Starting phenix.real_space_refine on Tue Dec 31 03:49:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hxb_35075/12_2024/8hxb_35075.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hxb_35075/12_2024/8hxb_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_35075/12_2024/8hxb_35075.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hxb_35075/12_2024/8hxb_35075.map" model { file = "/net/cci-nas-00/data/ceres_data/8hxb_35075/12_2024/8hxb_35075.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hxb_35075/12_2024/8hxb_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-5532/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: 5.45, 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=3, symmetry=0 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 160 " - pdb=" SG CYS A 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: 3.33 Conformation dependent library (CDL) restraints added in 2.0 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: 2.03 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: 5.49 Time building geometry restraints manager: 3.86 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: 7392 13.42 - 26.84: 1194 26.84 - 40.26: 362 40.26 - 53.68: 123 53.68 - 67.10: 64 Dihedral angle restraints: 9135 sinusoidal: 3675 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 9132 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: 1.97 - 2.56: 113 2.56 - 3.14: 10574 3.14 - 3.73: 22210 3.73 - 4.31: 32683 4.31 - 4.90: 55392 Nonbonded interactions: 120972 Sorted by model distance: nonbonded pdb=" SG CYS C 25 " pdb=" SG CYS D 130 " model vdw 1.970 3.760 nonbonded pdb=" SG CYS A 25 " pdb=" SG CYS B 130 " model vdw 1.986 3.760 nonbonded pdb=" SG CYS B 25 " pdb=" SG CYS C 130 " model vdw 2.006 3.760 nonbonded pdb=" SG CYS B 160 " pdb=" SG CYS B 205 " model vdw 2.022 3.760 nonbonded pdb=" SG CYS F 160 " pdb=" SG CYS F 205 " model vdw 2.023 3.760 ... (remaining 120967 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.93 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.060 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: 0.470 Check model and map are aligned: 0.100 Set scattering table: 0.150 Process input model: 31.830 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:15.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 50.500 ------------------------------------------------------------------------------- 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 15204 Z= 0.468 Angle : 1.150 15.068 20580 Z= 0.581 Chirality : 0.072 0.365 2286 Planarity : 0.006 0.039 2628 Dihedral : 16.218 67.096 5610 Min Nonbonded Distance : 1.970 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 *********************** 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 : 1.649 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: 1.0936 time to fit residues: 427.6843 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 : 1.943 ------------------------------------------------------------------------------- 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: 0.9990 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6780 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 15204 Z= 0.241 Angle : 0.624 9.472 20580 Z= 0.322 Chirality : 0.047 0.184 2286 Planarity : 0.004 0.039 2628 Dihedral : 5.175 30.273 2022 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 4.85 % Allowed : 20.94 % Favored : 74.21 % 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 : -0.73 (0.20), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 57 HIS 0.010 0.001 HIS I 124 PHE 0.020 0.002 PHE H 56 TYR 0.008 0.001 TYR F 74 ARG 0.005 0.001 ARG C 219 *********************** 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 311 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 228 time to evaluate : 1.681 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: 0.7879 (m) cc_final: 0.7640 (m) REVERT: A 186 SER cc_start: 0.8292 (m) cc_final: 0.7910 (p) REVERT: A 187 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.7424 (mt-10) REVERT: A 190 MET cc_start: 0.7826 (OUTLIER) cc_final: 0.7600 (mmm) REVERT: B 39 GLU cc_start: 0.7138 (tm-30) cc_final: 0.6791 (tp30) REVERT: B 47 ASP cc_start: 0.8353 (m-30) cc_final: 0.7940 (m-30) REVERT: B 55 GLU cc_start: 0.7999 (tp30) cc_final: 0.7451 (tp30) REVERT: B 84 ASP cc_start: 0.8158 (OUTLIER) cc_final: 0.7732 (t70) REVERT: B 101 LYS cc_start: 0.8666 (tppt) cc_final: 0.8285 (mmtp) REVERT: B 186 SER cc_start: 0.8350 (m) cc_final: 0.7970 (p) REVERT: C 39 GLU cc_start: 0.7429 (tm-30) cc_final: 0.6979 (tp30) REVERT: C 85 THR cc_start: 0.8496 (p) cc_final: 0.7083 (t) REVERT: C 101 LYS cc_start: 0.8625 (tppt) cc_final: 0.8271 (mmtp) REVERT: C 119 ILE cc_start: 0.8492 (OUTLIER) cc_final: 0.8052 (mm) REVERT: C 186 SER cc_start: 0.8215 (m) cc_final: 0.7752 (p) REVERT: C 190 MET cc_start: 0.7725 (mmp) cc_final: 0.7433 (mmm) REVERT: D 47 ASP cc_start: 0.8301 (m-30) cc_final: 0.8039 (m-30) REVERT: D 83 MET cc_start: 0.8573 (mmm) cc_final: 0.8029 (mmt) REVERT: D 85 THR cc_start: 0.8547 (p) cc_final: 0.7308 (t) REVERT: D 159 THR cc_start: 0.8585 (m) cc_final: 0.8318 (p) REVERT: D 184 HIS cc_start: 0.8397 (p90) cc_final: 0.8074 (p-80) REVERT: D 186 SER cc_start: 0.8206 (m) cc_final: 0.7848 (p) REVERT: E 39 GLU cc_start: 0.7144 (tm-30) cc_final: 0.6797 (tm-30) REVERT: E 55 GLU cc_start: 0.8138 (tp30) cc_final: 0.7707 (tp30) REVERT: E 64 ASP cc_start: 0.8082 (t0) cc_final: 0.7879 (OUTLIER) REVERT: E 85 THR cc_start: 0.8584 (p) cc_final: 0.7173 (t) REVERT: E 101 LYS cc_start: 0.8663 (tppt) cc_final: 0.8363 (tppt) REVERT: E 175 LEU cc_start: 0.7716 (OUTLIER) cc_final: 0.7418 (mm) REVERT: E 186 SER cc_start: 0.8490 (m) cc_final: 0.8084 (p) REVERT: F 47 ASP cc_start: 0.8459 (m-30) cc_final: 0.8068 (m-30) REVERT: F 80 MET cc_start: 0.8950 (ttm) cc_final: 0.8595 (ttt) REVERT: F 101 LYS cc_start: 0.8639 (tppt) cc_final: 0.8314 (mmtp) REVERT: F 141 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.8272 (tm-30) REVERT: F 186 SER cc_start: 0.8218 (m) cc_final: 0.7848 (p) REVERT: F 187 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7547 (mt-10) REVERT: G 100 LEU cc_start: 0.7259 (OUTLIER) cc_final: 0.7034 (mt) REVERT: G 120 MET cc_start: 0.7923 (ttp) cc_final: 0.7629 (ttt) REVERT: H 100 LEU cc_start: 0.7471 (OUTLIER) cc_final: 0.7138 (mt) REVERT: I 100 LEU cc_start: 0.7287 (OUTLIER) cc_final: 0.7023 (mt) REVERT: J 100 LEU cc_start: 0.6964 (OUTLIER) cc_final: 0.6725 (mt) REVERT: L 100 LEU cc_start: 0.7301 (OUTLIER) cc_final: 0.7052 (mt) outliers start: 83 outliers final: 42 residues processed: 282 average time/residue: 1.0505 time to fit residues: 333.0288 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 : 1.722 ------------------------------------------------------------------------------- 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 187 GLU Chi-restraints excluded: chain A residue 190 MET 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 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 175 LEU Chi-restraints excluded: chain E residue 193 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 187 GLU 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 90 optimal weight: 0.9990 chunk 50 optimal weight: 0.8980 chunk 136 optimal weight: 10.0000 chunk 111 optimal weight: 4.9990 chunk 45 optimal weight: 0.6980 chunk 163 optimal weight: 0.9980 chunk 176 optimal weight: 8.9990 chunk 145 optimal weight: 1.9990 chunk 162 optimal weight: 0.1980 chunk 55 optimal weight: 1.9990 chunk 131 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 116 HIS ** C 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6827 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15204 Z= 0.227 Angle : 0.586 8.405 20580 Z= 0.307 Chirality : 0.047 0.168 2286 Planarity : 0.004 0.037 2628 Dihedral : 4.991 33.190 2012 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 6.08 % Allowed : 19.94 % Favored : 73.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.20), residues: 1818 helix: None (None), residues: 0 sheet: -0.50 (0.17), residues: 840 loop : -0.55 (0.21), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 57 HIS 0.008 0.001 HIS I 124 PHE 0.020 0.001 PHE H 56 TYR 0.009 0.001 TYR B 183 ARG 0.006 0.000 ARG A 191 *********************** 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 321 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 217 time to evaluate : 1.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.6744 (tm-30) cc_final: 0.6309 (tm-30) REVERT: A 165 THR cc_start: 0.7821 (m) cc_final: 0.7575 (m) REVERT: A 184 HIS cc_start: 0.8761 (OUTLIER) cc_final: 0.8487 (p-80) REVERT: A 186 SER cc_start: 0.8257 (m) cc_final: 0.7832 (p) REVERT: B 39 GLU cc_start: 0.7150 (tm-30) cc_final: 0.6864 (tp30) REVERT: B 55 GLU cc_start: 0.8165 (tp30) cc_final: 0.7678 (tp30) REVERT: B 119 ILE cc_start: 0.8349 (OUTLIER) cc_final: 0.7877 (mm) REVERT: B 138 ASP cc_start: 0.8033 (OUTLIER) cc_final: 0.7707 (m-30) REVERT: B 186 SER cc_start: 0.8261 (m) cc_final: 0.7840 (p) REVERT: C 39 GLU cc_start: 0.7235 (tm-30) cc_final: 0.6778 (tp30) REVERT: C 72 THR cc_start: 0.7899 (p) cc_final: 0.7332 (m) REVERT: C 85 THR cc_start: 0.8537 (p) cc_final: 0.7032 (t) REVERT: C 141 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.8276 (tm-30) REVERT: C 186 SER cc_start: 0.8193 (m) cc_final: 0.7712 (p) REVERT: C 187 GLU cc_start: 0.7863 (mt-10) cc_final: 0.7634 (mt-10) REVERT: C 190 MET cc_start: 0.7807 (mmp) cc_final: 0.7540 (mmm) REVERT: D 47 ASP cc_start: 0.8406 (m-30) cc_final: 0.8141 (m-30) REVERT: D 60 GLU cc_start: 0.6801 (tm-30) cc_final: 0.6340 (tm-30) REVERT: D 85 THR cc_start: 0.8582 (p) cc_final: 0.7319 (t) REVERT: D 165 THR cc_start: 0.7867 (m) cc_final: 0.7565 (m) REVERT: D 184 HIS cc_start: 0.8538 (p90) cc_final: 0.8226 (p-80) REVERT: D 186 SER cc_start: 0.8294 (m) cc_final: 0.7960 (p) REVERT: D 187 GLU cc_start: 0.7879 (mt-10) cc_final: 0.7670 (mt-10) REVERT: E 39 GLU cc_start: 0.7126 (tm-30) cc_final: 0.6844 (tp30) REVERT: E 60 GLU cc_start: 0.6393 (OUTLIER) cc_final: 0.5859 (tm-30) REVERT: E 85 THR cc_start: 0.8548 (p) cc_final: 0.7370 (t) REVERT: E 101 LYS cc_start: 0.8655 (tppt) cc_final: 0.8202 (mmtp) REVERT: E 138 ASP cc_start: 0.7956 (OUTLIER) cc_final: 0.7542 (m-30) REVERT: E 175 LEU cc_start: 0.7888 (OUTLIER) cc_final: 0.7566 (mm) REVERT: E 186 SER cc_start: 0.8301 (m) cc_final: 0.7919 (p) REVERT: F 39 GLU cc_start: 0.7170 (tm-30) cc_final: 0.6719 (tp30) REVERT: F 47 ASP cc_start: 0.8560 (m-30) cc_final: 0.8195 (m-30) REVERT: F 141 GLU cc_start: 0.8546 (OUTLIER) cc_final: 0.8195 (tm-30) REVERT: F 165 THR cc_start: 0.7846 (m) cc_final: 0.7591 (p) REVERT: F 186 SER cc_start: 0.8163 (m) cc_final: 0.7762 (p) REVERT: F 190 MET cc_start: 0.7849 (mmp) cc_final: 0.7629 (mmm) REVERT: F 220 GLU cc_start: 0.6152 (OUTLIER) cc_final: 0.5786 (mm-30) REVERT: G 100 LEU cc_start: 0.7262 (OUTLIER) cc_final: 0.7010 (mt) REVERT: G 120 MET cc_start: 0.8080 (ttp) cc_final: 0.7760 (ttt) REVERT: I 100 LEU cc_start: 0.7357 (OUTLIER) cc_final: 0.7069 (mt) REVERT: J 100 LEU cc_start: 0.7033 (OUTLIER) cc_final: 0.6791 (mt) REVERT: L 100 LEU cc_start: 0.7360 (OUTLIER) cc_final: 0.7086 (mt) outliers start: 104 outliers final: 45 residues processed: 296 average time/residue: 1.0875 time to fit residues: 363.0578 Evaluate side-chains 261 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 203 time to evaluate : 1.704 ------------------------------------------------------------------------------- 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 184 HIS Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 81 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 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 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 60 GLU 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 175 LEU 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 84 ASP Chi-restraints excluded: chain F residue 85 THR Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain F residue 141 GLU Chi-restraints excluded: chain F residue 143 ILE Chi-restraints excluded: chain F residue 152 THR Chi-restraints excluded: chain F residue 193 SER Chi-restraints excluded: chain F residue 220 GLU Chi-restraints excluded: chain G residue 100 LEU 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 161 optimal weight: 5.9990 chunk 123 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 78 optimal weight: 4.9990 chunk 109 optimal weight: 3.9990 chunk 164 optimal weight: 10.0000 chunk 173 optimal weight: 0.9980 chunk 85 optimal weight: 0.4980 chunk 155 optimal weight: 8.9990 chunk 46 optimal weight: 1.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 184 HIS B 116 HIS ** B 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 116 HIS ** E 176 HIS ** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6889 moved from start: 0.2910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 15204 Z= 0.348 Angle : 0.634 9.255 20580 Z= 0.334 Chirality : 0.050 0.169 2286 Planarity : 0.004 0.038 2628 Dihedral : 5.316 37.575 2012 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 5.61 % Allowed : 20.18 % Favored : 74.21 % 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: -0.85 (0.20), residues: 1818 helix: None (None), residues: 0 sheet: -0.50 (0.17), residues: 846 loop : -0.50 (0.21), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 34 HIS 0.010 0.001 HIS A 184 PHE 0.020 0.002 PHE K 56 TYR 0.011 0.002 TYR B 183 ARG 0.004 0.000 ARG A 219 *********************** 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 305 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 209 time to evaluate : 1.762 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: 0.7353 (tm-30) cc_final: 0.6955 (tp30) REVERT: A 49 ASN cc_start: 0.7753 (OUTLIER) cc_final: 0.7308 (m110) REVERT: A 60 GLU cc_start: 0.6838 (tm-30) cc_final: 0.6545 (tm-30) REVERT: A 84 ASP cc_start: 0.7922 (OUTLIER) cc_final: 0.7692 (t70) REVERT: A 88 ARG cc_start: 0.8798 (ptp-110) cc_final: 0.8586 (ptp-110) REVERT: A 165 THR cc_start: 0.7891 (m) cc_final: 0.7629 (m) REVERT: A 184 HIS cc_start: 0.8562 (OUTLIER) cc_final: 0.8143 (p-80) REVERT: A 186 SER cc_start: 0.8208 (m) cc_final: 0.7814 (p) REVERT: B 39 GLU cc_start: 0.7115 (tm-30) cc_final: 0.6804 (tp30) REVERT: B 83 MET cc_start: 0.8551 (mmt) cc_final: 0.8321 (mmm) REVERT: B 84 ASP cc_start: 0.8045 (OUTLIER) cc_final: 0.7797 (t70) REVERT: B 119 ILE cc_start: 0.8407 (OUTLIER) cc_final: 0.7917 (mm) REVERT: B 138 ASP cc_start: 0.8052 (OUTLIER) cc_final: 0.7675 (m-30) REVERT: B 186 SER cc_start: 0.8328 (m) cc_final: 0.7925 (p) REVERT: B 187 GLU cc_start: 0.7927 (mt-10) cc_final: 0.7720 (mt-10) REVERT: C 39 GLU cc_start: 0.7210 (tm-30) cc_final: 0.6819 (tp30) REVERT: C 72 THR cc_start: 0.7958 (p) cc_final: 0.7388 (m) REVERT: C 80 MET cc_start: 0.9179 (OUTLIER) cc_final: 0.8874 (ttt) REVERT: C 88 ARG cc_start: 0.8789 (ptp-110) cc_final: 0.8466 (ptp90) REVERT: C 141 GLU cc_start: 0.8661 (OUTLIER) cc_final: 0.8353 (tm-30) REVERT: C 186 SER cc_start: 0.8228 (m) cc_final: 0.7823 (p) REVERT: C 220 GLU cc_start: 0.6140 (OUTLIER) cc_final: 0.4605 (mp0) REVERT: D 39 GLU cc_start: 0.7344 (tm-30) cc_final: 0.6930 (tp30) REVERT: D 85 THR cc_start: 0.8618 (p) cc_final: 0.7499 (t) REVERT: D 165 THR cc_start: 0.7907 (OUTLIER) cc_final: 0.7620 (m) REVERT: D 186 SER cc_start: 0.8310 (m) cc_final: 0.8003 (p) REVERT: D 187 GLU cc_start: 0.7938 (mt-10) cc_final: 0.7729 (mt-10) REVERT: E 39 GLU cc_start: 0.7109 (tm-30) cc_final: 0.6776 (tp30) REVERT: E 58 MET cc_start: 0.8514 (ptm) cc_final: 0.8287 (ptm) REVERT: E 138 ASP cc_start: 0.8029 (OUTLIER) cc_final: 0.7625 (m-30) REVERT: E 175 LEU cc_start: 0.7885 (pp) cc_final: 0.7508 (mm) REVERT: E 186 SER cc_start: 0.8334 (m) cc_final: 0.7955 (p) REVERT: E 187 GLU cc_start: 0.7975 (mt-10) cc_final: 0.7749 (mt-10) REVERT: F 39 GLU cc_start: 0.7305 (tm-30) cc_final: 0.6907 (tp30) REVERT: F 47 ASP cc_start: 0.8615 (m-30) cc_final: 0.8285 (m-30) REVERT: F 60 GLU cc_start: 0.6559 (OUTLIER) cc_final: 0.6103 (tm-30) REVERT: F 72 THR cc_start: 0.7994 (p) cc_final: 0.7417 (m) REVERT: F 80 MET cc_start: 0.9048 (ttm) cc_final: 0.8814 (ttt) REVERT: F 141 GLU cc_start: 0.8659 (OUTLIER) cc_final: 0.8347 (tm-30) REVERT: F 165 THR cc_start: 0.7817 (m) cc_final: 0.7573 (p) REVERT: F 186 SER cc_start: 0.8232 (m) cc_final: 0.7847 (p) REVERT: F 187 GLU cc_start: 0.7980 (mt-10) cc_final: 0.7761 (mt-10) REVERT: F 220 GLU cc_start: 0.6416 (OUTLIER) cc_final: 0.6040 (mm-30) REVERT: G 100 LEU cc_start: 0.7318 (OUTLIER) cc_final: 0.7056 (mt) REVERT: G 120 MET cc_start: 0.8255 (ttp) cc_final: 0.7967 (ttt) REVERT: G 126 MET cc_start: 0.7958 (OUTLIER) cc_final: 0.7550 (ttp) REVERT: I 100 LEU cc_start: 0.7478 (OUTLIER) cc_final: 0.7145 (mt) REVERT: J 100 LEU cc_start: 0.7231 (OUTLIER) cc_final: 0.6969 (mt) REVERT: L 100 LEU cc_start: 0.7468 (OUTLIER) cc_final: 0.7132 (mt) outliers start: 96 outliers final: 53 residues processed: 278 average time/residue: 1.1564 time to fit residues: 356.9627 Evaluate side-chains 263 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 191 time to evaluate : 1.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 49 ASN Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 84 ASP 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 159 THR Chi-restraints excluded: chain A residue 184 HIS Chi-restraints excluded: chain A residue 190 MET 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 84 ASP 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 141 GLU Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 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 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 59 SER Chi-restraints excluded: chain E residue 60 GLU Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 138 ASP Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 193 SER Chi-restraints excluded: chain E residue 197 THR Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 59 SER Chi-restraints excluded: chain F residue 60 GLU Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 85 THR Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain F residue 141 GLU Chi-restraints excluded: chain F residue 143 ILE Chi-restraints excluded: chain F residue 152 THR Chi-restraints excluded: chain F residue 193 SER Chi-restraints excluded: chain F residue 220 GLU Chi-restraints excluded: chain G residue 100 LEU 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 K residue 100 LEU Chi-restraints excluded: chain K residue 120 MET 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 144 optimal weight: 0.6980 chunk 98 optimal weight: 0.0570 chunk 2 optimal weight: 0.9990 chunk 129 optimal weight: 0.1980 chunk 71 optimal weight: 0.4980 chunk 148 optimal weight: 0.9990 chunk 120 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 156 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 overall best weight: 0.4098 ------------------------------------------------------------------------------- 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** E 68 ASN E 171 ASN ** E 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 58 GLN K 109 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6832 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 15204 Z= 0.168 Angle : 0.536 7.150 20580 Z= 0.285 Chirality : 0.045 0.155 2286 Planarity : 0.003 0.035 2628 Dihedral : 4.954 33.700 2012 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 5.91 % Allowed : 21.05 % Favored : 73.04 % 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: -0.52 (0.17), residues: 846 loop : -0.42 (0.21), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 57 HIS 0.016 0.001 HIS A 184 PHE 0.020 0.001 PHE K 56 TYR 0.008 0.001 TYR A 183 ARG 0.003 0.000 ARG C 219 *********************** 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 297 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 196 time to evaluate : 1.746 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: 0.7252 (tm-30) cc_final: 0.6950 (tp30) REVERT: A 49 ASN cc_start: 0.7576 (p0) cc_final: 0.7247 (m110) REVERT: A 60 GLU cc_start: 0.6804 (tm-30) cc_final: 0.6362 (tm-30) REVERT: A 94 GLU cc_start: 0.8382 (mt-10) cc_final: 0.8168 (mt-10) REVERT: A 141 GLU cc_start: 0.8676 (OUTLIER) cc_final: 0.8378 (tm-30) REVERT: A 165 THR cc_start: 0.7861 (m) cc_final: 0.7611 (m) REVERT: A 186 SER cc_start: 0.8023 (m) cc_final: 0.7601 (p) REVERT: B 39 GLU cc_start: 0.7126 (tm-30) cc_final: 0.6784 (tp30) REVERT: B 49 ASN cc_start: 0.7678 (p0) cc_final: 0.7279 (m-40) REVERT: B 119 ILE cc_start: 0.8385 (OUTLIER) cc_final: 0.7911 (mm) REVERT: B 138 ASP cc_start: 0.7995 (OUTLIER) cc_final: 0.7711 (m-30) REVERT: B 186 SER cc_start: 0.8234 (m) cc_final: 0.7799 (p) REVERT: C 39 GLU cc_start: 0.7127 (tm-30) cc_final: 0.6723 (tp30) REVERT: C 80 MET cc_start: 0.9145 (OUTLIER) cc_final: 0.8820 (ttt) REVERT: C 101 LYS cc_start: 0.8625 (OUTLIER) cc_final: 0.7637 (mppt) REVERT: C 110 GLN cc_start: 0.8239 (tt0) cc_final: 0.7999 (tt0) REVERT: C 141 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.8104 (tm-30) REVERT: C 186 SER cc_start: 0.8276 (m) cc_final: 0.7816 (p) REVERT: D 85 THR cc_start: 0.8661 (p) cc_final: 0.7332 (t) REVERT: D 141 GLU cc_start: 0.8708 (OUTLIER) cc_final: 0.8408 (tm-30) REVERT: D 165 THR cc_start: 0.7836 (m) cc_final: 0.7575 (m) REVERT: D 186 SER cc_start: 0.8260 (m) cc_final: 0.7931 (p) REVERT: D 187 GLU cc_start: 0.7800 (mt-10) cc_final: 0.7580 (mt-10) REVERT: E 39 GLU cc_start: 0.7100 (tm-30) cc_final: 0.6772 (tp30) REVERT: E 58 MET cc_start: 0.8514 (ptm) cc_final: 0.8251 (ptm) REVERT: E 80 MET cc_start: 0.8971 (ttm) cc_final: 0.8620 (ttt) REVERT: E 84 ASP cc_start: 0.8006 (OUTLIER) cc_final: 0.7767 (t70) REVERT: E 138 ASP cc_start: 0.7960 (OUTLIER) cc_final: 0.7660 (m-30) REVERT: E 175 LEU cc_start: 0.7871 (OUTLIER) cc_final: 0.7457 (mm) REVERT: E 186 SER cc_start: 0.8253 (m) cc_final: 0.7830 (p) REVERT: E 187 GLU cc_start: 0.7825 (mt-10) cc_final: 0.7614 (mt-10) REVERT: F 39 GLU cc_start: 0.7123 (tm-30) cc_final: 0.6719 (tp30) REVERT: F 60 GLU cc_start: 0.6280 (OUTLIER) cc_final: 0.5903 (tm-30) REVERT: F 80 MET cc_start: 0.9037 (ttm) cc_final: 0.8777 (ttt) REVERT: F 101 LYS cc_start: 0.8607 (OUTLIER) cc_final: 0.7576 (mppt) REVERT: F 110 GLN cc_start: 0.8246 (tt0) cc_final: 0.8035 (tt0) REVERT: F 141 GLU cc_start: 0.8523 (OUTLIER) cc_final: 0.8230 (tm-30) REVERT: F 186 SER cc_start: 0.8164 (m) cc_final: 0.7742 (p) REVERT: G 63 LEU cc_start: 0.8196 (OUTLIER) cc_final: 0.7924 (mt) REVERT: G 100 LEU cc_start: 0.7215 (OUTLIER) cc_final: 0.6959 (mt) REVERT: G 120 MET cc_start: 0.8196 (ttp) cc_final: 0.7900 (ttt) REVERT: H 63 LEU cc_start: 0.8204 (OUTLIER) cc_final: 0.7958 (mt) REVERT: I 100 LEU cc_start: 0.7357 (OUTLIER) cc_final: 0.7033 (mt) REVERT: J 63 LEU cc_start: 0.8223 (OUTLIER) cc_final: 0.7914 (mt) REVERT: J 100 LEU cc_start: 0.7238 (OUTLIER) cc_final: 0.6997 (mt) REVERT: L 63 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.8036 (mt) REVERT: L 100 LEU cc_start: 0.7419 (OUTLIER) cc_final: 0.7100 (mt) outliers start: 101 outliers final: 40 residues processed: 271 average time/residue: 1.1413 time to fit residues: 344.4594 Evaluate side-chains 256 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 195 time to evaluate : 1.847 ------------------------------------------------------------------------------- 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 190 MET Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 127 GLU Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 193 SER Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 59 SER Chi-restraints excluded: chain C residue 80 MET Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 101 LYS Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 141 GLU Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 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 141 GLU Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 159 THR Chi-restraints excluded: chain E residue 59 SER Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain E residue 84 ASP 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 175 LEU Chi-restraints excluded: chain E residue 193 SER Chi-restraints excluded: chain F residue 59 SER Chi-restraints excluded: chain F residue 60 GLU Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 85 THR Chi-restraints excluded: chain F residue 101 LYS 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 G residue 63 LEU Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain G residue 126 MET Chi-restraints excluded: chain H 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 63 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 58 optimal weight: 0.1980 chunk 156 optimal weight: 10.0000 chunk 34 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 174 optimal weight: 8.9990 chunk 144 optimal weight: 0.4980 chunk 80 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 91 optimal weight: 0.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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** ** B 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 116 HIS ** D 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6895 moved from start: 0.3234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 15204 Z= 0.325 Angle : 0.601 8.035 20580 Z= 0.321 Chirality : 0.049 0.158 2286 Planarity : 0.004 0.037 2628 Dihedral : 5.270 37.043 2012 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 6.55 % Allowed : 21.58 % Favored : 71.87 % 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: -0.48 (0.18), residues: 846 loop : -0.45 (0.21), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 34 HIS 0.006 0.001 HIS I 124 PHE 0.023 0.002 PHE K 56 TYR 0.010 0.001 TYR B 183 ARG 0.003 0.000 ARG C 65 *********************** 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 301 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 189 time to evaluate : 1.698 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: 0.7306 (tm-30) cc_final: 0.6968 (tp30) REVERT: A 49 ASN cc_start: 0.7682 (p0) cc_final: 0.7321 (m110) REVERT: A 60 GLU cc_start: 0.6862 (tm-30) cc_final: 0.6516 (tm-30) REVERT: A 141 GLU cc_start: 0.8763 (OUTLIER) cc_final: 0.8389 (tm-30) REVERT: A 165 THR cc_start: 0.7878 (m) cc_final: 0.7638 (m) REVERT: A 186 SER cc_start: 0.8226 (m) cc_final: 0.7781 (p) REVERT: B 39 GLU cc_start: 0.7151 (tm-30) cc_final: 0.6830 (tp30) REVERT: B 49 ASN cc_start: 0.7725 (p0) cc_final: 0.7346 (m-40) REVERT: B 60 GLU cc_start: 0.6947 (tm-30) cc_final: 0.6641 (tm-30) REVERT: B 119 ILE cc_start: 0.8468 (OUTLIER) cc_final: 0.7957 (mm) REVERT: B 138 ASP cc_start: 0.8031 (OUTLIER) cc_final: 0.7670 (m-30) REVERT: B 186 SER cc_start: 0.8328 (m) cc_final: 0.7905 (p) REVERT: B 187 GLU cc_start: 0.7856 (mt-10) cc_final: 0.7624 (mt-10) REVERT: C 39 GLU cc_start: 0.7291 (tm-30) cc_final: 0.6877 (tp30) REVERT: C 72 THR cc_start: 0.7991 (p) cc_final: 0.7448 (m) REVERT: C 80 MET cc_start: 0.9186 (OUTLIER) cc_final: 0.8895 (ttt) REVERT: C 101 LYS cc_start: 0.8664 (OUTLIER) cc_final: 0.7653 (mppt) REVERT: C 141 GLU cc_start: 0.8619 (OUTLIER) cc_final: 0.8299 (tm-30) REVERT: C 186 SER cc_start: 0.8344 (m) cc_final: 0.7923 (p) REVERT: D 39 GLU cc_start: 0.7303 (tm-30) cc_final: 0.6890 (tp30) REVERT: D 49 ASN cc_start: 0.7731 (OUTLIER) cc_final: 0.7326 (m110) REVERT: D 72 THR cc_start: 0.8084 (p) cc_final: 0.7421 (m) REVERT: D 141 GLU cc_start: 0.8810 (OUTLIER) cc_final: 0.8380 (tm-30) REVERT: D 165 THR cc_start: 0.7872 (OUTLIER) cc_final: 0.7598 (m) REVERT: D 169 LYS cc_start: 0.8474 (OUTLIER) cc_final: 0.7833 (pmtt) REVERT: D 186 SER cc_start: 0.8302 (m) cc_final: 0.7986 (p) REVERT: D 187 GLU cc_start: 0.7904 (mt-10) cc_final: 0.7667 (mt-10) REVERT: E 39 GLU cc_start: 0.7112 (tm-30) cc_final: 0.6788 (tp30) REVERT: E 49 ASN cc_start: 0.7780 (p0) cc_final: 0.7333 (m-40) REVERT: E 58 MET cc_start: 0.8551 (ptm) cc_final: 0.8312 (ptm) REVERT: E 60 GLU cc_start: 0.6502 (tm-30) cc_final: 0.6147 (tm-30) REVERT: E 84 ASP cc_start: 0.8003 (OUTLIER) cc_final: 0.7711 (t70) REVERT: E 138 ASP cc_start: 0.8041 (OUTLIER) cc_final: 0.7689 (m-30) REVERT: E 175 LEU cc_start: 0.7858 (pp) cc_final: 0.7428 (mm) REVERT: E 186 SER cc_start: 0.8334 (m) cc_final: 0.7920 (p) REVERT: F 39 GLU cc_start: 0.7292 (tm-30) cc_final: 0.6898 (tp30) REVERT: F 47 ASP cc_start: 0.8589 (m-30) cc_final: 0.8264 (m-30) REVERT: F 60 GLU cc_start: 0.6472 (OUTLIER) cc_final: 0.6003 (tm-30) REVERT: F 72 THR cc_start: 0.7941 (p) cc_final: 0.7409 (m) REVERT: F 80 MET cc_start: 0.9064 (ttm) cc_final: 0.8774 (ttt) REVERT: F 101 LYS cc_start: 0.8653 (OUTLIER) cc_final: 0.7640 (mppt) REVERT: F 141 GLU cc_start: 0.8639 (OUTLIER) cc_final: 0.8319 (tm-30) REVERT: F 186 SER cc_start: 0.8353 (m) cc_final: 0.7956 (p) REVERT: F 220 GLU cc_start: 0.6406 (OUTLIER) cc_final: 0.5964 (mm-30) REVERT: G 63 LEU cc_start: 0.8224 (OUTLIER) cc_final: 0.7960 (mt) REVERT: G 100 LEU cc_start: 0.7337 (OUTLIER) cc_final: 0.7073 (mt) REVERT: G 120 MET cc_start: 0.8297 (ttp) cc_final: 0.7993 (ttt) REVERT: H 63 LEU cc_start: 0.8275 (OUTLIER) cc_final: 0.8074 (mt) REVERT: I 63 LEU cc_start: 0.8210 (OUTLIER) cc_final: 0.7863 (mt) REVERT: I 100 LEU cc_start: 0.7494 (OUTLIER) cc_final: 0.7134 (mt) REVERT: J 63 LEU cc_start: 0.8259 (OUTLIER) cc_final: 0.7963 (mt) REVERT: J 100 LEU cc_start: 0.7362 (OUTLIER) cc_final: 0.7103 (mt) REVERT: J 118 THR cc_start: 0.7388 (OUTLIER) cc_final: 0.7015 (t) REVERT: L 63 LEU cc_start: 0.8226 (OUTLIER) cc_final: 0.8022 (mt) outliers start: 112 outliers final: 58 residues processed: 279 average time/residue: 1.1283 time to fit residues: 350.5875 Evaluate side-chains 265 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 182 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 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 190 MET 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 85 THR Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 127 GLU Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 193 SER Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 59 SER Chi-restraints excluded: chain C residue 60 GLU Chi-restraints excluded: chain C residue 80 MET Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 101 LYS Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 141 GLU Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 193 SER Chi-restraints excluded: chain 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 124 THR Chi-restraints excluded: chain D residue 141 GLU Chi-restraints excluded: chain D residue 143 ILE Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 159 THR Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 169 LYS Chi-restraints excluded: chain D residue 193 SER Chi-restraints excluded: chain E residue 59 SER Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain E residue 84 ASP Chi-restraints excluded: chain E residue 85 THR 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 101 LYS Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain F residue 141 GLU Chi-restraints excluded: chain F residue 143 ILE Chi-restraints excluded: chain F residue 152 THR Chi-restraints excluded: chain F residue 193 SER Chi-restraints excluded: chain F residue 220 GLU Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain I residue 63 LEU Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain J residue 63 LEU Chi-restraints excluded: chain J residue 100 LEU Chi-restraints excluded: chain J residue 118 THR Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain L residue 63 LEU Chi-restraints excluded: chain L residue 100 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 167 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 99 optimal weight: 5.9990 chunk 127 optimal weight: 8.9990 chunk 98 optimal weight: 0.9980 chunk 146 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 173 optimal weight: 0.8980 chunk 108 optimal weight: 0.9980 chunk 105 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 58 GLN H 109 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6878 moved from start: 0.3301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15204 Z= 0.254 Angle : 0.560 6.710 20580 Z= 0.300 Chirality : 0.047 0.154 2286 Planarity : 0.003 0.036 2628 Dihedral : 5.130 35.113 2012 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 5.91 % Allowed : 22.51 % Favored : 71.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.49 (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 G 57 HIS 0.005 0.001 HIS I 124 PHE 0.022 0.001 PHE K 56 TYR 0.008 0.001 TYR B 183 ARG 0.002 0.000 ARG F 111 *********************** 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 286 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 185 time to evaluate : 1.584 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: 0.7274 (tm-30) cc_final: 0.6904 (tp30) REVERT: A 49 ASN cc_start: 0.7676 (OUTLIER) cc_final: 0.7371 (m110) REVERT: A 60 GLU cc_start: 0.6888 (tm-30) cc_final: 0.6484 (tm-30) REVERT: A 141 GLU cc_start: 0.8653 (OUTLIER) cc_final: 0.8307 (tm-30) REVERT: A 164 GLU cc_start: 0.7555 (mm-30) cc_final: 0.7312 (mm-30) REVERT: A 165 THR cc_start: 0.7875 (OUTLIER) cc_final: 0.7630 (m) REVERT: A 186 SER cc_start: 0.8265 (m) cc_final: 0.7844 (p) REVERT: B 39 GLU cc_start: 0.7152 (tm-30) cc_final: 0.6817 (tp30) REVERT: B 49 ASN cc_start: 0.7699 (p0) cc_final: 0.7378 (m-40) REVERT: B 60 GLU cc_start: 0.6857 (tm-30) cc_final: 0.6543 (tm-30) REVERT: B 119 ILE cc_start: 0.8437 (OUTLIER) cc_final: 0.7900 (mm) REVERT: B 138 ASP cc_start: 0.7960 (OUTLIER) cc_final: 0.7665 (m-30) REVERT: B 186 SER cc_start: 0.8307 (m) cc_final: 0.7867 (p) REVERT: B 187 GLU cc_start: 0.7798 (mt-10) cc_final: 0.7569 (mt-10) REVERT: C 39 GLU cc_start: 0.7159 (tm-30) cc_final: 0.6736 (tp30) REVERT: C 72 THR cc_start: 0.7915 (p) cc_final: 0.7405 (m) REVERT: C 80 MET cc_start: 0.9172 (OUTLIER) cc_final: 0.8845 (ttt) REVERT: C 141 GLU cc_start: 0.8569 (OUTLIER) cc_final: 0.8252 (tm-30) REVERT: C 186 SER cc_start: 0.8362 (m) cc_final: 0.7926 (p) REVERT: D 39 GLU cc_start: 0.7280 (tm-30) cc_final: 0.6902 (tp30) REVERT: D 49 ASN cc_start: 0.7666 (OUTLIER) cc_final: 0.7331 (m110) REVERT: D 141 GLU cc_start: 0.8705 (OUTLIER) cc_final: 0.8335 (tm-30) REVERT: D 165 THR cc_start: 0.7852 (m) cc_final: 0.7588 (m) REVERT: D 186 SER cc_start: 0.8295 (m) cc_final: 0.7985 (p) REVERT: E 39 GLU cc_start: 0.7084 (tm-30) cc_final: 0.6755 (tp30) REVERT: E 49 ASN cc_start: 0.7736 (p0) cc_final: 0.7346 (m110) REVERT: E 58 MET cc_start: 0.8576 (ptm) cc_final: 0.8362 (ptm) REVERT: E 60 GLU cc_start: 0.6435 (tm-30) cc_final: 0.6084 (tm-30) REVERT: E 84 ASP cc_start: 0.8013 (OUTLIER) cc_final: 0.7726 (t70) REVERT: E 138 ASP cc_start: 0.7980 (OUTLIER) cc_final: 0.7637 (m-30) REVERT: E 186 SER cc_start: 0.8307 (m) cc_final: 0.7881 (p) REVERT: F 39 GLU cc_start: 0.7264 (tm-30) cc_final: 0.6868 (tp30) REVERT: F 55 GLU cc_start: 0.8091 (tp30) cc_final: 0.7837 (tp30) REVERT: F 80 MET cc_start: 0.9112 (ttm) cc_final: 0.8818 (ttt) REVERT: F 141 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.8274 (tm-30) REVERT: F 186 SER cc_start: 0.8347 (m) cc_final: 0.7922 (p) REVERT: F 220 GLU cc_start: 0.6472 (OUTLIER) cc_final: 0.6020 (mm-30) REVERT: G 63 LEU cc_start: 0.8212 (OUTLIER) cc_final: 0.7943 (mt) REVERT: G 100 LEU cc_start: 0.7327 (OUTLIER) cc_final: 0.7054 (mt) REVERT: G 118 THR cc_start: 0.7314 (OUTLIER) cc_final: 0.7035 (t) REVERT: G 120 MET cc_start: 0.8311 (ttp) cc_final: 0.8005 (ttt) REVERT: H 63 LEU cc_start: 0.8221 (OUTLIER) cc_final: 0.8014 (mt) REVERT: I 63 LEU cc_start: 0.8190 (OUTLIER) cc_final: 0.7851 (mt) REVERT: I 100 LEU cc_start: 0.7463 (OUTLIER) cc_final: 0.7089 (mt) REVERT: J 63 LEU cc_start: 0.8242 (OUTLIER) cc_final: 0.7950 (mt) REVERT: J 100 LEU cc_start: 0.7285 (OUTLIER) cc_final: 0.7049 (mt) REVERT: J 118 THR cc_start: 0.7309 (OUTLIER) cc_final: 0.7062 (t) REVERT: L 63 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.8020 (mt) outliers start: 101 outliers final: 52 residues processed: 265 average time/residue: 1.1386 time to fit residues: 336.8927 Evaluate side-chains 263 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 188 time to evaluate : 1.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 49 ASN Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 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 165 THR Chi-restraints excluded: chain A residue 190 MET 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 85 THR Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 127 GLU Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 193 SER Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 59 SER Chi-restraints excluded: chain C residue 80 MET 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 197 THR Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 49 ASN Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 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 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 84 ASP Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 138 ASP Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 197 THR Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 59 SER Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 85 THR Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain F residue 141 GLU Chi-restraints excluded: chain F residue 143 ILE Chi-restraints excluded: chain F residue 152 THR Chi-restraints excluded: chain F residue 193 SER Chi-restraints excluded: chain F residue 220 GLU Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain I residue 63 LEU Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain J residue 63 LEU Chi-restraints excluded: chain J residue 100 LEU Chi-restraints excluded: chain J residue 118 THR Chi-restraints excluded: chain L residue 63 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 107 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 chunk 52 optimal weight: 0.0270 chunk 34 optimal weight: 2.9990 chunk 33 optimal weight: 0.0770 chunk 110 optimal weight: 1.9990 chunk 118 optimal weight: 0.0570 chunk 85 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 136 optimal weight: 9.9990 overall best weight: 0.4116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6837 moved from start: 0.3306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 15204 Z= 0.163 Angle : 0.520 8.200 20580 Z= 0.280 Chirality : 0.045 0.152 2286 Planarity : 0.003 0.034 2628 Dihedral : 4.883 32.868 2012 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 5.03 % Allowed : 23.92 % Favored : 71.05 % 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: -0.77 (0.20), residues: 1818 helix: None (None), residues: 0 sheet: -0.49 (0.18), residues: 846 loop : -0.40 (0.21), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP I 57 HIS 0.005 0.001 HIS I 124 PHE 0.022 0.001 PHE K 56 TYR 0.005 0.001 TYR A 74 ARG 0.002 0.000 ARG C 219 *********************** 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 282 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 196 time to evaluate : 1.674 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: 0.7250 (tm-30) cc_final: 0.6803 (tp30) REVERT: A 49 ASN cc_start: 0.7614 (p0) cc_final: 0.7380 (m110) REVERT: A 60 GLU cc_start: 0.6801 (tm-30) cc_final: 0.6383 (tm-30) REVERT: A 141 GLU cc_start: 0.8549 (OUTLIER) cc_final: 0.8230 (tm-30) REVERT: A 165 THR cc_start: 0.7861 (m) cc_final: 0.7628 (m) REVERT: A 186 SER cc_start: 0.8174 (m) cc_final: 0.7753 (p) REVERT: B 39 GLU cc_start: 0.7180 (tm-30) cc_final: 0.6834 (tp30) REVERT: B 49 ASN cc_start: 0.7624 (p0) cc_final: 0.7332 (m-40) REVERT: B 60 GLU cc_start: 0.6750 (tm-30) cc_final: 0.6423 (tm-30) REVERT: B 80 MET cc_start: 0.8974 (ttm) cc_final: 0.8660 (ttt) REVERT: B 119 ILE cc_start: 0.8432 (OUTLIER) cc_final: 0.7918 (mm) REVERT: B 138 ASP cc_start: 0.7970 (OUTLIER) cc_final: 0.7723 (m-30) REVERT: B 186 SER cc_start: 0.8228 (m) cc_final: 0.7773 (p) REVERT: B 187 GLU cc_start: 0.7716 (mt-10) cc_final: 0.7495 (mt-10) REVERT: C 39 GLU cc_start: 0.7117 (tm-30) cc_final: 0.6651 (tp30) REVERT: C 80 MET cc_start: 0.9136 (ttm) cc_final: 0.8849 (ttt) REVERT: C 110 GLN cc_start: 0.8210 (tt0) cc_final: 0.7996 (tt0) REVERT: C 186 SER cc_start: 0.8358 (m) cc_final: 0.7898 (p) REVERT: D 39 GLU cc_start: 0.7267 (tm-30) cc_final: 0.6898 (tp30) REVERT: D 49 ASN cc_start: 0.7652 (p0) cc_final: 0.7333 (m110) REVERT: D 141 GLU cc_start: 0.8619 (OUTLIER) cc_final: 0.8270 (tm-30) REVERT: D 165 THR cc_start: 0.7845 (m) cc_final: 0.7589 (m) REVERT: D 186 SER cc_start: 0.8256 (m) cc_final: 0.7927 (p) REVERT: E 39 GLU cc_start: 0.7142 (tm-30) cc_final: 0.6767 (tp30) REVERT: E 49 ASN cc_start: 0.7648 (p0) cc_final: 0.7281 (m110) REVERT: E 58 MET cc_start: 0.8524 (ptm) cc_final: 0.8305 (ptm) REVERT: E 60 GLU cc_start: 0.6278 (tm-30) cc_final: 0.5928 (tm-30) REVERT: E 80 MET cc_start: 0.8952 (ttm) cc_final: 0.8635 (ttt) REVERT: E 138 ASP cc_start: 0.7969 (OUTLIER) cc_final: 0.7723 (m-30) REVERT: E 186 SER cc_start: 0.8227 (m) cc_final: 0.7773 (p) REVERT: E 190 MET cc_start: 0.7801 (mmm) cc_final: 0.7493 (mmp) REVERT: F 39 GLU cc_start: 0.7254 (tm-30) cc_final: 0.6873 (tp30) REVERT: F 47 ASP cc_start: 0.8438 (m-30) cc_final: 0.8064 (m-30) REVERT: F 80 MET cc_start: 0.9054 (ttm) cc_final: 0.8784 (ttt) REVERT: F 141 GLU cc_start: 0.8432 (OUTLIER) cc_final: 0.8099 (tm-30) REVERT: F 186 SER cc_start: 0.8338 (m) cc_final: 0.7895 (p) REVERT: G 63 LEU cc_start: 0.8196 (OUTLIER) cc_final: 0.7925 (mt) REVERT: G 100 LEU cc_start: 0.7283 (OUTLIER) cc_final: 0.7027 (mt) REVERT: G 118 THR cc_start: 0.7179 (OUTLIER) cc_final: 0.6972 (t) REVERT: G 120 MET cc_start: 0.8229 (ttp) cc_final: 0.7951 (ttt) REVERT: H 63 LEU cc_start: 0.8204 (OUTLIER) cc_final: 0.7999 (mt) REVERT: I 63 LEU cc_start: 0.8168 (OUTLIER) cc_final: 0.7838 (mt) REVERT: I 100 LEU cc_start: 0.7459 (OUTLIER) cc_final: 0.7097 (mt) REVERT: J 63 LEU cc_start: 0.8236 (OUTLIER) cc_final: 0.7952 (mt) REVERT: J 100 LEU cc_start: 0.7222 (OUTLIER) cc_final: 0.6971 (mt) REVERT: L 63 LEU cc_start: 0.8213 (OUTLIER) cc_final: 0.8007 (mt) outliers start: 86 outliers final: 47 residues processed: 262 average time/residue: 1.1372 time to fit residues: 333.0794 Evaluate side-chains 255 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 193 time to evaluate : 1.791 ------------------------------------------------------------------------------- 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 190 MET 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 85 THR Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 127 GLU Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 193 SER Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 59 SER Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 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 197 THR 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 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 E residue 59 SER Chi-restraints excluded: chain E residue 84 ASP Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 138 ASP Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 193 SER Chi-restraints excluded: chain 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 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 63 LEU Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain I residue 63 LEU Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain J residue 63 LEU Chi-restraints excluded: chain J residue 100 LEU Chi-restraints excluded: chain L residue 63 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 157 optimal weight: 0.0770 chunk 166 optimal weight: 7.9990 chunk 151 optimal weight: 5.9990 chunk 161 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 126 optimal weight: 0.1980 chunk 49 optimal weight: 4.9990 chunk 146 optimal weight: 10.0000 chunk 152 optimal weight: 7.9990 chunk 106 optimal weight: 2.9990 overall best weight: 1.8544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 ASN ** E 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 110 GLN ** F 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 58 GLN H 109 GLN H 127 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6915 moved from start: 0.3531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 15204 Z= 0.417 Angle : 0.640 7.695 20580 Z= 0.342 Chirality : 0.051 0.162 2286 Planarity : 0.004 0.047 2628 Dihedral : 5.400 39.253 2012 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 5.32 % Allowed : 24.15 % Favored : 70.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.42 (0.18), residues: 846 loop : -0.52 (0.21), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 34 HIS 0.007 0.001 HIS I 124 PHE 0.029 0.002 PHE K 56 TYR 0.011 0.002 TYR B 183 ARG 0.006 0.000 ARG E 219 *********************** 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 277 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 186 time to evaluate : 1.724 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: 0.7306 (tm-30) cc_final: 0.6968 (tp30) REVERT: A 49 ASN cc_start: 0.7779 (OUTLIER) cc_final: 0.7418 (m110) REVERT: A 60 GLU cc_start: 0.6948 (tm-30) cc_final: 0.6540 (tm-30) REVERT: A 141 GLU cc_start: 0.8793 (OUTLIER) cc_final: 0.8449 (tm-30) REVERT: A 164 GLU cc_start: 0.7593 (mm-30) cc_final: 0.7354 (mm-30) REVERT: A 165 THR cc_start: 0.7893 (m) cc_final: 0.7636 (m) REVERT: A 186 SER cc_start: 0.8335 (m) cc_final: 0.7938 (p) REVERT: B 39 GLU cc_start: 0.7145 (tm-30) cc_final: 0.6836 (tp30) REVERT: B 49 ASN cc_start: 0.7711 (p0) cc_final: 0.7397 (m-40) REVERT: B 119 ILE cc_start: 0.8486 (OUTLIER) cc_final: 0.7958 (mm) REVERT: B 138 ASP cc_start: 0.8027 (OUTLIER) cc_final: 0.7718 (m-30) REVERT: B 186 SER cc_start: 0.8351 (m) cc_final: 0.7946 (p) REVERT: B 187 GLU cc_start: 0.7887 (mt-10) cc_final: 0.7668 (mt-10) REVERT: C 39 GLU cc_start: 0.7254 (tm-30) cc_final: 0.6847 (tp30) REVERT: C 72 THR cc_start: 0.8015 (p) cc_final: 0.7482 (m) REVERT: C 80 MET cc_start: 0.9187 (OUTLIER) cc_final: 0.8888 (ttt) REVERT: C 186 SER cc_start: 0.8404 (m) cc_final: 0.8009 (p) REVERT: D 39 GLU cc_start: 0.7307 (tm-30) cc_final: 0.6962 (tp30) REVERT: D 49 ASN cc_start: 0.7801 (OUTLIER) cc_final: 0.7412 (m110) REVERT: D 141 GLU cc_start: 0.8823 (OUTLIER) cc_final: 0.8419 (tm-30) REVERT: D 165 THR cc_start: 0.7880 (m) cc_final: 0.7611 (m) REVERT: D 186 SER cc_start: 0.8330 (m) cc_final: 0.8049 (p) REVERT: E 39 GLU cc_start: 0.7122 (tm-30) cc_final: 0.6822 (tp30) REVERT: E 49 ASN cc_start: 0.7755 (p0) cc_final: 0.7365 (m-40) REVERT: E 58 MET cc_start: 0.8567 (ptm) cc_final: 0.8321 (ptm) REVERT: E 60 GLU cc_start: 0.6561 (tm-30) cc_final: 0.6227 (tm-30) REVERT: E 84 ASP cc_start: 0.7985 (OUTLIER) cc_final: 0.7693 (t70) REVERT: E 119 ILE cc_start: 0.8453 (OUTLIER) cc_final: 0.7953 (mm) REVERT: E 138 ASP cc_start: 0.8032 (OUTLIER) cc_final: 0.7716 (m-30) REVERT: E 186 SER cc_start: 0.8345 (m) cc_final: 0.7948 (p) REVERT: F 39 GLU cc_start: 0.7299 (tm-30) cc_final: 0.6931 (tp30) REVERT: F 47 ASP cc_start: 0.8531 (m-30) cc_final: 0.8223 (m-30) REVERT: F 72 THR cc_start: 0.8006 (p) cc_final: 0.7464 (m) REVERT: F 80 MET cc_start: 0.9091 (ttm) cc_final: 0.8836 (ttt) REVERT: F 141 GLU cc_start: 0.8767 (OUTLIER) cc_final: 0.8445 (tm-30) REVERT: F 186 SER cc_start: 0.8407 (m) cc_final: 0.8023 (p) REVERT: G 63 LEU cc_start: 0.8212 (OUTLIER) cc_final: 0.7964 (mt) REVERT: G 100 LEU cc_start: 0.7353 (OUTLIER) cc_final: 0.7110 (mt) REVERT: G 120 MET cc_start: 0.8361 (ttp) cc_final: 0.8049 (ttt) REVERT: I 63 LEU cc_start: 0.8203 (OUTLIER) cc_final: 0.7899 (mt) REVERT: J 63 LEU cc_start: 0.8263 (OUTLIER) cc_final: 0.7990 (mt) REVERT: J 100 LEU cc_start: 0.7451 (OUTLIER) cc_final: 0.7214 (mt) REVERT: L 63 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.8075 (mt) outliers start: 91 outliers final: 56 residues processed: 260 average time/residue: 1.1835 time to fit residues: 342.6248 Evaluate side-chains 250 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 177 time to evaluate : 1.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ASN 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 190 MET 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 85 THR Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 193 SER Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 59 SER Chi-restraints excluded: chain C residue 80 MET Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 85 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 197 THR Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 49 ASN Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 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 193 SER Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 59 SER Chi-restraints excluded: chain E residue 84 ASP 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 G residue 63 LEU Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain G residue 118 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 K residue 120 MET Chi-restraints excluded: chain L residue 63 LEU Chi-restraints excluded: chain L residue 100 LEU Chi-restraints excluded: chain L residue 126 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 170 optimal weight: 9.9990 chunk 104 optimal weight: 0.0980 chunk 81 optimal weight: 0.6980 chunk 118 optimal weight: 0.7980 chunk 179 optimal weight: 0.9990 chunk 165 optimal weight: 9.9990 chunk 142 optimal weight: 0.3980 chunk 14 optimal weight: 0.6980 chunk 110 optimal weight: 0.8980 chunk 87 optimal weight: 0.6980 chunk 113 optimal weight: 0.7980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 ASN ** E 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 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6853 moved from start: 0.3461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15204 Z= 0.183 Angle : 0.534 7.916 20580 Z= 0.287 Chirality : 0.045 0.156 2286 Planarity : 0.003 0.034 2628 Dihedral : 4.956 35.033 2012 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 4.04 % Allowed : 25.61 % Favored : 70.35 % 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: -0.76 (0.20), residues: 1818 helix: None (None), residues: 0 sheet: -0.46 (0.18), residues: 846 loop : -0.43 (0.21), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP I 57 HIS 0.005 0.001 HIS I 124 PHE 0.022 0.001 PHE K 56 TYR 0.007 0.001 TYR A 74 ARG 0.005 0.000 ARG E 219 ********************** 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 260 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 191 time to evaluate : 1.655 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: 0.7224 (tm-30) cc_final: 0.6824 (tp30) REVERT: A 49 ASN cc_start: 0.7658 (p0) cc_final: 0.7385 (m110) REVERT: A 60 GLU cc_start: 0.6806 (tm-30) cc_final: 0.6388 (tm-30) REVERT: A 141 GLU cc_start: 0.8618 (OUTLIER) cc_final: 0.8304 (tm-30) REVERT: A 165 THR cc_start: 0.7863 (m) cc_final: 0.7623 (m) REVERT: A 186 SER cc_start: 0.8287 (m) cc_final: 0.7847 (p) REVERT: B 39 GLU cc_start: 0.7218 (tm-30) cc_final: 0.6838 (tp30) REVERT: B 49 ASN cc_start: 0.7620 (p0) cc_final: 0.7368 (m110) REVERT: B 60 GLU cc_start: 0.6719 (tm-30) cc_final: 0.6445 (tm-30) REVERT: B 80 MET cc_start: 0.8984 (ttm) cc_final: 0.8660 (ttt) REVERT: B 119 ILE cc_start: 0.8428 (OUTLIER) cc_final: 0.7901 (mm) REVERT: B 138 ASP cc_start: 0.7928 (OUTLIER) cc_final: 0.7640 (m-30) REVERT: B 186 SER cc_start: 0.8252 (m) cc_final: 0.7817 (p) REVERT: C 39 GLU cc_start: 0.7270 (tm-30) cc_final: 0.6934 (tp30) REVERT: C 80 MET cc_start: 0.9143 (ttm) cc_final: 0.8842 (ttt) REVERT: C 110 GLN cc_start: 0.8307 (tt0) cc_final: 0.8090 (tt0) REVERT: C 186 SER cc_start: 0.8344 (m) cc_final: 0.7904 (p) REVERT: D 39 GLU cc_start: 0.7338 (tm-30) cc_final: 0.6905 (tp30) REVERT: D 49 ASN cc_start: 0.7700 (p0) cc_final: 0.7393 (m110) REVERT: D 141 GLU cc_start: 0.8634 (OUTLIER) cc_final: 0.8287 (tm-30) REVERT: D 165 THR cc_start: 0.7800 (m) cc_final: 0.7559 (m) REVERT: D 186 SER cc_start: 0.8243 (m) cc_final: 0.7940 (p) REVERT: E 39 GLU cc_start: 0.7204 (tm-30) cc_final: 0.6834 (tp30) REVERT: E 49 ASN cc_start: 0.7631 (p0) cc_final: 0.7317 (m110) REVERT: E 60 GLU cc_start: 0.6308 (tm-30) cc_final: 0.5965 (tm-30) REVERT: E 80 MET cc_start: 0.8955 (ttm) cc_final: 0.8623 (ttt) REVERT: E 94 GLU cc_start: 0.8369 (mt-10) cc_final: 0.7996 (mt-10) REVERT: E 119 ILE cc_start: 0.8393 (OUTLIER) cc_final: 0.7909 (mm) REVERT: E 138 ASP cc_start: 0.7986 (OUTLIER) cc_final: 0.7717 (m-30) REVERT: E 186 SER cc_start: 0.8251 (m) cc_final: 0.7806 (p) REVERT: E 187 GLU cc_start: 0.7775 (mt-10) cc_final: 0.7573 (mt-10) REVERT: F 39 GLU cc_start: 0.7349 (tm-30) cc_final: 0.6947 (tp30) REVERT: F 80 MET cc_start: 0.9083 (ttm) cc_final: 0.8789 (ttt) REVERT: F 141 GLU cc_start: 0.8532 (OUTLIER) cc_final: 0.8231 (tm-30) REVERT: F 186 SER cc_start: 0.8336 (m) cc_final: 0.7918 (p) REVERT: F 220 GLU cc_start: 0.5962 (OUTLIER) cc_final: 0.5248 (mt-10) REVERT: G 63 LEU cc_start: 0.8201 (OUTLIER) cc_final: 0.7938 (mt) REVERT: G 100 LEU cc_start: 0.7328 (OUTLIER) cc_final: 0.7108 (mt) REVERT: G 118 THR cc_start: 0.7117 (OUTLIER) cc_final: 0.6909 (t) REVERT: G 120 MET cc_start: 0.8297 (ttp) cc_final: 0.7978 (ttt) REVERT: I 63 LEU cc_start: 0.8142 (OUTLIER) cc_final: 0.7852 (mt) REVERT: J 63 LEU cc_start: 0.8221 (OUTLIER) cc_final: 0.7956 (mt) REVERT: J 100 LEU cc_start: 0.7358 (OUTLIER) cc_final: 0.7111 (mt) REVERT: L 63 LEU cc_start: 0.8256 (OUTLIER) cc_final: 0.8022 (mt) outliers start: 69 outliers final: 48 residues processed: 248 average time/residue: 1.1930 time to fit residues: 329.6092 Evaluate side-chains 252 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 189 time to evaluate : 1.695 ------------------------------------------------------------------------------- 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 190 MET 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 85 THR Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 193 SER Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 59 SER Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 85 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 197 THR 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 141 GLU 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 84 ASP Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain E residue 138 ASP Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 193 SER Chi-restraints excluded: chain E residue 197 THR Chi-restraints excluded: chain F residue 59 SER Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 85 THR Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain F residue 141 GLU Chi-restraints excluded: chain F residue 143 ILE Chi-restraints excluded: chain F residue 152 THR Chi-restraints excluded: chain F residue 193 SER Chi-restraints excluded: chain F residue 220 GLU Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain I residue 63 LEU Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain I residue 126 MET Chi-restraints excluded: chain J residue 63 LEU Chi-restraints excluded: chain J residue 100 LEU Chi-restraints excluded: chain L 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 152 optimal weight: 0.3980 chunk 43 optimal weight: 0.0270 chunk 131 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 143 optimal weight: 4.9990 chunk 59 optimal weight: 0.9990 chunk 146 optimal weight: 9.9990 chunk 18 optimal weight: 0.4980 chunk 26 optimal weight: 2.9990 chunk 125 optimal weight: 8.9990 overall best weight: 0.9842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 110 GLN ** F 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.197135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.132722 restraints weight = 13294.459| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 2.89 r_work: 0.3164 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3047 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3047 r_free = 0.3047 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 786 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3010 r_free = 0.3010 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 775 | |-----------------------------------------------------------------------------| r_final: 0.3010 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.3523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15204 Z= 0.260 Angle : 0.571 7.764 20580 Z= 0.305 Chirality : 0.047 0.157 2286 Planarity : 0.003 0.036 2628 Dihedral : 5.069 38.540 2012 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 4.97 % Allowed : 24.80 % Favored : 70.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.76 (0.20), residues: 1818 helix: None (None), residues: 0 sheet: -0.43 (0.18), residues: 846 loop : -0.46 (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 0.027 0.001 PHE K 56 TYR 0.009 0.001 TYR A 74 ARG 0.005 0.000 ARG E 219 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5777.74 seconds wall clock time: 105 minutes 56.62 seconds (6356.62 seconds total)