (m) REVERT: B 39 GLU cc_start: 0.7901 (tm-30) cc_final: 0.7642 (tp30) REVERT: B 42 ILE cc_start: 0.8455 (OUTLIER) cc_final: 0.8226 (mp) REVERT: B 49 ASN cc_start: 0.8039 (p0) cc_final: 0.7608 (m-40) REVERT: B 55 GLU cc_start: 0.8726 (tp30) cc_final: 0.8359 (tp30) REVERT: B 119 ILE cc_start: 0.8722 (OUTLIER) cc_final: 0.8151 (mm) REVERT: B 138 ASP cc_start: 0.8041 (OUTLIER) cc_final: 0.7740 (m-30) REVERT: C 39 GLU cc_start: 0.7954 (tm-30) cc_final: 0.7642 (tp30) REVERT: C 55 GLU cc_start: 0.8652 (tp30) cc_final: 0.8294 (tp30) REVERT: C 141 GLU cc_start: 0.8708 (OUTLIER) cc_final: 0.8244 (tm-30) REVERT: D 141 GLU cc_start: 0.8801 (OUTLIER) cc_final: 0.8471 (tm-30) REVERT: D 165 THR cc_start: 0.8375 (m) cc_final: 0.8043 (m) REVERT: E 39 GLU cc_start: 0.7884 (tm-30) cc_final: 0.7618 (tp30) REVERT: E 55 GLU cc_start: 0.8640 (tp30) cc_final: 0.8276 (tp30) REVERT: E 58 MET cc_start: 0.8904 (ptm) cc_final: 0.8629 (ptm) REVERT: E 138 ASP cc_start: 0.8142 (OUTLIER) cc_final: 0.7839 (m-30) REVERT: E 187 GLU cc_start: 0.8113 (mt-10) cc_final: 0.7889 (mt-10) REVERT: F 39 GLU cc_start: 0.7946 (tm-30) cc_final: 0.7608 (tp30) REVERT: F 141 GLU cc_start: 0.8674 (OUTLIER) cc_final: 0.8175 (tm-30) REVERT: F 220 GLU cc_start: 0.6777 (OUTLIER) cc_final: 0.6318 (mm-30) REVERT: G 126 MET cc_start: 0.7946 (OUTLIER) cc_final: 0.7481 (ttp) REVERT: I 100 LEU cc_start: 0.7125 (OUTLIER) cc_final: 0.6905 (mt) REVERT: J 100 LEU cc_start: 0.6951 (OUTLIER) cc_final: 0.6735 (mt) REVERT: L 100 LEU cc_start: 0.7159 (OUTLIER) cc_final: 0.6930 (mt) outliers start: 94 outliers final: 46 residues processed: 259 average time/residue: 1.0843 time to fit residues: 313.4826 Evaluate side-chains 246 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 187 time to evaluate : 1.529 ------------------------------------------------------------------------------- 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 159 THR Chi-restraints excluded: chain A residue 193 SER Chi-restraints excluded: chain B residue 42 ILE 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 82 ILE Chi-restraints excluded: chain B residue 104 VAL 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 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 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 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 141 GLU Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 159 THR Chi-restraints excluded: chain D residue 193 SER Chi-restraints excluded: chain E residue 59 SER 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 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 G residue 126 MET 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 69 optimal weight: 0.4980 chunk 91 optimal weight: 0.9980 chunk 93 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 118 optimal weight: 0.0270 chunk 64 optimal weight: 0.9980 chunk 129 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 overall best weight: 0.5838 ------------------------------------------------------------------------------- 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 = 0.4174 r_free = 0.4174 target = 0.200788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.133230 restraints weight = 13034.156| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 3.00 r_work: 0.3171 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3102 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3102 r_free = 0.3102 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 789 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3101 r_free = 0.3101 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 789 | |-----------------------------------------------------------------------------| r_final: 0.3101 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.2987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15228 Z= 0.127 Angle : 0.537 7.041 20628 Z= 0.286 Chirality : 0.046 0.149 2286 Planarity : 0.003 0.035 2628 Dihedral : 4.939 32.894 2012 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 6.67 % Allowed : 21.11 % Favored : 72.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.20), residues: 1818 helix: None (None), residues: 0 sheet: -0.50 (0.17), residues: 846 loop : -0.43 (0.21), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP I 57 HIS 0.006 0.001 HIS I 124 PHE 0.019 0.001 PHE K 56 TYR 0.006 0.001 TYR E 74 ARG 0.006 0.000 ARG A 191 Details of bonding type rmsd hydrogen bonds : bond 0.03585 ( 509) hydrogen bonds : angle 6.22501 ( 1365) SS BOND : bond 0.00223 ( 24) SS BOND : angle 0.47238 ( 48) covalent geometry : bond 0.00290 (15204) covalent geometry : angle 0.53711 (20580) *********************** 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: 114 poor density : 190 time to evaluate : 1.564 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: 0.8013 (tm-30) cc_final: 0.7767 (tp30) REVERT: A 49 ASN cc_start: 0.7856 (p0) cc_final: 0.7569 (m110) REVERT: A 165 THR cc_start: 0.8356 (m) cc_final: 0.8014 (m) REVERT: B 39 GLU cc_start: 0.7908 (tm-30) cc_final: 0.7655 (tp30) REVERT: B 49 ASN cc_start: 0.8005 (p0) cc_final: 0.7644 (m-40) REVERT: B 119 ILE cc_start: 0.8724 (OUTLIER) cc_final: 0.8172 (mm) REVERT: B 138 ASP cc_start: 0.8073 (OUTLIER) cc_final: 0.7824 (m-30) REVERT: C 39 GLU cc_start: 0.7914 (tm-30) cc_final: 0.7508 (tp30) REVERT: C 141 GLU cc_start: 0.8558 (OUTLIER) cc_final: 0.8067 (tm-30) REVERT: C 220 GLU cc_start: 0.6559 (OUTLIER) cc_final: 0.5020 (mp0) REVERT: D 47 ASP cc_start: 0.8753 (m-30) cc_final: 0.8504 (m-30) REVERT: D 49 ASN cc_start: 0.7925 (OUTLIER) cc_final: 0.7532 (m110) REVERT: D 141 GLU cc_start: 0.8746 (OUTLIER) cc_final: 0.8546 (tm-30) REVERT: D 165 THR cc_start: 0.8369 (m) cc_final: 0.8032 (m) REVERT: D 169 LYS cc_start: 0.8580 (OUTLIER) cc_final: 0.7978 (pmtt) REVERT: D 220 GLU cc_start: 0.6880 (OUTLIER) cc_final: 0.5536 (mp0) REVERT: E 39 GLU cc_start: 0.7859 (tm-30) cc_final: 0.7585 (tp30) REVERT: E 49 ASN cc_start: 0.7984 (p0) cc_final: 0.7587 (m-40) REVERT: E 55 GLU cc_start: 0.8615 (tp30) cc_final: 0.8259 (tp30) REVERT: E 58 MET cc_start: 0.8894 (ptm) cc_final: 0.8654 (ptm) REVERT: E 80 MET cc_start: 0.9029 (ttm) cc_final: 0.8808 (ttt) REVERT: E 138 ASP cc_start: 0.8077 (OUTLIER) cc_final: 0.7822 (m-30) REVERT: F 39 GLU cc_start: 0.7889 (tm-30) cc_final: 0.7573 (tp30) REVERT: F 47 ASP cc_start: 0.8774 (m-30) cc_final: 0.8483 (m-30) REVERT: F 83 MET cc_start: 0.8722 (OUTLIER) cc_final: 0.7781 (mmm) REVERT: F 141 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.8067 (tm-30) REVERT: F 220 GLU cc_start: 0.6640 (OUTLIER) cc_final: 0.6176 (mm-30) REVERT: I 100 LEU cc_start: 0.7124 (OUTLIER) cc_final: 0.6897 (mt) REVERT: J 63 LEU cc_start: 0.7050 (OUTLIER) cc_final: 0.6799 (mt) REVERT: J 100 LEU cc_start: 0.6927 (OUTLIER) cc_final: 0.6722 (mt) REVERT: L 100 LEU cc_start: 0.7207 (OUTLIER) cc_final: 0.6969 (mt) outliers start: 114 outliers final: 49 residues processed: 281 average time/residue: 0.9637 time to fit residues: 304.4035 Evaluate side-chains 246 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 181 time to evaluate : 1.489 ------------------------------------------------------------------------------- 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 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 104 VAL 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 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 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 82 ILE 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 D residue 220 GLU Chi-restraints excluded: chain E residue 59 SER 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 81 THR Chi-restraints excluded: chain F residue 83 MET 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 100 LEU Chi-restraints excluded: chain J residue 63 LEU Chi-restraints excluded: chain J 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 51 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 106 optimal weight: 0.9990 chunk 89 optimal weight: 3.9990 chunk 152 optimal weight: 0.5980 chunk 86 optimal weight: 0.9980 chunk 149 optimal weight: 3.9990 chunk 46 optimal weight: 0.7980 chunk 133 optimal weight: 7.9990 chunk 169 optimal weight: 6.9990 chunk 73 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 184 HIS ** B 129 ASN ** 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** 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 = 0.4148 r_free = 0.4148 target = 0.198327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.134415 restraints weight = 13140.152| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 2.72 r_work: 0.3081 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3066 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3066 r_free = 0.3066 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 789 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3065 r_free = 0.3065 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 788 | |-----------------------------------------------------------------------------| r_final: 0.3065 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.3164 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= 0.149 Angle : 0.545 6.474 20628 Z= 0.293 Chirality : 0.046 0.149 2286 Planarity : 0.003 0.035 2628 Dihedral : 5.002 34.758 2012 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 6.14 % Allowed : 22.22 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.20), residues: 1818 helix: None (None), residues: 0 sheet: -0.51 (0.18), residues: 846 loop : -0.45 (0.21), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP L 93 HIS 0.006 0.001 HIS I 124 PHE 0.019 0.001 PHE K 56 TYR 0.007 0.001 TYR B 183 ARG 0.004 0.000 ARG A 191 Details of bonding type rmsd hydrogen bonds : bond 0.03643 ( 509) hydrogen bonds : angle 6.21557 ( 1365) SS BOND : bond 0.00233 ( 24) SS BOND : angle 0.53364 ( 48) covalent geometry : bond 0.00344 (15204) covalent geometry : angle 0.54545 (20580) *********************** 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 284 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 179 time to evaluate : 1.729 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: 0.8386 (m) cc_final: 0.8029 (m) REVERT: B 39 GLU cc_start: 0.7847 (tm-30) cc_final: 0.7643 (tp30) REVERT: B 49 ASN cc_start: 0.8055 (p0) cc_final: 0.7803 (m-40) REVERT: B 119 ILE cc_start: 0.8771 (OUTLIER) cc_final: 0.8159 (mm) REVERT: B 138 ASP cc_start: 0.8000 (OUTLIER) cc_final: 0.7738 (m-30) REVERT: C 39 GLU cc_start: 0.7873 (tm-30) cc_final: 0.7571 (tp30) REVERT: C 110 GLN cc_start: 0.8367 (tt0) cc_final: 0.8163 (tt0) REVERT: C 141 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.8063 (tm-30) REVERT: C 220 GLU cc_start: 0.6619 (OUTLIER) cc_final: 0.5064 (mp0) REVERT: D 39 GLU cc_start: 0.8000 (tm-30) cc_final: 0.7796 (tp30) REVERT: D 49 ASN cc_start: 0.7998 (OUTLIER) cc_final: 0.7710 (m110) REVERT: D 165 THR cc_start: 0.8368 (OUTLIER) cc_final: 0.8011 (m) REVERT: D 169 LYS cc_start: 0.8618 (OUTLIER) cc_final: 0.8031 (pmtt) REVERT: D 220 GLU cc_start: 0.6955 (OUTLIER) cc_final: 0.5568 (mp0) REVERT: E 39 GLU cc_start: 0.7839 (tm-30) cc_final: 0.7603 (tp30) REVERT: E 49 ASN cc_start: 0.8048 (p0) cc_final: 0.7747 (m-40) REVERT: E 58 MET cc_start: 0.8908 (ptm) cc_final: 0.8693 (ptm) REVERT: E 60 GLU cc_start: 0.7862 (tm-30) cc_final: 0.7599 (tm-30) REVERT: E 80 MET cc_start: 0.9020 (ttm) cc_final: 0.8815 (ttt) REVERT: E 119 ILE cc_start: 0.8729 (OUTLIER) cc_final: 0.8143 (mm) REVERT: E 138 ASP cc_start: 0.8053 (OUTLIER) cc_final: 0.7801 (m-30) REVERT: F 39 GLU cc_start: 0.7874 (tm-30) cc_final: 0.7579 (tp30) REVERT: F 141 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.8135 (tm-30) REVERT: F 220 GLU cc_start: 0.6787 (OUTLIER) cc_final: 0.6282 (mm-30) REVERT: I 63 LEU cc_start: 0.7057 (OUTLIER) cc_final: 0.6744 (mt) REVERT: I 100 LEU cc_start: 0.7272 (OUTLIER) cc_final: 0.7009 (mt) REVERT: J 63 LEU cc_start: 0.7224 (OUTLIER) cc_final: 0.6977 (mt) REVERT: J 100 LEU cc_start: 0.7025 (OUTLIER) cc_final: 0.6816 (mt) REVERT: L 100 LEU cc_start: 0.7247 (OUTLIER) cc_final: 0.6999 (mt) REVERT: L 126 MET cc_start: 0.7911 (ttp) cc_final: 0.7691 (ptm) outliers start: 105 outliers final: 49 residues processed: 262 average time/residue: 1.0450 time to fit residues: 306.9596 Evaluate side-chains 251 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 185 time to evaluate : 1.690 ------------------------------------------------------------------------------- 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 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 104 VAL 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 81 THR Chi-restraints excluded: chain C residue 85 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 82 ILE Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 143 ILE Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 159 THR Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 169 LYS 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 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 F residue 220 GLU 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 J residue 100 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 40 optimal weight: 3.9990 chunk 3 optimal weight: 0.3980 chunk 70 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 157 optimal weight: 5.9990 chunk 122 optimal weight: 0.1980 chunk 52 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 18 optimal weight: 0.3980 chunk 10 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 110 GLN ** 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 = 0.4156 r_free = 0.4156 target = 0.198837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.133906 restraints weight = 13042.279| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 3.01 r_work: 0.3107 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2970 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2970 r_free = 0.2970 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 = 0.2970 r_free = 0.2970 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 788 | |-----------------------------------------------------------------------------| r_final: 0.2970 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.3271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15228 Z= 0.148 Angle : 0.544 6.667 20628 Z= 0.292 Chirality : 0.046 0.156 2286 Planarity : 0.003 0.035 2628 Dihedral : 4.973 34.927 2012 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 5.44 % Allowed : 22.92 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.20), residues: 1818 helix: None (None), residues: 0 sheet: -0.52 (0.18), residues: 846 loop : -0.44 (0.21), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP L 57 HIS 0.006 0.001 HIS I 124 PHE 0.019 0.001 PHE K 56 TYR 0.008 0.001 TYR A 74 ARG 0.004 0.000 ARG A 191 Details of bonding type rmsd hydrogen bonds : bond 0.03630 ( 509) hydrogen bonds : angle 6.19867 ( 1365) SS BOND : bond 0.00241 ( 24) SS BOND : angle 0.53287 ( 48) covalent geometry : bond 0.00340 (15204) covalent geometry : angle 0.54408 (20580) *********************** 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 278 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 185 time to evaluate : 1.526 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: 0.8471 (m) cc_final: 0.8143 (m) REVERT: B 39 GLU cc_start: 0.7999 (tm-30) cc_final: 0.7767 (tp30) REVERT: B 49 ASN cc_start: 0.8132 (p0) cc_final: 0.7813 (m-40) REVERT: B 119 ILE cc_start: 0.8817 (OUTLIER) cc_final: 0.8269 (mm) REVERT: B 138 ASP cc_start: 0.8179 (OUTLIER) cc_final: 0.7930 (m-30) REVERT: C 39 GLU cc_start: 0.7968 (tm-30) cc_final: 0.7639 (tp30) REVERT: C 110 GLN cc_start: 0.8377 (tt0) cc_final: 0.8150 (tt0) REVERT: C 141 GLU cc_start: 0.8615 (OUTLIER) cc_final: 0.8102 (tm-30) REVERT: D 39 GLU cc_start: 0.8101 (tm-30) cc_final: 0.7878 (tp30) REVERT: D 47 ASP cc_start: 0.8802 (m-30) cc_final: 0.8551 (m-30) REVERT: D 49 ASN cc_start: 0.8035 (OUTLIER) cc_final: 0.7726 (m110) REVERT: D 165 THR cc_start: 0.8475 (OUTLIER) cc_final: 0.8140 (m) REVERT: D 220 GLU cc_start: 0.6943 (OUTLIER) cc_final: 0.5559 (mp0) REVERT: E 39 GLU cc_start: 0.7946 (tm-30) cc_final: 0.7675 (tp30) REVERT: E 49 ASN cc_start: 0.8123 (p0) cc_final: 0.7770 (m-40) REVERT: E 60 GLU cc_start: 0.7814 (tm-30) cc_final: 0.7561 (tm-30) REVERT: E 119 ILE cc_start: 0.8764 (OUTLIER) cc_final: 0.8192 (mm) REVERT: E 138 ASP cc_start: 0.8215 (OUTLIER) cc_final: 0.7988 (m-30) REVERT: F 39 GLU cc_start: 0.8037 (tm-30) cc_final: 0.7706 (tp30) REVERT: F 47 ASP cc_start: 0.8872 (m-30) cc_final: 0.8603 (m-30) REVERT: F 141 GLU cc_start: 0.8648 (OUTLIER) cc_final: 0.8129 (tm-30) REVERT: F 220 GLU cc_start: 0.6865 (OUTLIER) cc_final: 0.6346 (mm-30) REVERT: I 63 LEU cc_start: 0.7216 (OUTLIER) cc_final: 0.6860 (mt) REVERT: I 100 LEU cc_start: 0.7297 (OUTLIER) cc_final: 0.7022 (mt) REVERT: J 63 LEU cc_start: 0.7303 (OUTLIER) cc_final: 0.7054 (mt) REVERT: J 100 LEU cc_start: 0.7055 (OUTLIER) cc_final: 0.6843 (mt) REVERT: L 126 MET cc_start: 0.8067 (ttp) cc_final: 0.7855 (ptm) outliers start: 93 outliers final: 55 residues processed: 264 average time/residue: 0.9574 time to fit residues: 285.3828 Evaluate side-chains 248 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 179 time to evaluate : 1.526 ------------------------------------------------------------------------------- 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 82 ILE Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 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 104 VAL 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 81 THR Chi-restraints excluded: chain C residue 85 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 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 82 ILE 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 127 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 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 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 J residue 63 LEU Chi-restraints excluded: chain J 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 13 optimal weight: 1.9990 chunk 96 optimal weight: 0.7980 chunk 149 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 89 optimal weight: 3.9990 chunk 151 optimal weight: 8.9990 chunk 94 optimal weight: 0.5980 chunk 83 optimal weight: 0.0170 chunk 91 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 overall best weight: 0.6618 ------------------------------------------------------------------------------- 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 = 0.4152 r_free = 0.4152 target = 0.198714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.135682 restraints weight = 13116.736| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 1.87 r_work: 0.3141 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3012 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3012 r_free = 0.3012 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 788 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3012 r_free = 0.3012 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 788 | |-----------------------------------------------------------------------------| r_final: 0.3012 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.3323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15228 Z= 0.134 Angle : 0.535 9.358 20628 Z= 0.286 Chirality : 0.046 0.155 2286 Planarity : 0.003 0.035 2628 Dihedral : 4.906 34.187 2012 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 5.32 % Allowed : 23.27 % Favored : 71.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.20), residues: 1818 helix: None (None), residues: 0 sheet: -0.55 (0.18), residues: 846 loop : -0.43 (0.21), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP I 57 HIS 0.005 0.001 HIS I 124 PHE 0.017 0.001 PHE K 56 TYR 0.007 0.001 TYR E 74 ARG 0.004 0.000 ARG A 191 Details of bonding type rmsd hydrogen bonds : bond 0.03521 ( 509) hydrogen bonds : angle 6.19588 ( 1365) SS BOND : bond 0.00203 ( 24) SS BOND : angle 0.50492 ( 48) covalent geometry : bond 0.00305 (15204) covalent geometry : angle 0.53488 (20580) *********************** 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 276 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 185 time to evaluate : 1.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 GLU cc_start: 0.8651 (tp30) cc_final: 0.8148 (tp30) REVERT: A 141 GLU cc_start: 0.8777 (OUTLIER) cc_final: 0.8365 (tm-30) REVERT: A 165 THR cc_start: 0.8401 (m) cc_final: 0.8090 (m) REVERT: B 39 GLU cc_start: 0.7963 (tm-30) cc_final: 0.7723 (tp30) REVERT: B 49 ASN cc_start: 0.8042 (p0) cc_final: 0.7752 (m-40) REVERT: B 55 GLU cc_start: 0.8552 (tp30) cc_final: 0.8086 (tp30) REVERT: B 119 ILE cc_start: 0.8766 (OUTLIER) cc_final: 0.8185 (mm) REVERT: B 138 ASP cc_start: 0.8104 (OUTLIER) cc_final: 0.7864 (m-30) REVERT: C 39 GLU cc_start: 0.7938 (tm-30) cc_final: 0.7604 (tp30) REVERT: C 141 GLU cc_start: 0.8545 (OUTLIER) cc_final: 0.8257 (tm-30) REVERT: D 39 GLU cc_start: 0.8051 (tm-30) cc_final: 0.7815 (tp30) REVERT: D 47 ASP cc_start: 0.8759 (m-30) cc_final: 0.8499 (m-30) REVERT: D 49 ASN cc_start: 0.7995 (OUTLIER) cc_final: 0.7692 (m110) REVERT: D 165 THR cc_start: 0.8437 (OUTLIER) cc_final: 0.8091 (m) REVERT: E 39 GLU cc_start: 0.7909 (tm-30) cc_final: 0.7652 (tp30) REVERT: E 49 ASN cc_start: 0.8031 (p0) cc_final: 0.7723 (m-40) REVERT: E 60 GLU cc_start: 0.7747 (tm-30) cc_final: 0.7496 (tm-30) REVERT: E 119 ILE cc_start: 0.8729 (OUTLIER) cc_final: 0.8175 (mm) REVERT: E 138 ASP cc_start: 0.8120 (OUTLIER) cc_final: 0.7902 (m-30) REVERT: F 39 GLU cc_start: 0.7981 (tm-30) cc_final: 0.7640 (tp30) REVERT: F 141 GLU cc_start: 0.8603 (OUTLIER) cc_final: 0.8095 (tm-30) REVERT: I 63 LEU cc_start: 0.7148 (OUTLIER) cc_final: 0.6809 (mt) REVERT: I 100 LEU cc_start: 0.7325 (OUTLIER) cc_final: 0.7038 (mt) REVERT: J 63 LEU cc_start: 0.7247 (OUTLIER) cc_final: 0.7009 (mt) REVERT: J 100 LEU cc_start: 0.7063 (OUTLIER) cc_final: 0.6852 (mt) REVERT: L 126 MET cc_start: 0.8005 (ttp) cc_final: 0.7783 (ptm) outliers start: 91 outliers final: 54 residues processed: 261 average time/residue: 1.0511 time to fit residues: 308.6628 Evaluate side-chains 253 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 186 time to evaluate : 1.574 ------------------------------------------------------------------------------- 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 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 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 59 SER Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 104 VAL 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 81 THR Chi-restraints excluded: chain C residue 85 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 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 82 ILE 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 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 193 SER 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 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 I residue 63 LEU Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain J residue 63 LEU Chi-restraints excluded: chain J 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 111 optimal weight: 0.9990 chunk 101 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 62 optimal weight: 0.0570 chunk 149 optimal weight: 4.9990 chunk 51 optimal weight: 0.6980 chunk 78 optimal weight: 0.0270 chunk 16 optimal weight: 2.9990 chunk 179 optimal weight: 0.0270 chunk 148 optimal weight: 0.0000 chunk 59 optimal weight: 0.5980 overall best weight: 0.1418 ------------------------------------------------------------------------------- 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 129 ASN ** B 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 129 ASN ** D 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 184 HIS ** E 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 = 0.4217 r_free = 0.4217 target = 0.205591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.145304 restraints weight = 13089.641| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 2.46 r_work: 0.3211 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3076 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3076 r_free = 0.3076 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 788 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3075 r_free = 0.3075 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 791 | |-----------------------------------------------------------------------------| r_final: 0.3075 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.3374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 15228 Z= 0.086 Angle : 0.497 8.728 20628 Z= 0.266 Chirality : 0.044 0.154 2286 Planarity : 0.003 0.033 2628 Dihedral : 4.587 32.850 2012 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 3.51 % Allowed : 25.15 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.20), residues: 1818 helix: None (None), residues: 0 sheet: -0.50 (0.18), residues: 846 loop : -0.43 (0.21), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 57 HIS 0.004 0.001 HIS I 124 PHE 0.016 0.001 PHE K 56 TYR 0.006 0.001 TYR B 46 ARG 0.007 0.000 ARG A 191 Details of bonding type rmsd hydrogen bonds : bond 0.03131 ( 509) hydrogen bonds : angle 6.07684 ( 1365) SS BOND : bond 0.00116 ( 24) SS BOND : angle 0.40530 ( 48) covalent geometry : bond 0.00186 (15204) covalent geometry : angle 0.49697 (20580) *********************** 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 270 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 210 time to evaluate : 1.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 THR cc_start: 0.8483 (OUTLIER) cc_final: 0.7824 (t) REVERT: A 141 GLU cc_start: 0.8672 (OUTLIER) cc_final: 0.8176 (tm-30) REVERT: A 165 THR cc_start: 0.8352 (m) cc_final: 0.8042 (m) REVERT: B 39 GLU cc_start: 0.7914 (tm-30) cc_final: 0.7699 (tp30) REVERT: B 47 ASP cc_start: 0.8655 (m-30) cc_final: 0.8348 (m-30) REVERT: B 49 ASN cc_start: 0.7990 (p0) cc_final: 0.7743 (m-40) REVERT: B 60 GLU cc_start: 0.7258 (tm-30) cc_final: 0.6802 (tm-30) REVERT: B 119 ILE cc_start: 0.8735 (OUTLIER) cc_final: 0.8185 (mm) REVERT: C 39 GLU cc_start: 0.7926 (tm-30) cc_final: 0.7677 (tp30) REVERT: C 85 THR cc_start: 0.8466 (p) cc_final: 0.7575 (t) REVERT: C 141 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7834 (tm-30) REVERT: D 47 ASP cc_start: 0.8738 (m-30) cc_final: 0.8480 (m-30) REVERT: D 49 ASN cc_start: 0.7924 (p0) cc_final: 0.7702 (m110) REVERT: D 85 THR cc_start: 0.8446 (p) cc_final: 0.7851 (t) REVERT: D 165 THR cc_start: 0.8401 (m) cc_final: 0.8081 (m) REVERT: E 32 ARG cc_start: 0.8169 (mtp180) cc_final: 0.7961 (mtt90) REVERT: E 39 GLU cc_start: 0.8008 (tm-30) cc_final: 0.7791 (tp30) REVERT: E 49 ASN cc_start: 0.7999 (p0) cc_final: 0.7706 (m-40) REVERT: E 119 ILE cc_start: 0.8724 (OUTLIER) cc_final: 0.8177 (mm) REVERT: F 47 ASP cc_start: 0.8777 (m-30) cc_final: 0.8451 (m-30) REVERT: F 141 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.7984 (tm-30) REVERT: F 184 HIS cc_start: 0.8900 (p90) cc_final: 0.8679 (p90) REVERT: I 63 LEU cc_start: 0.7270 (OUTLIER) cc_final: 0.6928 (mt) REVERT: I 100 LEU cc_start: 0.7262 (OUTLIER) cc_final: 0.6995 (mt) REVERT: J 63 LEU cc_start: 0.7327 (OUTLIER) cc_final: 0.7091 (mt) REVERT: J 100 LEU cc_start: 0.7069 (OUTLIER) cc_final: 0.6851 (mt) REVERT: L 100 LEU cc_start: 0.7090 (OUTLIER) cc_final: 0.6865 (mt) outliers start: 60 outliers final: 26 residues processed: 255 average time/residue: 1.0884 time to fit residues: 310.5176 Evaluate side-chains 239 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 202 time to evaluate : 1.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 124 THR 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 81 THR Chi-restraints excluded: chain B residue 119 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 141 GLU Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 143 ILE Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 159 THR Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain F residue 81 THR 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 I residue 63 LEU Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain J residue 63 LEU Chi-restraints excluded: chain J 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 69 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 160 optimal weight: 10.0000 chunk 8 optimal weight: 0.6980 chunk 35 optimal weight: 0.5980 chunk 20 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 146 optimal weight: 6.9990 chunk 150 optimal weight: 10.0000 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** H 127 ASN ** I 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.194522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.126419 restraints weight = 13133.570| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 3.25 r_work: 0.3033 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2904 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2904 ------------------------------------------------------------------------------- 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: 791 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2900 r_free = 0.2900 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 789 | |-----------------------------------------------------------------------------| r_final: 0.2900 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.3599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 15228 Z= 0.269 Angle : 0.655 13.467 20628 Z= 0.347 Chirality : 0.051 0.163 2286 Planarity : 0.004 0.037 2628 Dihedral : 5.324 40.542 2012 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 3.63 % Allowed : 25.61 % Favored : 70.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.20), residues: 1818 helix: None (None), residues: 0 sheet: -0.43 (0.18), residues: 834 loop : -0.55 (0.20), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 34 HIS 0.007 0.001 HIS I 124 PHE 0.018 0.002 PHE K 56 TYR 0.010 0.002 TYR A 20 ARG 0.004 0.001 ARG E 65 Details of bonding type rmsd hydrogen bonds : bond 0.04151 ( 509) hydrogen bonds : angle 6.33463 ( 1365) SS BOND : bond 0.00441 ( 24) SS BOND : angle 0.90198 ( 48) covalent geometry : bond 0.00635 (15204) covalent geometry : angle 0.65399 (20580) ********************** 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 240 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 178 time to evaluate : 1.693 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: 0.8986 (OUTLIER) cc_final: 0.8601 (tm-30) REVERT: A 164 GLU cc_start: 0.8388 (mm-30) cc_final: 0.8111 (mm-30) REVERT: A 165 THR cc_start: 0.8486 (m) cc_final: 0.8148 (m) REVERT: B 39 GLU cc_start: 0.8054 (tm-30) cc_final: 0.7826 (tp30) REVERT: B 49 ASN cc_start: 0.8226 (p0) cc_final: 0.7859 (m-40) REVERT: B 119 ILE cc_start: 0.8873 (OUTLIER) cc_final: 0.8320 (mm) REVERT: C 39 GLU cc_start: 0.8078 (tm-30) cc_final: 0.7786 (tp30) REVERT: C 55 GLU cc_start: 0.8839 (tp30) cc_final: 0.8553 (tp30) REVERT: C 60 GLU cc_start: 0.7785 (tm-30) cc_final: 0.7394 (tm-30) REVERT: C 72 THR cc_start: 0.8880 (p) cc_final: 0.8297 (m) REVERT: C 138 ASP cc_start: 0.8366 (OUTLIER) cc_final: 0.8013 (t70) REVERT: C 141 GLU cc_start: 0.8874 (OUTLIER) cc_final: 0.8443 (tm-30) REVERT: D 49 ASN cc_start: 0.8232 (p0) cc_final: 0.7871 (m110) REVERT: D 165 THR cc_start: 0.8518 (m) cc_final: 0.8174 (m) REVERT: E 39 GLU cc_start: 0.8043 (tm-30) cc_final: 0.7807 (tp30) REVERT: E 49 ASN cc_start: 0.8205 (p0) cc_final: 0.7826 (m-40) REVERT: E 60 GLU cc_start: 0.7639 (tm-30) cc_final: 0.7357 (tm-30) REVERT: E 119 ILE cc_start: 0.8864 (OUTLIER) cc_final: 0.8290 (mm) REVERT: F 72 THR cc_start: 0.8884 (p) cc_final: 0.8287 (m) REVERT: F 138 ASP cc_start: 0.8358 (OUTLIER) cc_final: 0.7953 (t70) REVERT: F 141 GLU cc_start: 0.8892 (OUTLIER) cc_final: 0.8433 (tm-30) REVERT: I 63 LEU cc_start: 0.7172 (OUTLIER) cc_final: 0.6875 (mt) REVERT: J 63 LEU cc_start: 0.7265 (OUTLIER) cc_final: 0.7034 (mt) outliers start: 62 outliers final: 36 residues processed: 227 average time/residue: 1.0451 time to fit residues: 265.3437 Evaluate side-chains 229 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 184 time to evaluate : 1.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 SER 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 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 81 THR Chi-restraints excluded: chain B residue 119 ILE 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 85 THR Chi-restraints excluded: chain C residue 138 ASP 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 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 143 ILE Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 159 THR 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 143 ILE Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 197 THR Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 85 THR Chi-restraints excluded: chain F residue 138 ASP 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 J residue 63 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 54 optimal weight: 0.7980 chunk 48 optimal weight: 0.6980 chunk 139 optimal weight: 1.9990 chunk 124 optimal weight: 10.0000 chunk 133 optimal weight: 1.9990 chunk 61 optimal weight: 0.0980 chunk 174 optimal weight: 9.9990 chunk 62 optimal weight: 0.5980 chunk 91 optimal weight: 0.8980 chunk 98 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 184 HIS ** B 129 ASN ** 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** 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** ** H 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.199026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.135861 restraints weight = 13106.451| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 1.92 r_work: 0.3141 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3059 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3059 r_free = 0.3059 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 = 0.3058 r_free = 0.3058 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 790 | |-----------------------------------------------------------------------------| r_final: 0.3058 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.3564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15228 Z= 0.135 Angle : 0.558 13.775 20628 Z= 0.296 Chirality : 0.046 0.156 2286 Planarity : 0.003 0.035 2628 Dihedral : 5.066 36.497 2012 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 3.16 % Allowed : 26.20 % Favored : 70.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.08 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.20), residues: 1818 helix: None (None), residues: 0 sheet: -0.56 (0.18), residues: 846 loop : -0.43 (0.21), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP I 57 HIS 0.005 0.001 HIS I 124 PHE 0.015 0.001 PHE I 56 TYR 0.007 0.001 TYR A 74 ARG 0.006 0.000 ARG A 191 Details of bonding type rmsd hydrogen bonds : bond 0.03487 ( 509) hydrogen bonds : angle 6.17486 ( 1365) SS BOND : bond 0.00386 ( 24) SS BOND : angle 1.16338 ( 48) covalent geometry : bond 0.00309 (15204) covalent geometry : angle 0.55596 (20580) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12259.63 seconds wall clock time: 211 minutes 22.04 seconds (12682.04 seconds total)