Starting phenix.real_space_refine on Fri Jun 13 05:32:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hxb_35075/06_2025/8hxb_35075.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hxb_35075/06_2025/8hxb_35075.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hxb_35075/06_2025/8hxb_35075.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hxb_35075/06_2025/8hxb_35075.map" model { file = "/net/cci-nas-00/data/ceres_data/8hxb_35075/06_2025/8hxb_35075.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hxb_35075/06_2025/8hxb_35075.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.061 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 120 5.16 5 C 9378 2.51 5 N 2514 2.21 5 O 2880 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 5.22, per 1000 atoms: 0.35 Number of scatterers: 14892 At special positions: 0 Unit cell: (160.55, 175.75, 65.55, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 120 16.00 O 2880 8.00 N 2514 7.00 C 9378 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS A 25 " - pdb=" SG CYS B 130 " distance=1.99 Simple disulfide: pdb=" SG CYS A 56 " - pdb=" SG CYS A 217 " distance=2.03 Simple disulfide: pdb=" SG CYS A 125 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 130 " - pdb=" SG CYS F 25 " distance=2.06 Simple disulfide: pdb=" SG CYS A 160 " - pdb=" SG CYS A 205 " distance=2.02 Simple disulfide: pdb=" SG CYS C 25 " - pdb=" SG CYS D 130 " distance=1.97 Simple disulfide: pdb=" SG CYS B 25 " - pdb=" SG CYS C 130 " distance=2.01 Simple disulfide: pdb=" SG CYS E 25 " - pdb=" SG CYS F 130 " distance=2.11 Simple disulfide: pdb=" SG CYS D 25 " - pdb=" SG CYS E 130 " distance=2.09 Simple disulfide: pdb=" SG CYS C 56 " - pdb=" SG CYS C 217 " distance=2.03 Simple disulfide: pdb=" SG CYS B 56 " - pdb=" SG CYS B 217 " distance=2.03 Simple disulfide: pdb=" SG CYS E 56 " - pdb=" SG CYS E 217 " distance=2.03 Simple disulfide: pdb=" SG CYS D 56 " - pdb=" SG CYS D 217 " distance=2.03 Simple disulfide: pdb=" SG CYS F 56 " - pdb=" SG CYS F 217 " distance=2.03 Simple disulfide: pdb=" SG CYS C 125 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS B 125 " - pdb=" SG CYS B 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 125 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS D 125 " - pdb=" SG CYS D 157 " distance=2.03 Simple disulfide: pdb=" SG CYS F 125 " - pdb=" SG CYS F 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 160 " - pdb=" SG CYS C 205 " distance=2.02 Simple disulfide: pdb=" SG CYS B 160 " - pdb=" SG CYS B 205 " distance=2.02 Simple disulfide: pdb=" SG CYS E 160 " - pdb=" SG CYS E 205 " distance=2.02 Simple disulfide: pdb=" SG CYS D 160 " - pdb=" SG CYS D 205 " distance=2.02 Simple disulfide: pdb=" SG CYS F 160 " - pdb=" SG CYS F 205 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.98 Conformation dependent library (CDL) restraints added in 1.7 seconds 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3516 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 29 sheets defined 4.9% alpha, 42.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.87 Creating SS restraints... Processing helix chain 'A' and resid 187 through 191 Processing helix chain 'B' and resid 187 through 191 Processing helix chain 'C' and resid 187 through 191 Processing helix chain 'D' and resid 187 through 191 Processing helix chain 'E' and resid 187 through 191 Processing helix chain 'F' and resid 187 through 191 Processing helix chain 'G' and resid 49 through 53 removed outlier: 3.845A pdb=" N GLU G 52 " --> pdb=" O SER G 49 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU G 53 " --> pdb=" O LEU G 50 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 49 through 53' Processing helix chain 'G' and resid 79 through 83 Processing helix chain 'H' and resid 49 through 53 removed outlier: 3.845A pdb=" N GLU H 52 " --> pdb=" O SER H 49 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU H 53 " --> pdb=" O LEU H 50 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 49 through 53' Processing helix chain 'H' and resid 79 through 83 Processing helix chain 'I' and resid 49 through 53 removed outlier: 3.845A pdb=" N GLU I 52 " --> pdb=" O SER I 49 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU I 53 " --> pdb=" O LEU I 50 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 49 through 53' Processing helix chain 'I' and resid 79 through 83 Processing helix chain 'J' and resid 49 through 53 removed outlier: 3.845A pdb=" N GLU J 52 " --> pdb=" O SER J 49 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU J 53 " --> pdb=" O LEU J 50 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 49 through 53' Processing helix chain 'J' and resid 79 through 83 Processing helix chain 'K' and resid 49 through 53 removed outlier: 3.846A pdb=" N GLU K 52 " --> pdb=" O SER K 49 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU K 53 " --> pdb=" O LEU K 50 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 49 through 53' Processing helix chain 'K' and resid 79 through 83 Processing helix chain 'L' and resid 49 through 53 removed outlier: 3.845A pdb=" N GLU L 52 " --> pdb=" O SER L 49 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU L 53 " --> pdb=" O LEU L 50 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 49 through 53' Processing helix chain 'L' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 22 through 23 removed outlier: 4.350A pdb=" N CYS B 130 " --> pdb=" O THR A 23 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 181 through 184 removed outlier: 5.575A pdb=" N PHE A 36 " --> pdb=" O THR A 108 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N THR A 108 " --> pdb=" O PHE A 36 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA A 38 " --> pdb=" O LEU A 106 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LYS A 101 " --> pdb=" O VAL A 96 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N VAL A 96 " --> pdb=" O LYS A 101 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N SER A 103 " --> pdb=" O GLU A 94 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N GLU A 94 " --> pdb=" O SER A 103 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N LEU A 105 " --> pdb=" O ALA A 92 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ALA A 92 " --> pdb=" O LEU A 105 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N PHE A 107 " --> pdb=" O VAL A 90 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 181 through 184 removed outlier: 9.387A pdb=" N SER A 193 " --> pdb=" O HIS G 124 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N HIS G 124 " --> pdb=" O SER A 193 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N GLY A 195 " --> pdb=" O ARG G 122 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ILE G 112 " --> pdb=" O ILE G 123 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N GLN G 125 " --> pdb=" O CYS G 110 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N CYS G 110 " --> pdb=" O GLN G 125 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N ASN G 127 " --> pdb=" O TYR G 108 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N TYR G 108 " --> pdb=" O ASN G 127 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N TRP G 57 " --> pdb=" O ASN G 66 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ASN G 66 " --> pdb=" O TRP G 57 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 57 through 63 Processing sheet with id=AA5, first strand: chain 'A' and resid 130 through 131 removed outlier: 4.388A pdb=" N CYS A 130 " --> pdb=" O THR F 23 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 22 through 23 removed outlier: 4.337A pdb=" N CYS C 130 " --> pdb=" O THR B 23 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 181 through 184 removed outlier: 5.576A pdb=" N PHE B 36 " --> pdb=" O THR B 108 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N THR B 108 " --> pdb=" O PHE B 36 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA B 38 " --> pdb=" O LEU B 106 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LYS B 101 " --> pdb=" O VAL B 96 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N VAL B 96 " --> pdb=" O LYS B 101 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N SER B 103 " --> pdb=" O GLU B 94 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N GLU B 94 " --> pdb=" O SER B 103 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N LEU B 105 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ALA B 92 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N PHE B 107 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 181 through 184 removed outlier: 9.372A pdb=" N SER B 193 " --> pdb=" O HIS H 124 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N HIS H 124 " --> pdb=" O SER B 193 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N GLY B 195 " --> pdb=" O ARG H 122 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ILE H 112 " --> pdb=" O ILE H 123 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N GLN H 125 " --> pdb=" O CYS H 110 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N CYS H 110 " --> pdb=" O GLN H 125 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N ASN H 127 " --> pdb=" O TYR H 108 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N TYR H 108 " --> pdb=" O ASN H 127 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N TRP H 57 " --> pdb=" O ASN H 66 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ASN H 66 " --> pdb=" O TRP H 57 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 57 through 63 Processing sheet with id=AB1, first strand: chain 'C' and resid 22 through 23 removed outlier: 4.362A pdb=" N CYS D 130 " --> pdb=" O THR C 23 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 181 through 184 removed outlier: 5.576A pdb=" N PHE C 36 " --> pdb=" O THR C 108 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N THR C 108 " --> pdb=" O PHE C 36 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA C 38 " --> pdb=" O LEU C 106 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N LYS C 101 " --> pdb=" O VAL C 96 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N VAL C 96 " --> pdb=" O LYS C 101 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N SER C 103 " --> pdb=" O GLU C 94 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N GLU C 94 " --> pdb=" O SER C 103 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N LEU C 105 " --> pdb=" O ALA C 92 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ALA C 92 " --> pdb=" O LEU C 105 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N PHE C 107 " --> pdb=" O VAL C 90 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 181 through 184 removed outlier: 9.416A pdb=" N SER C 193 " --> pdb=" O HIS I 124 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N HIS I 124 " --> pdb=" O SER C 193 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N GLY C 195 " --> pdb=" O ARG I 122 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ILE I 112 " --> pdb=" O ILE I 123 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N GLN I 125 " --> pdb=" O CYS I 110 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N CYS I 110 " --> pdb=" O GLN I 125 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N ASN I 127 " --> pdb=" O TYR I 108 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N TYR I 108 " --> pdb=" O ASN I 127 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N TRP I 57 " --> pdb=" O ASN I 66 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ASN I 66 " --> pdb=" O TRP I 57 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 57 through 63 Processing sheet with id=AB5, first strand: chain 'D' and resid 181 through 184 removed outlier: 5.576A pdb=" N PHE D 36 " --> pdb=" O THR D 108 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N THR D 108 " --> pdb=" O PHE D 36 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA D 38 " --> pdb=" O LEU D 106 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LYS D 101 " --> pdb=" O VAL D 96 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N VAL D 96 " --> pdb=" O LYS D 101 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N SER D 103 " --> pdb=" O GLU D 94 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N GLU D 94 " --> pdb=" O SER D 103 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N LEU D 105 " --> pdb=" O ALA D 92 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ALA D 92 " --> pdb=" O LEU D 105 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N PHE D 107 " --> pdb=" O VAL D 90 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 181 through 184 removed outlier: 9.355A pdb=" N SER D 193 " --> pdb=" O HIS J 124 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N HIS J 124 " --> pdb=" O SER D 193 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N GLY D 195 " --> pdb=" O ARG J 122 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ILE J 112 " --> pdb=" O ILE J 123 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N GLN J 125 " --> pdb=" O CYS J 110 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N CYS J 110 " --> pdb=" O GLN J 125 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N ASN J 127 " --> pdb=" O TYR J 108 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N TYR J 108 " --> pdb=" O ASN J 127 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TRP J 57 " --> pdb=" O ASN J 66 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ASN J 66 " --> pdb=" O TRP J 57 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 57 through 63 Processing sheet with id=AB8, first strand: chain 'E' and resid 22 through 23 removed outlier: 4.399A pdb=" N CYS F 130 " --> pdb=" O THR E 23 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 181 through 184 removed outlier: 5.576A pdb=" N PHE E 36 " --> pdb=" O THR E 108 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N THR E 108 " --> pdb=" O PHE E 36 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA E 38 " --> pdb=" O LEU E 106 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LYS E 101 " --> pdb=" O VAL E 96 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N VAL E 96 " --> pdb=" O LYS E 101 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N SER E 103 " --> pdb=" O GLU E 94 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N GLU E 94 " --> pdb=" O SER E 103 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N LEU E 105 " --> pdb=" O ALA E 92 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ALA E 92 " --> pdb=" O LEU E 105 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N PHE E 107 " --> pdb=" O VAL E 90 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 181 through 184 removed outlier: 9.183A pdb=" N SER E 193 " --> pdb=" O HIS K 124 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N HIS K 124 " --> pdb=" O SER E 193 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N GLY E 195 " --> pdb=" O ARG K 122 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ILE K 112 " --> pdb=" O ILE K 123 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N GLN K 125 " --> pdb=" O CYS K 110 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N CYS K 110 " --> pdb=" O GLN K 125 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N ASN K 127 " --> pdb=" O TYR K 108 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N TYR K 108 " --> pdb=" O ASN K 127 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N TRP K 57 " --> pdb=" O ASN K 66 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ASN K 66 " --> pdb=" O TRP K 57 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 57 through 63 Processing sheet with id=AC3, first strand: chain 'F' and resid 181 through 184 removed outlier: 5.575A pdb=" N PHE F 36 " --> pdb=" O THR F 108 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N THR F 108 " --> pdb=" O PHE F 36 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA F 38 " --> pdb=" O LEU F 106 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LYS F 101 " --> pdb=" O VAL F 96 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N VAL F 96 " --> pdb=" O LYS F 101 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N SER F 103 " --> pdb=" O GLU F 94 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N GLU F 94 " --> pdb=" O SER F 103 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N LEU F 105 " --> pdb=" O ALA F 92 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ALA F 92 " --> pdb=" O LEU F 105 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N PHE F 107 " --> pdb=" O VAL F 90 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 181 through 184 removed outlier: 9.417A pdb=" N SER F 193 " --> pdb=" O HIS L 124 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N HIS L 124 " --> pdb=" O SER F 193 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N GLY F 195 " --> pdb=" O ARG L 122 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ILE L 112 " --> pdb=" O ILE L 123 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N GLN L 125 " --> pdb=" O CYS L 110 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N CYS L 110 " --> pdb=" O GLN L 125 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N ASN L 127 " --> pdb=" O TYR L 108 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N TYR L 108 " --> pdb=" O ASN L 127 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TRP L 57 " --> pdb=" O ASN L 66 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ASN L 66 " --> pdb=" O TRP L 57 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 57 through 63 Processing sheet with id=AC6, first strand: chain 'G' and resid 35 through 39 Processing sheet with id=AC7, first strand: chain 'H' and resid 35 through 39 Processing sheet with id=AC8, first strand: chain 'I' and resid 35 through 39 Processing sheet with id=AC9, first strand: chain 'J' and resid 35 through 39 Processing sheet with id=AD1, first strand: chain 'K' and resid 35 through 39 Processing sheet with id=AD2, first strand: chain 'L' and resid 35 through 39 527 hydrogen bonds defined for protein. 1365 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.19 Time building geometry restraints manager: 3.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4602 1.33 - 1.46: 3122 1.46 - 1.58: 7300 1.58 - 1.70: 6 1.70 - 1.82: 174 Bond restraints: 15204 Sorted by residual: bond pdb=" CA GLU I 52 " pdb=" CB GLU I 52 " ideal model delta sigma weight residual 1.539 1.665 -0.125 4.88e-02 4.20e+02 6.60e+00 bond pdb=" CA GLU H 52 " pdb=" CB GLU H 52 " ideal model delta sigma weight residual 1.539 1.665 -0.125 4.88e-02 4.20e+02 6.58e+00 bond pdb=" CA GLU K 52 " pdb=" CB GLU K 52 " ideal model delta sigma weight residual 1.539 1.665 -0.125 4.88e-02 4.20e+02 6.58e+00 bond pdb=" CA GLU G 52 " pdb=" CB GLU G 52 " ideal model delta sigma weight residual 1.539 1.664 -0.125 4.88e-02 4.20e+02 6.54e+00 bond pdb=" CA GLU L 52 " pdb=" CB GLU L 52 " ideal model delta sigma weight residual 1.539 1.664 -0.125 4.88e-02 4.20e+02 6.51e+00 ... (remaining 15199 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.01: 20027 3.01 - 6.03: 446 6.03 - 9.04: 71 9.04 - 12.05: 24 12.05 - 15.07: 12 Bond angle restraints: 20580 Sorted by residual: angle pdb=" CA LEU K 50 " pdb=" CB LEU K 50 " pdb=" CG LEU K 50 " ideal model delta sigma weight residual 116.30 131.37 -15.07 3.50e+00 8.16e-02 1.85e+01 angle pdb=" CA LEU H 50 " pdb=" CB LEU H 50 " pdb=" CG LEU H 50 " ideal model delta sigma weight residual 116.30 131.36 -15.06 3.50e+00 8.16e-02 1.85e+01 angle pdb=" CA LEU J 50 " pdb=" CB LEU J 50 " pdb=" CG LEU J 50 " ideal model delta sigma weight residual 116.30 131.36 -15.06 3.50e+00 8.16e-02 1.85e+01 angle pdb=" CA LEU G 50 " pdb=" CB LEU G 50 " pdb=" CG LEU G 50 " ideal model delta sigma weight residual 116.30 131.36 -15.06 3.50e+00 8.16e-02 1.85e+01 angle pdb=" CA LEU L 50 " pdb=" CB LEU L 50 " pdb=" CG LEU L 50 " ideal model delta sigma weight residual 116.30 131.35 -15.05 3.50e+00 8.16e-02 1.85e+01 ... (remaining 20575 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.42: 7423 13.42 - 26.84: 1205 26.84 - 40.26: 372 40.26 - 53.68: 134 53.68 - 67.10: 64 Dihedral angle restraints: 9198 sinusoidal: 3738 harmonic: 5460 Sorted by residual: dihedral pdb=" CA LEU F 40 " pdb=" C LEU F 40 " pdb=" N THR F 41 " pdb=" CA THR F 41 " ideal model delta harmonic sigma weight residual -180.00 -158.91 -21.09 0 5.00e+00 4.00e-02 1.78e+01 dihedral pdb=" CA LEU E 40 " pdb=" C LEU E 40 " pdb=" N THR E 41 " pdb=" CA THR E 41 " ideal model delta harmonic sigma weight residual -180.00 -158.93 -21.07 0 5.00e+00 4.00e-02 1.78e+01 dihedral pdb=" CA LEU D 40 " pdb=" C LEU D 40 " pdb=" N THR D 41 " pdb=" CA THR D 41 " ideal model delta harmonic sigma weight residual 180.00 -158.95 -21.05 0 5.00e+00 4.00e-02 1.77e+01 ... (remaining 9195 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 1651 0.073 - 0.146: 545 0.146 - 0.219: 66 0.219 - 0.292: 12 0.292 - 0.365: 12 Chirality restraints: 2286 Sorted by residual: chirality pdb=" CB ILE E 209 " pdb=" CA ILE E 209 " pdb=" CG1 ILE E 209 " pdb=" CG2 ILE E 209 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.36 2.00e-01 2.50e+01 3.33e+00 chirality pdb=" CB ILE F 209 " pdb=" CA ILE F 209 " pdb=" CG1 ILE F 209 " pdb=" CG2 ILE F 209 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.36 2.00e-01 2.50e+01 3.31e+00 chirality pdb=" CB ILE C 209 " pdb=" CA ILE C 209 " pdb=" CG1 ILE C 209 " pdb=" CG2 ILE C 209 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.36 2.00e-01 2.50e+01 3.31e+00 ... (remaining 2283 not shown) Planarity restraints: 2628 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE F 209 " 0.018 2.00e-02 2.50e+03 3.60e-02 1.29e+01 pdb=" C ILE F 209 " -0.062 2.00e-02 2.50e+03 pdb=" O ILE F 209 " 0.024 2.00e-02 2.50e+03 pdb=" N LYS F 210 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE C 209 " -0.018 2.00e-02 2.50e+03 3.59e-02 1.29e+01 pdb=" C ILE C 209 " 0.062 2.00e-02 2.50e+03 pdb=" O ILE C 209 " -0.024 2.00e-02 2.50e+03 pdb=" N LYS C 210 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE E 209 " -0.018 2.00e-02 2.50e+03 3.59e-02 1.29e+01 pdb=" C ILE E 209 " 0.062 2.00e-02 2.50e+03 pdb=" O ILE E 209 " -0.024 2.00e-02 2.50e+03 pdb=" N LYS E 210 " -0.021 2.00e-02 2.50e+03 ... (remaining 2625 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 119 2.61 - 3.18: 11407 3.18 - 3.75: 22478 3.75 - 4.33: 32184 4.33 - 4.90: 54721 Nonbonded interactions: 120909 Sorted by model distance: nonbonded pdb=" SG CYS I 40 " pdb=" SG CYS I 110 " model vdw 2.032 3.760 nonbonded pdb=" SG CYS H 40 " pdb=" SG CYS H 110 " model vdw 2.032 3.760 nonbonded pdb=" SG CYS J 40 " pdb=" SG CYS J 110 " model vdw 2.032 3.760 nonbonded pdb=" SG CYS K 40 " pdb=" SG CYS K 110 " model vdw 2.032 3.760 nonbonded pdb=" SG CYS G 40 " pdb=" SG CYS G 110 " model vdw 2.033 3.760 ... (remaining 120904 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.11 Found NCS groups: ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'H' selection = chain 'K' selection = chain 'J' selection = chain 'L' } ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.93 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.530 Check model and map are aligned: 0.080 Set scattering table: 0.130 Process input model: 29.090 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6682 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.125 15228 Z= 0.297 Angle : 1.151 15.068 20628 Z= 0.581 Chirality : 0.072 0.365 2286 Planarity : 0.006 0.039 2628 Dihedral : 16.218 67.096 5610 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 1.64 % Allowed : 26.78 % Favored : 71.58 % Cbeta Deviations : 0.34 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.18), residues: 1818 helix: None (None), residues: 0 sheet: -0.55 (0.17), residues: 834 loop : -1.29 (0.18), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP G 57 HIS 0.023 0.002 HIS G 124 PHE 0.023 0.003 PHE G 88 TYR 0.045 0.003 TYR G 82 ARG 0.005 0.001 ARG L 122 Details of bonding type rmsd hydrogen bonds : bond 0.17704 ( 509) hydrogen bonds : angle 8.40269 ( 1365) SS BOND : bond 0.02690 ( 24) SS BOND : angle 1.52119 ( 48) covalent geometry : bond 0.00712 (15204) covalent geometry : angle 1.15047 (20580) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 333 time to evaluate : 1.629 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: 1.0950 time to fit residues: 428.2560 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 : 1.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain D residue 209 ILE Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 209 ILE Chi-restraints excluded: chain F residue 143 ILE Chi-restraints excluded: chain F residue 209 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 151 optimal weight: 1.9990 chunk 136 optimal weight: 9.9990 chunk 75 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 92 optimal weight: 0.7980 chunk 72 optimal weight: 0.7980 chunk 141 optimal weight: 0.0980 chunk 54 optimal weight: 1.9990 chunk 85 optimal weight: 0.6980 chunk 105 optimal weight: 0.7980 chunk 163 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 ASN A 129 ASN A 162 ASN ** A 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 68 ASN ** B 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 162 ASN ** B 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 68 ASN ** C 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 162 ASN C 173 HIS ** C 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 68 ASN ** D 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 162 ASN ** D 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 162 ASN F 68 ASN F 129 ASN F 162 ASN ** F 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.207821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.178363 restraints weight = 12798.450| |-----------------------------------------------------------------------------| r_work (start): 0.3911 rms_B_bonded: 0.89 r_work: 0.3520 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.3272 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3249 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3249 r_free = 0.3249 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 786 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3211 r_free = 0.3211 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 788 | |-----------------------------------------------------------------------------| r_final: 0.3211 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 15228 Z= 0.147 Angle : 0.621 9.575 20628 Z= 0.321 Chirality : 0.048 0.190 2286 Planarity : 0.004 0.040 2628 Dihedral : 5.160 30.050 2022 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 4.85 % Allowed : 21.05 % Favored : 74.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.19), residues: 1818 helix: None (None), residues: 0 sheet: -0.50 (0.17), residues: 852 loop : -0.74 (0.20), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 57 HIS 0.011 0.001 HIS I 124 PHE 0.019 0.002 PHE H 56 TYR 0.008 0.001 TYR F 74 ARG 0.005 0.000 ARG C 219 Details of bonding type rmsd hydrogen bonds : bond 0.04196 ( 509) hydrogen bonds : angle 6.46450 ( 1365) SS BOND : bond 0.00252 ( 24) SS BOND : angle 0.66101 ( 48) covalent geometry : bond 0.00355 (15204) covalent geometry : angle 0.62122 (20580) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 230 time to evaluate : 1.641 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: 0.8335 (m) cc_final: 0.8018 (m) REVERT: B 47 ASP cc_start: 0.8573 (m-30) cc_final: 0.8284 (m-30) REVERT: B 55 GLU cc_start: 0.8542 (tp30) cc_final: 0.7749 (tp30) REVERT: B 84 ASP cc_start: 0.8372 (OUTLIER) cc_final: 0.8095 (t70) REVERT: C 85 THR cc_start: 0.8603 (p) cc_final: 0.7108 (t) REVERT: C 119 ILE cc_start: 0.8755 (OUTLIER) cc_final: 0.8226 (mm) REVERT: D 47 ASP cc_start: 0.8619 (m-30) cc_final: 0.8410 (m-30) REVERT: D 83 MET cc_start: 0.8554 (mmm) cc_final: 0.8201 (mmt) REVERT: D 85 THR cc_start: 0.8665 (p) cc_final: 0.7287 (t) REVERT: D 164 GLU cc_start: 0.8428 (mm-30) cc_final: 0.8213 (mm-30) REVERT: E 39 GLU cc_start: 0.7872 (tm-30) cc_final: 0.7659 (tm-30) REVERT: E 85 THR cc_start: 0.8723 (p) cc_final: 0.7141 (t) REVERT: E 101 LYS cc_start: 0.8515 (tppt) cc_final: 0.8313 (tppt) REVERT: F 47 ASP cc_start: 0.8660 (m-30) cc_final: 0.8344 (m-30) REVERT: F 119 ILE cc_start: 0.8814 (OUTLIER) cc_final: 0.8041 (mm) REVERT: F 141 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.7969 (tm-30) REVERT: G 100 LEU cc_start: 0.7155 (OUTLIER) cc_final: 0.6914 (mt) REVERT: H 100 LEU cc_start: 0.7317 (OUTLIER) cc_final: 0.6963 (mt) REVERT: I 100 LEU cc_start: 0.7057 (OUTLIER) cc_final: 0.6802 (mt) REVERT: J 100 LEU cc_start: 0.6773 (OUTLIER) cc_final: 0.6509 (mt) REVERT: L 100 LEU cc_start: 0.7151 (OUTLIER) cc_final: 0.6903 (mt) outliers start: 83 outliers final: 44 residues processed: 289 average time/residue: 1.3194 time to fit residues: 428.0129 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 : 1.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 193 SER Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 193 SER Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 59 SER Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 193 SER Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 143 ILE Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 193 SER Chi-restraints excluded: chain E residue 59 SER Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain E residue 138 ASP Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 193 SER Chi-restraints excluded: chain F residue 59 SER Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 84 ASP Chi-restraints excluded: chain F residue 85 THR Chi-restraints excluded: chain F residue 119 ILE Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain F residue 141 GLU Chi-restraints excluded: chain F residue 143 ILE Chi-restraints excluded: chain F residue 152 THR Chi-restraints excluded: chain F residue 193 SER Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain J residue 100 LEU Chi-restraints excluded: chain L residue 100 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 152 optimal weight: 6.9990 chunk 15 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 88 optimal weight: 0.9980 chunk 106 optimal weight: 0.8980 chunk 9 optimal weight: 6.9990 chunk 64 optimal weight: 0.7980 chunk 139 optimal weight: 4.9990 chunk 94 optimal weight: 0.8980 chunk 96 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 184 HIS ** B 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 184 HIS ** E 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.201079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.133997 restraints weight = 12989.187| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 2.58 r_work: 0.3152 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3024 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3024 r_free = 0.3024 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 788 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3022 r_free = 0.3022 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 790 | |-----------------------------------------------------------------------------| r_final: 0.3022 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 15228 Z= 0.164 Angle : 0.595 8.498 20628 Z= 0.312 Chirality : 0.048 0.169 2286 Planarity : 0.004 0.038 2628 Dihedral : 5.052 32.514 2012 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 6.08 % Allowed : 20.23 % Favored : 73.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.20), residues: 1818 helix: None (None), residues: 0 sheet: -0.50 (0.17), residues: 840 loop : -0.54 (0.21), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 34 HIS 0.008 0.001 HIS I 124 PHE 0.020 0.001 PHE H 56 TYR 0.010 0.001 TYR B 183 ARG 0.004 0.000 ARG A 191 Details of bonding type rmsd hydrogen bonds : bond 0.04046 ( 509) hydrogen bonds : angle 6.25539 ( 1365) SS BOND : bond 0.00326 ( 24) SS BOND : angle 0.65193 ( 48) covalent geometry : bond 0.00383 (15204) covalent geometry : angle 0.59445 (20580) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 211 time to evaluate : 1.582 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: 0.8428 (m) cc_final: 0.8095 (m) REVERT: B 39 GLU cc_start: 0.7950 (tm-30) cc_final: 0.7742 (tp30) REVERT: B 55 GLU cc_start: 0.8690 (tp30) cc_final: 0.8256 (tp30) REVERT: B 84 ASP cc_start: 0.8128 (OUTLIER) cc_final: 0.7841 (t70) REVERT: B 119 ILE cc_start: 0.8737 (OUTLIER) cc_final: 0.8153 (mm) REVERT: B 138 ASP cc_start: 0.8083 (OUTLIER) cc_final: 0.7740 (m-30) REVERT: C 39 GLU cc_start: 0.8022 (tm-30) cc_final: 0.7697 (tp30) REVERT: C 80 MET cc_start: 0.9149 (OUTLIER) cc_final: 0.8880 (ttt) REVERT: C 85 THR cc_start: 0.8759 (p) cc_final: 0.7198 (t) REVERT: D 60 GLU cc_start: 0.7782 (tm-30) cc_final: 0.7247 (tm-30) REVERT: D 85 THR cc_start: 0.8710 (p) cc_final: 0.7434 (t) REVERT: D 165 THR cc_start: 0.8434 (OUTLIER) cc_final: 0.8071 (m) REVERT: D 170 ILE cc_start: 0.8652 (tp) cc_final: 0.8435 (tp) REVERT: E 39 GLU cc_start: 0.7957 (tm-30) cc_final: 0.7703 (tp30) REVERT: E 55 GLU cc_start: 0.8644 (tp30) cc_final: 0.8242 (tp30) REVERT: E 65 ARG cc_start: 0.8701 (mtp180) cc_final: 0.8483 (mtp180) REVERT: E 101 LYS cc_start: 0.8727 (tppt) cc_final: 0.8423 (mmtp) REVERT: E 187 GLU cc_start: 0.8087 (mt-10) cc_final: 0.7849 (mt-10) REVERT: F 39 GLU cc_start: 0.7958 (tm-30) cc_final: 0.7661 (tp30) REVERT: F 47 ASP cc_start: 0.8847 (m-30) cc_final: 0.8569 (m-30) REVERT: F 141 GLU cc_start: 0.8648 (OUTLIER) cc_final: 0.8112 (tm-30) REVERT: F 207 LEU cc_start: 0.7168 (OUTLIER) cc_final: 0.6934 (mp) REVERT: G 100 LEU cc_start: 0.7062 (OUTLIER) cc_final: 0.6852 (mt) REVERT: H 111 ILE cc_start: 0.8080 (OUTLIER) cc_final: 0.7792 (mm) REVERT: I 100 LEU cc_start: 0.7074 (OUTLIER) cc_final: 0.6859 (mt) REVERT: J 100 LEU cc_start: 0.6865 (OUTLIER) cc_final: 0.6657 (mt) REVERT: L 100 LEU cc_start: 0.7129 (OUTLIER) cc_final: 0.6917 (mt) outliers start: 104 outliers final: 45 residues processed: 289 average time/residue: 1.0572 time to fit residues: 341.2857 Evaluate side-chains 257 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 200 time to evaluate : 1.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 193 SER Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 60 GLU Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 84 ASP 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 80 MET Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 193 SER Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain D residue 101 LYS Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 143 ILE Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 193 SER Chi-restraints excluded: chain E residue 59 SER Chi-restraints excluded: chain E residue 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 84 ASP Chi-restraints excluded: chain F residue 85 THR Chi-restraints excluded: chain F residue 141 GLU Chi-restraints excluded: chain F residue 143 ILE Chi-restraints excluded: chain F residue 152 THR Chi-restraints excluded: chain F residue 193 SER Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain G residue 120 MET Chi-restraints excluded: chain H residue 111 ILE 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 L residue 100 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 27 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 95 optimal weight: 0.0060 chunk 48 optimal weight: 0.8980 chunk 143 optimal weight: 0.7980 chunk 101 optimal weight: 2.9990 chunk 53 optimal weight: 0.5980 chunk 88 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 HIS ** A 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 184 HIS B 116 HIS ** B 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 116 HIS ** C 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 184 HIS E 68 ASN ** E 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.199142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.133592 restraints weight = 13079.816| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 3.06 r_work: 0.3121 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2982 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2982 r_free = 0.2982 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 790 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2981 r_free = 0.2981 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 791 | |-----------------------------------------------------------------------------| r_final: 0.2981 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.2739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15228 Z= 0.134 Angle : 0.549 7.536 20628 Z= 0.291 Chirality : 0.046 0.159 2286 Planarity : 0.003 0.036 2628 Dihedral : 4.960 33.163 2012 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 5.67 % Allowed : 20.88 % Favored : 73.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.20), residues: 1818 helix: None (None), residues: 0 sheet: -0.49 (0.17), residues: 846 loop : -0.47 (0.21), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP L 57 HIS 0.006 0.001 HIS I 124 PHE 0.020 0.001 PHE K 56 TYR 0.007 0.001 TYR D 74 ARG 0.005 0.000 ARG A 191 Details of bonding type rmsd hydrogen bonds : bond 0.03676 ( 509) hydrogen bonds : angle 6.20421 ( 1365) SS BOND : bond 0.00227 ( 24) SS BOND : angle 0.49742 ( 48) covalent geometry : bond 0.00308 (15204) covalent geometry : angle 0.54956 (20580) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 202 time to evaluate : 1.673 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: 0.8111 (tm-30) cc_final: 0.7891 (tp30) REVERT: A 49 ASN cc_start: 0.7964 (p0) cc_final: 0.7594 (m110) REVERT: A 84 ASP cc_start: 0.8097 (OUTLIER) cc_final: 0.7892 (t70) REVERT: A 94 GLU cc_start: 0.8656 (mt-10) cc_final: 0.8326 (mt-10) REVERT: A 141 GLU cc_start: 0.8743 (OUTLIER) cc_final: 0.8338 (tm-30) REVERT: A 165 THR cc_start: 0.8475 (m) cc_final: 0.8170 (m) REVERT: B 39 GLU cc_start: 0.8005 (tm-30) cc_final: 0.7776 (tp30) REVERT: B 47 ASP cc_start: 0.8756 (m-30) cc_final: 0.8367 (m-30) REVERT: B 55 GLU cc_start: 0.8766 (tp30) cc_final: 0.8335 (tp30) REVERT: B 83 MET cc_start: 0.8595 (mmt) cc_final: 0.8391 (mmt) REVERT: B 119 ILE cc_start: 0.8783 (OUTLIER) cc_final: 0.8242 (mm) REVERT: B 138 ASP cc_start: 0.8139 (OUTLIER) cc_final: 0.7877 (m-30) REVERT: C 39 GLU cc_start: 0.8054 (tm-30) cc_final: 0.7679 (tp30) REVERT: C 141 GLU cc_start: 0.8643 (OUTLIER) cc_final: 0.8073 (tm-30) REVERT: C 220 GLU cc_start: 0.6607 (OUTLIER) cc_final: 0.5293 (mp0) REVERT: D 47 ASP cc_start: 0.8818 (m-30) cc_final: 0.8574 (m-30) REVERT: D 85 THR cc_start: 0.8748 (p) cc_final: 0.7384 (t) REVERT: D 165 THR cc_start: 0.8451 (m) cc_final: 0.8108 (m) REVERT: E 39 GLU cc_start: 0.7982 (tm-30) cc_final: 0.7736 (tp30) REVERT: E 65 ARG cc_start: 0.8752 (mtp180) cc_final: 0.8530 (mtp180) REVERT: E 80 MET cc_start: 0.9037 (ttm) cc_final: 0.8809 (ttt) REVERT: E 138 ASP cc_start: 0.8195 (OUTLIER) cc_final: 0.7921 (m-30) REVERT: F 39 GLU cc_start: 0.8024 (tm-30) cc_final: 0.7663 (tp30) REVERT: F 47 ASP cc_start: 0.8885 (m-30) cc_final: 0.8618 (m-30) REVERT: F 141 GLU cc_start: 0.8612 (OUTLIER) cc_final: 0.8020 (tm-30) REVERT: G 126 MET cc_start: 0.8050 (OUTLIER) cc_final: 0.7637 (ttp) REVERT: I 100 LEU cc_start: 0.7095 (OUTLIER) cc_final: 0.6882 (mt) REVERT: J 100 LEU cc_start: 0.6929 (OUTLIER) cc_final: 0.6725 (mt) REVERT: L 100 LEU cc_start: 0.7131 (OUTLIER) cc_final: 0.6915 (mt) outliers start: 97 outliers final: 49 residues processed: 274 average time/residue: 1.1443 time to fit residues: 348.8318 Evaluate side-chains 252 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 191 time to evaluate : 1.684 ------------------------------------------------------------------------------- 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 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 141 GLU Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 193 SER Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 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 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 82 ILE Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 143 ILE Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 159 THR Chi-restraints excluded: chain D residue 193 SER Chi-restraints excluded: chain E residue 59 SER Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 138 ASP Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 193 SER Chi-restraints excluded: chain E residue 197 THR Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 59 SER Chi-restraints excluded: chain F residue 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 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 L residue 100 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 69 optimal weight: 0.6980 chunk 91 optimal weight: 0.9990 chunk 93 optimal weight: 0.5980 chunk 8 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 118 optimal weight: 0.9990 chunk 64 optimal weight: 0.9980 chunk 129 optimal weight: 0.8980 chunk 18 optimal weight: 0.4980 chunk 54 optimal weight: 0.9990 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 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 184 HIS ** E 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.199723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.131600 restraints weight = 13036.082| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 2.84 r_work: 0.3170 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3032 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3032 r_free = 0.3032 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 791 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3031 r_free = 0.3031 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 790 | |-----------------------------------------------------------------------------| r_final: 0.3031 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.2949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15228 Z= 0.143 Angle : 0.547 7.072 20628 Z= 0.291 Chirality : 0.046 0.154 2286 Planarity : 0.003 0.035 2628 Dihedral : 4.952 33.655 2012 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 5.85 % Allowed : 21.17 % Favored : 72.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.20), residues: 1818 helix: None (None), residues: 0 sheet: -0.50 (0.17), residues: 846 loop : -0.45 (0.21), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP L 57 HIS 0.006 0.001 HIS I 124 PHE 0.020 0.001 PHE K 56 TYR 0.007 0.001 TYR D 74 ARG 0.004 0.000 ARG A 191 Details of bonding type rmsd hydrogen bonds : bond 0.03654 ( 509) hydrogen bonds : angle 6.18173 ( 1365) SS BOND : bond 0.00238 ( 24) SS BOND : angle 0.51034 ( 48) covalent geometry : bond 0.00328 (15204) covalent geometry : angle 0.54719 (20580) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 189 time to evaluate : 1.539 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: 0.8025 (tm-30) cc_final: 0.7801 (tp30) REVERT: A 49 ASN cc_start: 0.7925 (p0) cc_final: 0.7628 (m110) REVERT: A 94 GLU cc_start: 0.8725 (mt-10) cc_final: 0.8384 (mt-10) REVERT: A 165 THR cc_start: 0.8376 (m) cc_final: 0.8052 (m) REVERT: B 39 GLU cc_start: 0.7909 (tm-30) cc_final: 0.7683 (tp30) REVERT: B 49 ASN cc_start: 0.8044 (p0) cc_final: 0.7685 (m-40) REVERT: B 119 ILE cc_start: 0.8769 (OUTLIER) cc_final: 0.8220 (mm) REVERT: B 138 ASP cc_start: 0.8087 (OUTLIER) cc_final: 0.7816 (m-30) REVERT: C 39 GLU cc_start: 0.7928 (tm-30) cc_final: 0.7598 (tp30) REVERT: C 110 GLN cc_start: 0.8349 (tt0) cc_final: 0.8145 (tt0) REVERT: C 141 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.8069 (tm-30) REVERT: C 220 GLU cc_start: 0.6541 (OUTLIER) cc_final: 0.4982 (mp0) REVERT: D 47 ASP cc_start: 0.8760 (m-30) cc_final: 0.8527 (m-30) REVERT: D 85 THR cc_start: 0.8779 (p) cc_final: 0.7453 (t) REVERT: D 165 THR cc_start: 0.8419 (m) cc_final: 0.8050 (m) REVERT: E 39 GLU cc_start: 0.7872 (tm-30) cc_final: 0.7638 (tp30) REVERT: E 55 GLU cc_start: 0.8688 (tp30) cc_final: 0.8300 (tp30) REVERT: E 65 ARG cc_start: 0.8682 (mtp180) cc_final: 0.8442 (mtp180) REVERT: E 80 MET cc_start: 0.9049 (ttm) cc_final: 0.8808 (ttt) REVERT: E 138 ASP cc_start: 0.8089 (OUTLIER) cc_final: 0.7847 (m-30) REVERT: F 39 GLU cc_start: 0.7958 (tm-30) cc_final: 0.7698 (tp30) REVERT: F 110 GLN cc_start: 0.8342 (tt0) cc_final: 0.8138 (tt0) REVERT: F 141 GLU cc_start: 0.8598 (OUTLIER) cc_final: 0.8105 (tm-30) REVERT: G 63 LEU cc_start: 0.7121 (OUTLIER) cc_final: 0.6909 (mt) REVERT: G 126 MET cc_start: 0.7936 (OUTLIER) cc_final: 0.7491 (ttp) REVERT: I 100 LEU cc_start: 0.7130 (OUTLIER) cc_final: 0.6892 (mt) REVERT: J 63 LEU cc_start: 0.7185 (OUTLIER) cc_final: 0.6915 (mt) REVERT: J 100 LEU cc_start: 0.6983 (OUTLIER) cc_final: 0.6776 (mt) REVERT: L 100 LEU cc_start: 0.7217 (OUTLIER) cc_final: 0.6975 (mt) outliers start: 100 outliers final: 49 residues processed: 273 average time/residue: 1.0658 time to fit residues: 325.4381 Evaluate side-chains 244 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 183 time to evaluate : 1.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 193 SER Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 193 SER Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 59 SER Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 141 GLU Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 193 SER Chi-restraints excluded: chain C residue 220 GLU Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 143 ILE Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 159 THR Chi-restraints excluded: chain D residue 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 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 126 MET 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 100 LEU Chi-restraints excluded: chain L residue 100 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 51 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 106 optimal weight: 0.9980 chunk 89 optimal weight: 3.9990 chunk 152 optimal weight: 0.0370 chunk 86 optimal weight: 0.5980 chunk 149 optimal weight: 0.0980 chunk 46 optimal weight: 0.9990 chunk 133 optimal weight: 7.9990 chunk 169 optimal weight: 5.9990 chunk 73 optimal weight: 1.9990 overall best weight: 0.5460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 184 HIS ** B 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 184 HIS ** E 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.201591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.140689 restraints weight = 13082.800| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 2.46 r_work: 0.3149 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3011 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3011 r_free = 0.3011 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 790 | |-----------------------------------------------------------------------------| |-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: 789 | |-----------------------------------------------------------------------------| r_final: 0.3010 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.3083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15228 Z= 0.121 Angle : 0.526 12.762 20628 Z= 0.280 Chirality : 0.045 0.153 2286 Planarity : 0.003 0.035 2628 Dihedral : 4.833 34.084 2012 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 5.73 % Allowed : 21.87 % Favored : 72.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.20), residues: 1818 helix: None (None), residues: 0 sheet: -0.48 (0.17), residues: 840 loop : -0.51 (0.21), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 93 HIS 0.005 0.001 HIS I 124 PHE 0.019 0.001 PHE K 56 TYR 0.006 0.001 TYR D 74 ARG 0.003 0.000 ARG A 191 Details of bonding type rmsd hydrogen bonds : bond 0.03448 ( 509) hydrogen bonds : angle 6.12847 ( 1365) SS BOND : bond 0.00183 ( 24) SS BOND : angle 0.46146 ( 48) covalent geometry : bond 0.00273 (15204) covalent geometry : angle 0.52606 (20580) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 186 time to evaluate : 1.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 ASN cc_start: 0.7951 (p0) cc_final: 0.7699 (m110) REVERT: A 165 THR cc_start: 0.8423 (m) cc_final: 0.8105 (m) REVERT: B 39 GLU cc_start: 0.7967 (tm-30) cc_final: 0.7745 (tp30) REVERT: B 49 ASN cc_start: 0.8064 (p0) cc_final: 0.7767 (m-40) REVERT: B 119 ILE cc_start: 0.8795 (OUTLIER) cc_final: 0.8245 (mm) REVERT: B 138 ASP cc_start: 0.8122 (OUTLIER) cc_final: 0.7902 (m-30) REVERT: C 39 GLU cc_start: 0.7927 (tm-30) cc_final: 0.7623 (tp30) REVERT: C 141 GLU cc_start: 0.8507 (OUTLIER) cc_final: 0.8177 (tm-30) REVERT: C 165 THR cc_start: 0.8425 (m) cc_final: 0.8182 (m) REVERT: C 220 GLU cc_start: 0.6575 (OUTLIER) cc_final: 0.5020 (mp0) REVERT: D 47 ASP cc_start: 0.8827 (m-30) cc_final: 0.8593 (m-30) REVERT: D 49 ASN cc_start: 0.7968 (p0) cc_final: 0.7674 (m110) REVERT: D 85 THR cc_start: 0.8781 (p) cc_final: 0.7359 (t) REVERT: D 165 THR cc_start: 0.8366 (m) cc_final: 0.8002 (m) REVERT: E 39 GLU cc_start: 0.7940 (tm-30) cc_final: 0.7713 (tp30) REVERT: E 55 GLU cc_start: 0.8730 (tp30) cc_final: 0.8353 (tp30) REVERT: E 65 ARG cc_start: 0.8731 (mtp180) cc_final: 0.8473 (mtp180) REVERT: E 80 MET cc_start: 0.9025 (ttm) cc_final: 0.8805 (ttt) REVERT: F 39 GLU cc_start: 0.8000 (tm-30) cc_final: 0.7700 (tp30) REVERT: F 60 GLU cc_start: 0.7377 (OUTLIER) cc_final: 0.7117 (tm-30) REVERT: F 141 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.7995 (tm-30) REVERT: I 63 LEU cc_start: 0.7214 (OUTLIER) cc_final: 0.6877 (mt) REVERT: I 100 LEU cc_start: 0.7261 (OUTLIER) cc_final: 0.7005 (mt) REVERT: I 126 MET cc_start: 0.8091 (ttp) cc_final: 0.7870 (ptm) REVERT: J 63 LEU cc_start: 0.7341 (OUTLIER) cc_final: 0.7081 (mt) REVERT: J 100 LEU cc_start: 0.6985 (OUTLIER) cc_final: 0.6782 (mt) REVERT: L 100 LEU cc_start: 0.7258 (OUTLIER) cc_final: 0.6996 (mt) REVERT: L 126 MET cc_start: 0.8106 (ttp) cc_final: 0.7886 (ptm) outliers start: 98 outliers final: 47 residues processed: 261 average time/residue: 1.1690 time to fit residues: 343.5763 Evaluate side-chains 248 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 190 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 127 GLU Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 193 SER Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 193 SER Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 141 GLU Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 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 104 VAL Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 143 ILE Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 159 THR Chi-restraints excluded: chain D residue 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 124 THR Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 197 THR Chi-restraints excluded: chain F residue 48 ILE 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 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 100 LEU Chi-restraints excluded: chain L residue 100 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 40 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 70 optimal weight: 0.5980 chunk 91 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 157 optimal weight: 9.9990 chunk 122 optimal weight: 10.0000 chunk 52 optimal weight: 0.0670 chunk 80 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 10 optimal weight: 0.0030 overall best weight: 1.1332 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 184 HIS ** B 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 184 HIS ** E 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.198341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.130891 restraints weight = 12997.805| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 3.47 r_work: 0.3125 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2992 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2992 r_free = 0.2992 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 789 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2992 r_free = 0.2992 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 789 | |-----------------------------------------------------------------------------| r_final: 0.2992 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.3252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 15228 Z= 0.185 Angle : 0.572 11.281 20628 Z= 0.305 Chirality : 0.047 0.157 2286 Planarity : 0.003 0.036 2628 Dihedral : 5.058 36.303 2012 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 5.56 % Allowed : 22.28 % Favored : 72.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.20), residues: 1818 helix: None (None), residues: 0 sheet: -0.51 (0.18), residues: 846 loop : -0.46 (0.21), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 93 HIS 0.006 0.001 HIS I 124 PHE 0.019 0.001 PHE K 56 TYR 0.009 0.001 TYR A 74 ARG 0.005 0.000 ARG A 191 Details of bonding type rmsd hydrogen bonds : bond 0.03778 ( 509) hydrogen bonds : angle 6.21081 ( 1365) SS BOND : bond 0.00283 ( 24) SS BOND : angle 0.60184 ( 48) covalent geometry : bond 0.00427 (15204) covalent geometry : angle 0.57181 (20580) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 195 time to evaluate : 1.758 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: 0.8071 (tm-30) cc_final: 0.7865 (tp30) REVERT: A 49 ASN cc_start: 0.7971 (p0) cc_final: 0.7764 (m110) REVERT: A 141 GLU cc_start: 0.8823 (tm-30) cc_final: 0.8612 (tm-30) REVERT: A 165 THR cc_start: 0.8400 (m) cc_final: 0.8067 (m) REVERT: B 39 GLU cc_start: 0.7924 (tm-30) cc_final: 0.7709 (tp30) REVERT: B 49 ASN cc_start: 0.8082 (p0) cc_final: 0.7785 (m-40) REVERT: B 55 GLU cc_start: 0.8711 (tp30) cc_final: 0.8324 (tp30) REVERT: B 119 ILE cc_start: 0.8821 (OUTLIER) cc_final: 0.8278 (mm) REVERT: B 138 ASP cc_start: 0.8129 (OUTLIER) cc_final: 0.7824 (m-30) REVERT: C 39 GLU cc_start: 0.7988 (tm-30) cc_final: 0.7671 (tp30) REVERT: C 60 GLU cc_start: 0.7455 (OUTLIER) cc_final: 0.7235 (tt0) REVERT: C 88 ARG cc_start: 0.8978 (ptp-110) cc_final: 0.8744 (ptp90) REVERT: C 110 GLN cc_start: 0.8514 (tt0) cc_final: 0.8257 (tt0) REVERT: C 141 GLU cc_start: 0.8702 (OUTLIER) cc_final: 0.8254 (tm-30) REVERT: C 220 GLU cc_start: 0.6616 (OUTLIER) cc_final: 0.5089 (mp0) REVERT: D 39 GLU cc_start: 0.8093 (tm-30) cc_final: 0.7862 (tp30) REVERT: D 49 ASN cc_start: 0.8032 (p0) cc_final: 0.7752 (m110) REVERT: D 72 THR cc_start: 0.8839 (p) cc_final: 0.8104 (m) REVERT: D 85 THR cc_start: 0.8782 (p) cc_final: 0.7547 (t) REVERT: D 165 THR cc_start: 0.8481 (OUTLIER) cc_final: 0.8094 (m) REVERT: D 169 LYS cc_start: 0.8528 (OUTLIER) cc_final: 0.7925 (pmtt) REVERT: E 39 GLU cc_start: 0.7927 (tm-30) cc_final: 0.7689 (tp30) REVERT: E 49 ASN cc_start: 0.8094 (p0) cc_final: 0.7683 (m110) REVERT: F 39 GLU cc_start: 0.7993 (tm-30) cc_final: 0.7693 (tp30) REVERT: F 110 GLN cc_start: 0.8485 (tt0) cc_final: 0.8252 (tt0) REVERT: F 141 GLU cc_start: 0.8707 (OUTLIER) cc_final: 0.8222 (tm-30) REVERT: F 220 GLU cc_start: 0.6810 (OUTLIER) cc_final: 0.6113 (mt-10) REVERT: I 63 LEU cc_start: 0.7066 (OUTLIER) cc_final: 0.6715 (mt) REVERT: I 100 LEU cc_start: 0.7286 (OUTLIER) cc_final: 0.7024 (mt) REVERT: I 126 MET cc_start: 0.8019 (ttp) cc_final: 0.7716 (ptm) REVERT: J 63 LEU cc_start: 0.7182 (OUTLIER) cc_final: 0.6930 (mt) REVERT: L 126 MET cc_start: 0.8009 (ttp) cc_final: 0.7732 (ptm) outliers start: 95 outliers final: 55 residues processed: 271 average time/residue: 1.0783 time to fit residues: 326.4470 Evaluate side-chains 251 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 184 time to evaluate : 1.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 193 SER Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 193 SER Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 59 SER Chi-restraints excluded: chain C residue 60 GLU Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 141 GLU Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 193 SER Chi-restraints excluded: chain C residue 220 GLU Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain D residue 101 LYS Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 127 GLU Chi-restraints excluded: chain D residue 143 ILE Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 159 THR Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 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 124 THR Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 193 SER Chi-restraints excluded: chain E residue 197 THR Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 59 SER Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 85 THR Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain F residue 141 GLU Chi-restraints excluded: chain F residue 143 ILE Chi-restraints excluded: chain F residue 152 THR Chi-restraints excluded: chain F residue 193 SER Chi-restraints excluded: chain F residue 220 GLU Chi-restraints excluded: chain I residue 63 LEU Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain J residue 63 LEU Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain L residue 100 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 13 optimal weight: 2.9990 chunk 96 optimal weight: 0.7980 chunk 149 optimal weight: 4.9990 chunk 7 optimal weight: 0.9990 chunk 89 optimal weight: 2.9990 chunk 151 optimal weight: 8.9990 chunk 94 optimal weight: 0.2980 chunk 83 optimal weight: 2.9990 chunk 91 optimal weight: 0.5980 chunk 54 optimal weight: 0.5980 chunk 74 optimal weight: 0.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- 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 116 HIS ** D 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 184 HIS ** E 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.199965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.135668 restraints weight = 13045.141| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 2.77 r_work: 0.3108 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2976 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2976 r_free = 0.2976 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 789 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2976 r_free = 0.2976 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 789 | |-----------------------------------------------------------------------------| r_final: 0.2976 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.3293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15228 Z= 0.134 Angle : 0.540 11.095 20628 Z= 0.287 Chirality : 0.046 0.156 2286 Planarity : 0.003 0.035 2628 Dihedral : 4.919 34.377 2012 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 4.91 % Allowed : 22.92 % Favored : 72.16 % 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: -0.54 (0.18), residues: 846 loop : -0.46 (0.21), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 93 HIS 0.005 0.001 HIS I 124 PHE 0.017 0.001 PHE K 56 TYR 0.007 0.001 TYR A 74 ARG 0.006 0.000 ARG A 191 Details of bonding type rmsd hydrogen bonds : bond 0.03526 ( 509) hydrogen bonds : angle 6.18951 ( 1365) SS BOND : bond 0.00210 ( 24) SS BOND : angle 0.50598 ( 48) covalent geometry : bond 0.00306 (15204) covalent geometry : angle 0.54005 (20580) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 182 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 49 ASN cc_start: 0.7990 (p0) cc_final: 0.7786 (m110) REVERT: A 55 GLU cc_start: 0.8696 (tp30) cc_final: 0.8219 (tp30) REVERT: A 141 GLU cc_start: 0.8811 (OUTLIER) cc_final: 0.8581 (tm-30) REVERT: A 165 THR cc_start: 0.8441 (m) cc_final: 0.8113 (m) REVERT: B 39 GLU cc_start: 0.7956 (tm-30) cc_final: 0.7734 (tp30) REVERT: B 49 ASN cc_start: 0.8112 (p0) cc_final: 0.7827 (m-40) REVERT: B 55 GLU cc_start: 0.8696 (tp30) cc_final: 0.8289 (tp30) REVERT: B 119 ILE cc_start: 0.8833 (OUTLIER) cc_final: 0.8308 (mm) REVERT: B 138 ASP cc_start: 0.8183 (OUTLIER) cc_final: 0.7941 (m-30) REVERT: C 39 GLU cc_start: 0.7980 (tm-30) cc_final: 0.7641 (tp30) REVERT: C 141 GLU cc_start: 0.8577 (OUTLIER) cc_final: 0.8057 (tm-30) REVERT: D 49 ASN cc_start: 0.8065 (p0) cc_final: 0.7783 (m110) REVERT: D 55 GLU cc_start: 0.8684 (tp30) cc_final: 0.8172 (tp30) REVERT: D 85 THR cc_start: 0.8808 (p) cc_final: 0.7443 (t) REVERT: D 165 THR cc_start: 0.8459 (m) cc_final: 0.8133 (m) REVERT: E 39 GLU cc_start: 0.7970 (tm-30) cc_final: 0.7726 (tp30) REVERT: E 49 ASN cc_start: 0.8132 (p0) cc_final: 0.7726 (m110) REVERT: E 80 MET cc_start: 0.9012 (ttm) cc_final: 0.8800 (ttt) REVERT: E 119 ILE cc_start: 0.8754 (OUTLIER) cc_final: 0.8173 (mm) REVERT: F 39 GLU cc_start: 0.8044 (tm-30) cc_final: 0.7702 (tp30) REVERT: F 47 ASP cc_start: 0.8844 (m-30) cc_final: 0.8578 (m-30) REVERT: F 141 GLU cc_start: 0.8646 (OUTLIER) cc_final: 0.8112 (tm-30) REVERT: I 63 LEU cc_start: 0.7210 (OUTLIER) cc_final: 0.6863 (mt) REVERT: I 100 LEU cc_start: 0.7304 (OUTLIER) cc_final: 0.7031 (mt) REVERT: I 126 MET cc_start: 0.8097 (ttp) cc_final: 0.7844 (ptm) REVERT: J 63 LEU cc_start: 0.7298 (OUTLIER) cc_final: 0.7055 (mt) outliers start: 84 outliers final: 52 residues processed: 256 average time/residue: 1.0880 time to fit residues: 312.5964 Evaluate side-chains 243 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 182 time to evaluate : 2.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 193 SER Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 193 SER Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 59 SER Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 141 GLU Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 193 SER Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain D residue 101 LYS Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 127 GLU Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 159 THR Chi-restraints excluded: chain D residue 193 SER Chi-restraints excluded: chain E residue 59 SER Chi-restraints excluded: chain E residue 82 ILE 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 143 ILE Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 193 SER Chi-restraints excluded: chain E residue 197 THR Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 59 SER Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 85 THR Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain F residue 141 GLU Chi-restraints excluded: chain F residue 143 ILE Chi-restraints excluded: chain F residue 152 THR Chi-restraints excluded: chain F residue 193 SER Chi-restraints excluded: chain I residue 63 LEU Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain J residue 63 LEU Chi-restraints excluded: chain L residue 100 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 111 optimal weight: 0.4980 chunk 101 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 149 optimal weight: 3.9990 chunk 51 optimal weight: 0.7980 chunk 78 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 179 optimal weight: 4.9990 chunk 148 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 184 HIS ** B 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 184 HIS E 68 ASN ** E 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 127 ASN ** I 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 127 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.194796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.128410 restraints weight = 13091.468| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 2.50 r_work: 0.3089 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2914 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2914 r_free = 0.2914 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 789 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2914 r_free = 0.2914 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 789 | |-----------------------------------------------------------------------------| r_final: 0.2914 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.3477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 15228 Z= 0.220 Angle : 0.615 13.478 20628 Z= 0.325 Chirality : 0.049 0.161 2286 Planarity : 0.004 0.037 2628 Dihedral : 5.218 37.101 2012 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 4.91 % Allowed : 23.27 % Favored : 71.81 % 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 (0.18), residues: 846 loop : -0.50 (0.21), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 34 HIS 0.006 0.001 HIS I 124 PHE 0.018 0.002 PHE K 56 TYR 0.011 0.002 TYR A 74 ARG 0.005 0.000 ARG A 191 Details of bonding type rmsd hydrogen bonds : bond 0.03935 ( 509) hydrogen bonds : angle 6.28638 ( 1365) SS BOND : bond 0.00384 ( 24) SS BOND : angle 0.72646 ( 48) covalent geometry : bond 0.00513 (15204) covalent geometry : angle 0.61503 (20580) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 178 time to evaluate : 2.112 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 ASN cc_start: 0.8122 (p0) cc_final: 0.7855 (m110) REVERT: A 141 GLU cc_start: 0.8916 (OUTLIER) cc_final: 0.8519 (tm-30) REVERT: A 165 THR cc_start: 0.8517 (m) cc_final: 0.8210 (m) REVERT: B 39 GLU cc_start: 0.8033 (tm-30) cc_final: 0.7825 (tp30) REVERT: B 49 ASN cc_start: 0.8208 (p0) cc_final: 0.7882 (m-40) REVERT: B 55 GLU cc_start: 0.8831 (tp30) cc_final: 0.8493 (tp30) REVERT: B 119 ILE cc_start: 0.8891 (OUTLIER) cc_final: 0.8348 (mm) REVERT: B 138 ASP cc_start: 0.8227 (OUTLIER) cc_final: 0.7948 (m-30) REVERT: C 39 GLU cc_start: 0.8022 (tm-30) cc_final: 0.7775 (tp30) REVERT: C 72 THR cc_start: 0.8871 (p) cc_final: 0.8313 (m) REVERT: C 141 GLU cc_start: 0.8725 (OUTLIER) cc_final: 0.8260 (tm-30) REVERT: C 165 THR cc_start: 0.8584 (m) cc_final: 0.8365 (m) REVERT: D 49 ASN cc_start: 0.8193 (p0) cc_final: 0.7881 (m110) REVERT: D 85 THR cc_start: 0.8803 (p) cc_final: 0.7646 (t) REVERT: D 165 THR cc_start: 0.8555 (OUTLIER) cc_final: 0.8207 (m) REVERT: E 39 GLU cc_start: 0.8033 (tm-30) cc_final: 0.7822 (tp30) REVERT: E 49 ASN cc_start: 0.8270 (p0) cc_final: 0.7834 (m110) REVERT: E 119 ILE cc_start: 0.8839 (OUTLIER) cc_final: 0.8254 (mm) REVERT: E 138 ASP cc_start: 0.8279 (OUTLIER) cc_final: 0.8026 (t0) REVERT: F 39 GLU cc_start: 0.8093 (tm-30) cc_final: 0.7783 (tp30) REVERT: F 72 THR cc_start: 0.8858 (p) cc_final: 0.8300 (m) REVERT: F 110 GLN cc_start: 0.8580 (tt0) cc_final: 0.8356 (tt0) REVERT: F 141 GLU cc_start: 0.8738 (OUTLIER) cc_final: 0.8220 (tm-30) REVERT: I 63 LEU cc_start: 0.7252 (OUTLIER) cc_final: 0.6947 (mt) REVERT: J 63 LEU cc_start: 0.7351 (OUTLIER) cc_final: 0.7118 (mt) outliers start: 84 outliers final: 56 residues processed: 249 average time/residue: 1.3857 time to fit residues: 384.1681 Evaluate side-chains 240 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 174 time to evaluate : 3.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 193 SER Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 127 GLU Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 193 SER Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 59 SER Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 141 GLU Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 193 SER Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain D residue 101 LYS Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 143 ILE Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 159 THR Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 193 SER Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 59 SER Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain E residue 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 I residue 63 LEU Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain J residue 63 LEU Chi-restraints excluded: chain L residue 100 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 69 optimal weight: 0.9990 chunk 99 optimal weight: 0.9980 chunk 101 optimal weight: 0.6980 chunk 160 optimal weight: 10.0000 chunk 8 optimal weight: 0.5980 chunk 35 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 146 optimal weight: 9.9990 chunk 150 optimal weight: 10.0000 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 184 HIS ** B 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 184 HIS E 68 ASN ** E 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 125 GLN H 127 ASN K 125 GLN K 127 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.196699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.131277 restraints weight = 13157.463| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 2.66 r_work: 0.3116 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2983 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2983 r_free = 0.2983 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 789 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2982 r_free = 0.2982 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 789 | |-----------------------------------------------------------------------------| r_final: 0.2982 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.3494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15228 Z= 0.157 Angle : 0.573 13.425 20628 Z= 0.302 Chirality : 0.046 0.162 2286 Planarity : 0.003 0.036 2628 Dihedral : 5.055 34.601 2012 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 4.44 % Allowed : 24.33 % Favored : 71.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.20), residues: 1818 helix: None (None), residues: 0 sheet: -0.51 (0.18), residues: 846 loop : -0.47 (0.21), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP I 93 HIS 0.006 0.001 HIS I 124 PHE 0.014 0.001 PHE I 56 TYR 0.008 0.001 TYR A 74 ARG 0.005 0.000 ARG A 191 Details of bonding type rmsd hydrogen bonds : bond 0.03658 ( 509) hydrogen bonds : angle 6.26201 ( 1365) SS BOND : bond 0.00274 ( 24) SS BOND : angle 0.62134 ( 48) covalent geometry : bond 0.00362 (15204) covalent geometry : angle 0.57289 (20580) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 181 time to evaluate : 2.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 GLU cc_start: 0.8833 (OUTLIER) cc_final: 0.8587 (tm-30) REVERT: A 165 THR cc_start: 0.8406 (m) cc_final: 0.8090 (m) REVERT: B 39 GLU cc_start: 0.7970 (tm-30) cc_final: 0.7732 (tp30) REVERT: B 49 ASN cc_start: 0.8102 (p0) cc_final: 0.7829 (m110) REVERT: B 55 GLU cc_start: 0.8683 (tp30) cc_final: 0.8304 (tp30) REVERT: B 119 ILE cc_start: 0.8837 (OUTLIER) cc_final: 0.8295 (mm) REVERT: B 138 ASP cc_start: 0.8107 (OUTLIER) cc_final: 0.7833 (m-30) REVERT: C 39 GLU cc_start: 0.7982 (tm-30) cc_final: 0.7638 (tp30) REVERT: C 110 GLN cc_start: 0.8420 (tt0) cc_final: 0.8192 (tt0) REVERT: C 141 GLU cc_start: 0.8644 (OUTLIER) cc_final: 0.8210 (tm-30) REVERT: D 49 ASN cc_start: 0.8022 (p0) cc_final: 0.7778 (m110) REVERT: D 85 THR cc_start: 0.8808 (p) cc_final: 0.7533 (t) REVERT: D 165 THR cc_start: 0.8435 (m) cc_final: 0.8092 (m) REVERT: E 39 GLU cc_start: 0.7959 (tm-30) cc_final: 0.7704 (tp30) REVERT: E 49 ASN cc_start: 0.8106 (p0) cc_final: 0.7750 (m110) REVERT: E 119 ILE cc_start: 0.8771 (OUTLIER) cc_final: 0.8174 (mm) REVERT: E 138 ASP cc_start: 0.8166 (OUTLIER) cc_final: 0.7906 (t0) REVERT: F 39 GLU cc_start: 0.8014 (tm-30) cc_final: 0.7647 (tp30) REVERT: F 110 GLN cc_start: 0.8397 (tt0) cc_final: 0.8153 (tt0) REVERT: F 141 GLU cc_start: 0.8662 (OUTLIER) cc_final: 0.8152 (tm-30) REVERT: I 63 LEU cc_start: 0.7169 (OUTLIER) cc_final: 0.6880 (mt) REVERT: J 63 LEU cc_start: 0.7261 (OUTLIER) cc_final: 0.7032 (mt) outliers start: 76 outliers final: 56 residues processed: 249 average time/residue: 1.5454 time to fit residues: 429.3217 Evaluate side-chains 238 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 173 time to evaluate : 1.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 193 SER Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 127 GLU Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 193 SER Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 59 SER Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 141 GLU Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 193 SER Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain D residue 101 LYS Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 127 GLU Chi-restraints excluded: chain D residue 143 ILE Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 159 THR Chi-restraints excluded: chain D residue 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 119 ILE Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 138 ASP Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 193 SER Chi-restraints excluded: chain E residue 197 THR Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 59 SER Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 85 THR Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain F residue 141 GLU Chi-restraints excluded: chain F residue 143 ILE Chi-restraints excluded: chain F residue 152 THR Chi-restraints excluded: chain F residue 193 SER Chi-restraints excluded: chain I residue 63 LEU Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain J residue 63 LEU Chi-restraints excluded: chain L residue 100 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 54 optimal weight: 0.9980 chunk 48 optimal weight: 0.7980 chunk 139 optimal weight: 4.9990 chunk 124 optimal weight: 10.0000 chunk 133 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 174 optimal weight: 10.0000 chunk 62 optimal weight: 0.9980 chunk 91 optimal weight: 0.8980 chunk 98 optimal weight: 0.9980 chunk 11 optimal weight: 0.7980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 129 ASN ** A 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 184 HIS ** B 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 127 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.197976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.130800 restraints weight = 13054.381| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 2.66 r_work: 0.3062 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2930 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2930 r_free = 0.2930 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 789 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2930 r_free = 0.2930 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 788 | |-----------------------------------------------------------------------------| r_final: 0.2930 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.3544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15228 Z= 0.162 Angle : 0.578 13.358 20628 Z= 0.305 Chirality : 0.047 0.161 2286 Planarity : 0.003 0.036 2628 Dihedral : 5.042 35.178 2012 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 4.62 % Allowed : 24.21 % Favored : 71.17 % 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: -0.84 (0.20), residues: 1818 helix: None (None), residues: 0 sheet: -0.53 (0.18), residues: 846 loop : -0.47 (0.21), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP I 93 HIS 0.006 0.001 HIS I 124 PHE 0.013 0.001 PHE L 56 TYR 0.009 0.001 TYR D 183 ARG 0.005 0.000 ARG C 65 Details of bonding type rmsd hydrogen bonds : bond 0.03701 ( 509) hydrogen bonds : angle 6.26760 ( 1365) SS BOND : bond 0.00277 ( 24) SS BOND : angle 0.60211 ( 48) covalent geometry : bond 0.00375 (15204) covalent geometry : angle 0.57768 (20580) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14264.25 seconds wall clock time: 250 minutes 22.09 seconds (15022.09 seconds total)