Starting phenix.real_space_refine on Tue Nov 18 10:09:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6e0f_8946/11_2025/6e0f_8946.cif Found real_map, /net/cci-nas-00/data/ceres_data/6e0f_8946/11_2025/6e0f_8946.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6e0f_8946/11_2025/6e0f_8946.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6e0f_8946/11_2025/6e0f_8946.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6e0f_8946/11_2025/6e0f_8946.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6e0f_8946/11_2025/6e0f_8946.map" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.014 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 80 5.16 5 C 8700 2.51 5 N 2320 2.21 5 O 2550 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13650 Number of models: 1 Model: "" Number of chains: 1 Chain: "J" Number of atoms: 1365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1365 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 7, 'TRANS': 166} Restraints were copied for chains: A, I, E, G, F, B, C, D, H Time building chain proxies: 1.61, per 1000 atoms: 0.12 Number of scatterers: 13650 At special positions: 0 Unit cell: (133, 135, 61, 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 80 16.00 O 2550 8.00 N 2320 7.00 C 8700 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.10 Conformation dependent library (CDL) restraints added in 640.9 milliseconds 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3240 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 15 sheets defined 27.6% alpha, 17.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'J' and resid 61 through 64 removed outlier: 3.623A pdb=" N LYS J 64 " --> pdb=" O ASN J 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 61 through 64' Processing helix chain 'J' and resid 82 through 90 removed outlier: 4.199A pdb=" N PHE J 88 " --> pdb=" O GLU J 84 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER J 89 " --> pdb=" O ILE J 85 " (cutoff:3.500A) Processing helix chain 'J' and resid 92 through 97 removed outlier: 3.634A pdb=" N GLU J 96 " --> pdb=" O HIS J 92 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS J 97 " --> pdb=" O ALA J 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 92 through 97' Processing helix chain 'J' and resid 109 through 119 Processing helix chain 'J' and resid 181 through 198 removed outlier: 3.961A pdb=" N LEU J 189 " --> pdb=" O ALA J 185 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLN J 193 " --> pdb=" O LEU J 189 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASN J 198 " --> pdb=" O TYR J 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 64 removed outlier: 3.622A pdb=" N LYS A 64 " --> pdb=" O ASN A 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 61 through 64' Processing helix chain 'A' and resid 82 through 90 removed outlier: 4.200A pdb=" N PHE A 88 " --> pdb=" O GLU A 84 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER A 89 " --> pdb=" O ILE A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 97 removed outlier: 3.633A pdb=" N GLU A 96 " --> pdb=" O HIS A 92 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS A 97 " --> pdb=" O ALA A 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 92 through 97' Processing helix chain 'A' and resid 109 through 119 Processing helix chain 'A' and resid 181 through 198 removed outlier: 3.961A pdb=" N LEU A 189 " --> pdb=" O ALA A 185 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N GLN A 193 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASN A 198 " --> pdb=" O TYR A 194 " (cutoff:3.500A) Processing helix chain 'I' and resid 61 through 64 removed outlier: 3.623A pdb=" N LYS I 64 " --> pdb=" O ASN I 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 61 through 64' Processing helix chain 'I' and resid 82 through 90 removed outlier: 4.198A pdb=" N PHE I 88 " --> pdb=" O GLU I 84 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER I 89 " --> pdb=" O ILE I 85 " (cutoff:3.500A) Processing helix chain 'I' and resid 92 through 97 removed outlier: 3.633A pdb=" N GLU I 96 " --> pdb=" O HIS I 92 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS I 97 " --> pdb=" O ALA I 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 92 through 97' Processing helix chain 'I' and resid 109 through 119 Processing helix chain 'I' and resid 181 through 198 removed outlier: 3.960A pdb=" N LEU I 189 " --> pdb=" O ALA I 185 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLN I 193 " --> pdb=" O LEU I 189 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASN I 198 " --> pdb=" O TYR I 194 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 64 removed outlier: 3.623A pdb=" N LYS E 64 " --> pdb=" O ASN E 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 61 through 64' Processing helix chain 'E' and resid 82 through 90 removed outlier: 4.199A pdb=" N PHE E 88 " --> pdb=" O GLU E 84 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER E 89 " --> pdb=" O ILE E 85 " (cutoff:3.500A) Processing helix chain 'E' and resid 92 through 97 removed outlier: 3.634A pdb=" N GLU E 96 " --> pdb=" O HIS E 92 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS E 97 " --> pdb=" O ALA E 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 92 through 97' Processing helix chain 'E' and resid 109 through 119 Processing helix chain 'E' and resid 181 through 198 removed outlier: 3.961A pdb=" N LEU E 189 " --> pdb=" O ALA E 185 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLN E 193 " --> pdb=" O LEU E 189 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASN E 198 " --> pdb=" O TYR E 194 " (cutoff:3.500A) Processing helix chain 'G' and resid 61 through 64 removed outlier: 3.623A pdb=" N LYS G 64 " --> pdb=" O ASN G 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 61 through 64' Processing helix chain 'G' and resid 82 through 90 removed outlier: 4.199A pdb=" N PHE G 88 " --> pdb=" O GLU G 84 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER G 89 " --> pdb=" O ILE G 85 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 97 removed outlier: 3.634A pdb=" N GLU G 96 " --> pdb=" O HIS G 92 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS G 97 " --> pdb=" O ALA G 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 92 through 97' Processing helix chain 'G' and resid 109 through 119 Processing helix chain 'G' and resid 181 through 198 removed outlier: 3.960A pdb=" N LEU G 189 " --> pdb=" O ALA G 185 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N GLN G 193 " --> pdb=" O LEU G 189 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASN G 198 " --> pdb=" O TYR G 194 " (cutoff:3.500A) Processing helix chain 'F' and resid 61 through 64 removed outlier: 3.622A pdb=" N LYS F 64 " --> pdb=" O ASN F 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 61 through 64' Processing helix chain 'F' and resid 82 through 90 removed outlier: 4.199A pdb=" N PHE F 88 " --> pdb=" O GLU F 84 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER F 89 " --> pdb=" O ILE F 85 " (cutoff:3.500A) Processing helix chain 'F' and resid 92 through 97 removed outlier: 3.634A pdb=" N GLU F 96 " --> pdb=" O HIS F 92 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS F 97 " --> pdb=" O ALA F 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 92 through 97' Processing helix chain 'F' and resid 109 through 119 Processing helix chain 'F' and resid 181 through 198 removed outlier: 3.960A pdb=" N LEU F 189 " --> pdb=" O ALA F 185 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLN F 193 " --> pdb=" O LEU F 189 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASN F 198 " --> pdb=" O TYR F 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 64 removed outlier: 3.623A pdb=" N LYS B 64 " --> pdb=" O ASN B 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 61 through 64' Processing helix chain 'B' and resid 82 through 90 removed outlier: 4.198A pdb=" N PHE B 88 " --> pdb=" O GLU B 84 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER B 89 " --> pdb=" O ILE B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 97 removed outlier: 3.634A pdb=" N GLU B 96 " --> pdb=" O HIS B 92 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS B 97 " --> pdb=" O ALA B 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 92 through 97' Processing helix chain 'B' and resid 109 through 119 Processing helix chain 'B' and resid 181 through 198 removed outlier: 3.960A pdb=" N LEU B 189 " --> pdb=" O ALA B 185 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLN B 193 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASN B 198 " --> pdb=" O TYR B 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 64 removed outlier: 3.622A pdb=" N LYS C 64 " --> pdb=" O ASN C 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 61 through 64' Processing helix chain 'C' and resid 82 through 90 removed outlier: 4.199A pdb=" N PHE C 88 " --> pdb=" O GLU C 84 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER C 89 " --> pdb=" O ILE C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 97 removed outlier: 3.633A pdb=" N GLU C 96 " --> pdb=" O HIS C 92 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS C 97 " --> pdb=" O ALA C 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 92 through 97' Processing helix chain 'C' and resid 109 through 119 Processing helix chain 'C' and resid 181 through 198 removed outlier: 3.960A pdb=" N LEU C 189 " --> pdb=" O ALA C 185 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLN C 193 " --> pdb=" O LEU C 189 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASN C 198 " --> pdb=" O TYR C 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 64 removed outlier: 3.623A pdb=" N LYS D 64 " --> pdb=" O ASN D 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 61 through 64' Processing helix chain 'D' and resid 82 through 90 removed outlier: 4.199A pdb=" N PHE D 88 " --> pdb=" O GLU D 84 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER D 89 " --> pdb=" O ILE D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 97 removed outlier: 3.634A pdb=" N GLU D 96 " --> pdb=" O HIS D 92 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS D 97 " --> pdb=" O ALA D 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 92 through 97' Processing helix chain 'D' and resid 109 through 119 Processing helix chain 'D' and resid 181 through 198 removed outlier: 3.961A pdb=" N LEU D 189 " --> pdb=" O ALA D 185 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N GLN D 193 " --> pdb=" O LEU D 189 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASN D 198 " --> pdb=" O TYR D 194 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 64 removed outlier: 3.622A pdb=" N LYS H 64 " --> pdb=" O ASN H 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 61 through 64' Processing helix chain 'H' and resid 82 through 90 removed outlier: 4.198A pdb=" N PHE H 88 " --> pdb=" O GLU H 84 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER H 89 " --> pdb=" O ILE H 85 " (cutoff:3.500A) Processing helix chain 'H' and resid 92 through 97 removed outlier: 3.633A pdb=" N GLU H 96 " --> pdb=" O HIS H 92 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS H 97 " --> pdb=" O ALA H 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 92 through 97' Processing helix chain 'H' and resid 109 through 119 Processing helix chain 'H' and resid 181 through 198 removed outlier: 3.960A pdb=" N LEU H 189 " --> pdb=" O ALA H 185 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLN H 193 " --> pdb=" O LEU H 189 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASN H 198 " --> pdb=" O TYR H 194 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'J' and resid 54 through 59 Processing sheet with id=AA2, first strand: chain 'J' and resid 100 through 105 removed outlier: 6.251A pdb=" N TYR J 67 " --> pdb=" O GLN J 101 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N VAL J 103 " --> pdb=" O TYR J 67 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N VAL J 69 " --> pdb=" O VAL J 103 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N VAL J 105 " --> pdb=" O VAL J 69 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N PHE J 71 " --> pdb=" O VAL J 105 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N TYR A 67 " --> pdb=" O GLN A 101 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N VAL A 103 " --> pdb=" O TYR A 67 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N VAL A 69 " --> pdb=" O VAL A 103 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N VAL A 105 " --> pdb=" O VAL A 69 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N PHE A 71 " --> pdb=" O VAL A 105 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 54 through 59 Processing sheet with id=AA4, first strand: chain 'I' and resid 54 through 59 Processing sheet with id=AA5, first strand: chain 'I' and resid 100 through 105 removed outlier: 6.251A pdb=" N TYR I 67 " --> pdb=" O GLN I 101 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N VAL I 103 " --> pdb=" O TYR I 67 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N VAL I 69 " --> pdb=" O VAL I 103 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N VAL I 105 " --> pdb=" O VAL I 69 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N PHE I 71 " --> pdb=" O VAL I 105 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N TYR E 67 " --> pdb=" O GLN E 101 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N VAL E 103 " --> pdb=" O TYR E 67 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N VAL E 69 " --> pdb=" O VAL E 103 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N VAL E 105 " --> pdb=" O VAL E 69 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N PHE E 71 " --> pdb=" O VAL E 105 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 54 through 59 Processing sheet with id=AA7, first strand: chain 'G' and resid 54 through 59 Processing sheet with id=AA8, first strand: chain 'G' and resid 100 through 105 removed outlier: 6.251A pdb=" N TYR G 67 " --> pdb=" O GLN G 101 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N VAL G 103 " --> pdb=" O TYR G 67 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N VAL G 69 " --> pdb=" O VAL G 103 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N VAL G 105 " --> pdb=" O VAL G 69 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N PHE G 71 " --> pdb=" O VAL G 105 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N TYR C 67 " --> pdb=" O GLN C 101 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N VAL C 103 " --> pdb=" O TYR C 67 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N VAL C 69 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N VAL C 105 " --> pdb=" O VAL C 69 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N PHE C 71 " --> pdb=" O VAL C 105 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 54 through 59 Processing sheet with id=AB1, first strand: chain 'F' and resid 100 through 105 removed outlier: 6.251A pdb=" N TYR F 67 " --> pdb=" O GLN F 101 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N VAL F 103 " --> pdb=" O TYR F 67 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N VAL F 69 " --> pdb=" O VAL F 103 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N VAL F 105 " --> pdb=" O VAL F 69 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N PHE F 71 " --> pdb=" O VAL F 105 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N TYR B 67 " --> pdb=" O GLN B 101 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N VAL B 103 " --> pdb=" O TYR B 67 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N VAL B 69 " --> pdb=" O VAL B 103 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N VAL B 105 " --> pdb=" O VAL B 69 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N PHE B 71 " --> pdb=" O VAL B 105 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 54 through 59 Processing sheet with id=AB3, first strand: chain 'C' and resid 54 through 59 Processing sheet with id=AB4, first strand: chain 'D' and resid 54 through 59 Processing sheet with id=AB5, first strand: chain 'D' and resid 100 through 105 removed outlier: 6.251A pdb=" N TYR D 67 " --> pdb=" O GLN D 101 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N VAL D 103 " --> pdb=" O TYR D 67 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N VAL D 69 " --> pdb=" O VAL D 103 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N VAL D 105 " --> pdb=" O VAL D 69 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N PHE D 71 " --> pdb=" O VAL D 105 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N TYR H 67 " --> pdb=" O GLN H 101 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N VAL H 103 " --> pdb=" O TYR H 67 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N VAL H 69 " --> pdb=" O VAL H 103 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N VAL H 105 " --> pdb=" O VAL H 69 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N PHE H 71 " --> pdb=" O VAL H 105 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 54 through 59 410 hydrogen bonds defined for protein. 1140 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.13 Time building geometry restraints manager: 1.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4480 1.34 - 1.46: 2581 1.46 - 1.57: 6739 1.57 - 1.69: 0 1.69 - 1.81: 130 Bond restraints: 13930 Sorted by residual: bond pdb=" CB PHE D 71 " pdb=" CG PHE D 71 " ideal model delta sigma weight residual 1.502 1.435 0.067 2.30e-02 1.89e+03 8.55e+00 bond pdb=" CB PHE H 71 " pdb=" CG PHE H 71 " ideal model delta sigma weight residual 1.502 1.435 0.067 2.30e-02 1.89e+03 8.52e+00 bond pdb=" CB PHE E 71 " pdb=" CG PHE E 71 " ideal model delta sigma weight residual 1.502 1.435 0.067 2.30e-02 1.89e+03 8.49e+00 bond pdb=" CB PHE J 71 " pdb=" CG PHE J 71 " ideal model delta sigma weight residual 1.502 1.435 0.067 2.30e-02 1.89e+03 8.45e+00 bond pdb=" CB PHE F 71 " pdb=" CG PHE F 71 " ideal model delta sigma weight residual 1.502 1.435 0.067 2.30e-02 1.89e+03 8.41e+00 ... (remaining 13925 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.59: 17087 1.59 - 3.19: 1508 3.19 - 4.78: 185 4.78 - 6.38: 60 6.38 - 7.97: 20 Bond angle restraints: 18860 Sorted by residual: angle pdb=" N VAL F 38 " pdb=" CA VAL F 38 " pdb=" CB VAL F 38 " ideal model delta sigma weight residual 112.08 105.85 6.23 1.68e+00 3.54e-01 1.37e+01 angle pdb=" N VAL A 38 " pdb=" CA VAL A 38 " pdb=" CB VAL A 38 " ideal model delta sigma weight residual 112.08 105.88 6.20 1.68e+00 3.54e-01 1.36e+01 angle pdb=" N VAL I 38 " pdb=" CA VAL I 38 " pdb=" CB VAL I 38 " ideal model delta sigma weight residual 112.08 105.89 6.19 1.68e+00 3.54e-01 1.36e+01 angle pdb=" N VAL C 38 " pdb=" CA VAL C 38 " pdb=" CB VAL C 38 " ideal model delta sigma weight residual 112.08 105.89 6.19 1.68e+00 3.54e-01 1.36e+01 angle pdb=" N VAL J 38 " pdb=" CA VAL J 38 " pdb=" CB VAL J 38 " ideal model delta sigma weight residual 112.08 105.90 6.18 1.68e+00 3.54e-01 1.35e+01 ... (remaining 18855 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 9.34: 7092 9.34 - 18.69: 958 18.69 - 28.03: 210 28.03 - 37.38: 50 37.38 - 46.72: 40 Dihedral angle restraints: 8350 sinusoidal: 3310 harmonic: 5040 Sorted by residual: dihedral pdb=" CA ARG G 121 " pdb=" C ARG G 121 " pdb=" N LYS G 122 " pdb=" CA LYS G 122 " ideal model delta harmonic sigma weight residual -180.00 -159.56 -20.44 0 5.00e+00 4.00e-02 1.67e+01 dihedral pdb=" CA ARG F 121 " pdb=" C ARG F 121 " pdb=" N LYS F 122 " pdb=" CA LYS F 122 " ideal model delta harmonic sigma weight residual -180.00 -159.56 -20.44 0 5.00e+00 4.00e-02 1.67e+01 dihedral pdb=" CA ARG C 121 " pdb=" C ARG C 121 " pdb=" N LYS C 122 " pdb=" CA LYS C 122 " ideal model delta harmonic sigma weight residual -180.00 -159.57 -20.43 0 5.00e+00 4.00e-02 1.67e+01 ... (remaining 8347 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1294 0.054 - 0.108: 598 0.108 - 0.162: 168 0.162 - 0.215: 20 0.215 - 0.269: 20 Chirality restraints: 2100 Sorted by residual: chirality pdb=" CA TYR G 33 " pdb=" N TYR G 33 " pdb=" C TYR G 33 " pdb=" CB TYR G 33 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" CA TYR H 33 " pdb=" N TYR H 33 " pdb=" C TYR H 33 " pdb=" CB TYR H 33 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" CA TYR E 33 " pdb=" N TYR E 33 " pdb=" C TYR E 33 " pdb=" CB TYR E 33 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.80e+00 ... (remaining 2097 not shown) Planarity restraints: 2460 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP F 116 " 0.023 2.00e-02 2.50e+03 1.61e-02 6.45e+00 pdb=" CG TRP F 116 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 TRP F 116 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP F 116 " -0.011 2.00e-02 2.50e+03 pdb=" NE1 TRP F 116 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP F 116 " 0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP F 116 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 116 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 116 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP F 116 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP G 116 " -0.024 2.00e-02 2.50e+03 1.60e-02 6.43e+00 pdb=" CG TRP G 116 " 0.041 2.00e-02 2.50e+03 pdb=" CD1 TRP G 116 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP G 116 " 0.012 2.00e-02 2.50e+03 pdb=" NE1 TRP G 116 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP G 116 " -0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP G 116 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP G 116 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP G 116 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP G 116 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 116 " 0.023 2.00e-02 2.50e+03 1.60e-02 6.41e+00 pdb=" CG TRP B 116 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 TRP B 116 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP B 116 " -0.011 2.00e-02 2.50e+03 pdb=" NE1 TRP B 116 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 116 " 0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP B 116 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 116 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 116 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP B 116 " 0.000 2.00e-02 2.50e+03 ... (remaining 2457 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 137 2.58 - 3.16: 11462 3.16 - 3.74: 20443 3.74 - 4.32: 31323 4.32 - 4.90: 48905 Nonbonded interactions: 112270 Sorted by model distance: nonbonded pdb=" O ARG E 34 " pdb=" OG1 THR E 35 " model vdw 1.999 3.040 nonbonded pdb=" O ARG J 34 " pdb=" OG1 THR J 35 " model vdw 1.999 3.040 nonbonded pdb=" O ARG I 34 " pdb=" OG1 THR I 35 " model vdw 1.999 3.040 nonbonded pdb=" O ARG D 34 " pdb=" OG1 THR D 35 " model vdw 1.999 3.040 nonbonded pdb=" O ARG A 34 " pdb=" OG1 THR A 35 " model vdw 1.999 3.040 ... (remaining 112265 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: 0.05 Found NCS groups: ncs_group { reference = chain 'J' selection = chain 'A' selection = chain 'I' selection = chain 'E' selection = chain 'G' selection = chain 'F' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'H' } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 11.450 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.010 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: 0.010 Load rotamer database and sin/cos tables:1.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 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 : 0.010 0.067 13930 Z= 0.479 Angle : 1.010 7.971 18860 Z= 0.571 Chirality : 0.068 0.269 2100 Planarity : 0.006 0.048 2460 Dihedral : 9.643 46.720 5110 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.58 % Allowed : 8.14 % Favored : 91.28 % Rotamer: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.79 (0.16), residues: 1720 helix: -4.51 (0.09), residues: 500 sheet: -2.48 (0.23), residues: 390 loop : -2.53 (0.20), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 91 TYR 0.029 0.003 TYR B 67 PHE 0.023 0.006 PHE I 160 TRP 0.041 0.010 TRP F 116 HIS 0.009 0.003 HIS H 113 Details of bonding type rmsd covalent geometry : bond 0.01041 (13930) covalent geometry : angle 1.01012 (18860) hydrogen bonds : bond 0.29771 ( 410) hydrogen bonds : angle 10.94973 ( 1140) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 616 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 616 time to evaluate : 0.557 Fit side-chains REVERT: A 169 ARG cc_start: 0.8375 (mmm-85) cc_final: 0.8073 (mtt-85) REVERT: I 100 THR cc_start: 0.9030 (t) cc_final: 0.8811 (m) REVERT: I 109 SER cc_start: 0.8250 (t) cc_final: 0.8004 (m) REVERT: I 169 ARG cc_start: 0.8459 (mmm-85) cc_final: 0.8219 (mtp85) REVERT: E 169 ARG cc_start: 0.8421 (mmm-85) cc_final: 0.8131 (mtp85) REVERT: E 190 GLU cc_start: 0.7754 (tt0) cc_final: 0.7482 (tm-30) REVERT: G 62 ASP cc_start: 0.8340 (m-30) cc_final: 0.7944 (t0) REVERT: G 163 ASP cc_start: 0.7090 (p0) cc_final: 0.6789 (p0) REVERT: G 167 ILE cc_start: 0.8781 (mm) cc_final: 0.8579 (mt) REVERT: G 169 ARG cc_start: 0.8463 (mmm-85) cc_final: 0.7783 (mtt-85) REVERT: F 60 MET cc_start: 0.8230 (ttt) cc_final: 0.7535 (ttt) REVERT: F 62 ASP cc_start: 0.8086 (m-30) cc_final: 0.7823 (t0) REVERT: F 143 ARG cc_start: 0.8467 (ttm-80) cc_final: 0.8210 (ttm-80) REVERT: F 169 ARG cc_start: 0.8394 (mmm-85) cc_final: 0.8141 (mtp85) REVERT: B 73 TYR cc_start: 0.8959 (p90) cc_final: 0.8740 (p90) REVERT: B 164 LYS cc_start: 0.8135 (pttt) cc_final: 0.7933 (ptmt) REVERT: B 169 ARG cc_start: 0.8333 (mmm-85) cc_final: 0.8025 (mmt90) REVERT: C 99 ASN cc_start: 0.8348 (t0) cc_final: 0.8127 (t0) REVERT: D 60 MET cc_start: 0.8263 (ttt) cc_final: 0.6935 (ttt) REVERT: D 62 ASP cc_start: 0.8229 (m-30) cc_final: 0.7705 (t0) REVERT: D 108 ASP cc_start: 0.7915 (m-30) cc_final: 0.6922 (m-30) REVERT: D 169 ARG cc_start: 0.8256 (mmm-85) cc_final: 0.7994 (mtp85) outliers start: 0 outliers final: 0 residues processed: 616 average time/residue: 0.1324 time to fit residues: 115.0994 Evaluate side-chains 420 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 420 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 0.5980 chunk 91 optimal weight: 6.9990 chunk 149 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.158232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.132707 restraints weight = 18728.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.136942 restraints weight = 11402.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.139899 restraints weight = 8170.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.141937 restraints weight = 6445.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.143568 restraints weight = 5412.956| |-----------------------------------------------------------------------------| r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.2948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 13930 Z= 0.145 Angle : 0.652 8.082 18860 Z= 0.353 Chirality : 0.050 0.149 2100 Planarity : 0.005 0.042 2460 Dihedral : 5.437 17.449 1890 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 2.67 % Allowed : 16.92 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.48 (0.19), residues: 1720 helix: -3.06 (0.16), residues: 490 sheet: -2.60 (0.24), residues: 440 loop : -1.38 (0.24), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 169 TYR 0.017 0.002 TYR J 194 PHE 0.017 0.002 PHE D 77 TRP 0.017 0.002 TRP C 116 HIS 0.004 0.001 HIS D 170 Details of bonding type rmsd covalent geometry : bond 0.00302 (13930) covalent geometry : angle 0.65210 (18860) hydrogen bonds : bond 0.03872 ( 410) hydrogen bonds : angle 5.88625 ( 1140) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 561 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 522 time to evaluate : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: J 58 ILE cc_start: 0.8703 (mm) cc_final: 0.8448 (mt) REVERT: J 62 ASP cc_start: 0.8289 (m-30) cc_final: 0.7992 (t0) REVERT: J 84 GLU cc_start: 0.7818 (tp30) cc_final: 0.7610 (tp30) REVERT: J 108 ASP cc_start: 0.8091 (m-30) cc_final: 0.7761 (m-30) REVERT: A 57 ASP cc_start: 0.7773 (m-30) cc_final: 0.7557 (m-30) REVERT: A 62 ASP cc_start: 0.8196 (m-30) cc_final: 0.7702 (t0) REVERT: A 63 TYR cc_start: 0.8605 (m-80) cc_final: 0.8217 (m-80) REVERT: A 73 TYR cc_start: 0.8599 (p90) cc_final: 0.8292 (p90) REVERT: A 76 ASP cc_start: 0.7309 (OUTLIER) cc_final: 0.7034 (m-30) REVERT: I 48 GLN cc_start: 0.8779 (mt0) cc_final: 0.8386 (mt0) REVERT: I 62 ASP cc_start: 0.8104 (m-30) cc_final: 0.7679 (t0) REVERT: I 76 ASP cc_start: 0.7457 (OUTLIER) cc_final: 0.7202 (m-30) REVERT: I 108 ASP cc_start: 0.7737 (m-30) cc_final: 0.7490 (m-30) REVERT: I 169 ARG cc_start: 0.8266 (mmm-85) cc_final: 0.8011 (mmt90) REVERT: E 163 ASP cc_start: 0.7498 (m-30) cc_final: 0.7282 (m-30) REVERT: E 169 ARG cc_start: 0.8249 (mmm-85) cc_final: 0.7819 (mtp85) REVERT: G 62 ASP cc_start: 0.8329 (m-30) cc_final: 0.7936 (t0) REVERT: G 73 TYR cc_start: 0.8687 (p90) cc_final: 0.8353 (p90) REVERT: G 84 GLU cc_start: 0.7929 (tp30) cc_final: 0.7717 (tp30) REVERT: G 143 ARG cc_start: 0.8470 (ttm-80) cc_final: 0.8223 (ttm-80) REVERT: F 44 GLN cc_start: 0.7684 (mm-40) cc_final: 0.7119 (mm-40) REVERT: F 48 GLN cc_start: 0.8852 (mt0) cc_final: 0.8554 (mt0) REVERT: F 60 MET cc_start: 0.8369 (ttt) cc_final: 0.7991 (ttt) REVERT: F 62 ASP cc_start: 0.8248 (m-30) cc_final: 0.7890 (t0) REVERT: F 100 THR cc_start: 0.8822 (m) cc_final: 0.8611 (p) REVERT: F 169 ARG cc_start: 0.8271 (mmm-85) cc_final: 0.8057 (mmt90) REVERT: B 60 MET cc_start: 0.7511 (OUTLIER) cc_final: 0.6652 (ttp) REVERT: B 145 TYR cc_start: 0.9065 (m-10) cc_final: 0.8799 (m-80) REVERT: C 58 ILE cc_start: 0.8609 (mm) cc_final: 0.8360 (mt) REVERT: C 67 TYR cc_start: 0.8108 (m-10) cc_final: 0.7431 (m-10) REVERT: C 84 GLU cc_start: 0.7986 (tp30) cc_final: 0.7704 (tp30) REVERT: D 62 ASP cc_start: 0.8212 (m-30) cc_final: 0.7900 (t0) REVERT: D 63 TYR cc_start: 0.8550 (m-80) cc_final: 0.8284 (m-80) REVERT: D 67 TYR cc_start: 0.7894 (m-10) cc_final: 0.7297 (m-10) REVERT: D 76 ASP cc_start: 0.7359 (OUTLIER) cc_final: 0.6937 (m-30) REVERT: D 131 ILE cc_start: 0.9021 (mt) cc_final: 0.8685 (tt) REVERT: H 58 ILE cc_start: 0.8700 (mm) cc_final: 0.8416 (mt) REVERT: H 100 THR cc_start: 0.9013 (t) cc_final: 0.8786 (p) REVERT: H 145 TYR cc_start: 0.8979 (m-10) cc_final: 0.8777 (m-80) REVERT: H 169 ARG cc_start: 0.8482 (mmm-85) cc_final: 0.8232 (mtt-85) REVERT: H 197 GLU cc_start: 0.7499 (tt0) cc_final: 0.7283 (tt0) outliers start: 39 outliers final: 16 residues processed: 535 average time/residue: 0.1182 time to fit residues: 92.4082 Evaluate side-chains 463 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 443 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 109 SER Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 108 ASP Chi-restraints excluded: chain I residue 57 ASP Chi-restraints excluded: chain I residue 76 ASP Chi-restraints excluded: chain E residue 66 LYS Chi-restraints excluded: chain E residue 109 SER Chi-restraints excluded: chain G residue 68 ILE Chi-restraints excluded: chain G residue 109 SER Chi-restraints excluded: chain G residue 186 LEU Chi-restraints excluded: chain F residue 68 ILE Chi-restraints excluded: chain B residue 60 MET Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 76 ASP Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain H residue 109 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 168 optimal weight: 8.9990 chunk 167 optimal weight: 6.9990 chunk 164 optimal weight: 6.9990 chunk 32 optimal weight: 10.0000 chunk 31 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 chunk 94 optimal weight: 20.0000 chunk 111 optimal weight: 0.0570 chunk 48 optimal weight: 7.9990 chunk 21 optimal weight: 4.9990 chunk 68 optimal weight: 9.9990 overall best weight: 4.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 52 ASN A 59 ASN E 52 ASN G 193 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.149514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.122140 restraints weight = 19190.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.126139 restraints weight = 12102.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.128968 restraints weight = 8927.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.130988 restraints weight = 7195.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.132361 restraints weight = 6146.397| |-----------------------------------------------------------------------------| r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.3370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.035 13930 Z= 0.296 Angle : 0.710 7.563 18860 Z= 0.382 Chirality : 0.052 0.169 2100 Planarity : 0.005 0.038 2460 Dihedral : 5.299 18.956 1890 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 16.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 4.11 % Allowed : 17.33 % Favored : 78.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.83 (0.21), residues: 1720 helix: -2.07 (0.19), residues: 470 sheet: -2.17 (0.25), residues: 410 loop : -1.46 (0.25), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 157 TYR 0.020 0.002 TYR G 67 PHE 0.038 0.003 PHE A 88 TRP 0.017 0.004 TRP I 116 HIS 0.007 0.002 HIS E 113 Details of bonding type rmsd covalent geometry : bond 0.00665 (13930) covalent geometry : angle 0.71042 (18860) hydrogen bonds : bond 0.04235 ( 410) hydrogen bonds : angle 5.70894 ( 1140) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 559 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 499 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 58 ILE cc_start: 0.8815 (mm) cc_final: 0.8542 (mt) REVERT: J 84 GLU cc_start: 0.7821 (tp30) cc_final: 0.7611 (tp30) REVERT: J 190 GLU cc_start: 0.7911 (tt0) cc_final: 0.7588 (tm-30) REVERT: J 197 GLU cc_start: 0.8027 (tt0) cc_final: 0.7782 (tt0) REVERT: A 48 GLN cc_start: 0.8775 (mt0) cc_final: 0.8495 (mt0) REVERT: A 62 ASP cc_start: 0.8159 (m-30) cc_final: 0.7885 (t0) REVERT: A 64 LYS cc_start: 0.7643 (OUTLIER) cc_final: 0.7339 (ttmm) REVERT: A 67 TYR cc_start: 0.7932 (m-10) cc_final: 0.7563 (m-10) REVERT: A 147 VAL cc_start: 0.9303 (m) cc_final: 0.8917 (p) REVERT: A 186 LEU cc_start: 0.9193 (mt) cc_final: 0.8924 (mt) REVERT: A 190 GLU cc_start: 0.7979 (tt0) cc_final: 0.7717 (tm-30) REVERT: A 193 GLN cc_start: 0.8256 (OUTLIER) cc_final: 0.7817 (mp10) REVERT: I 59 ASN cc_start: 0.7410 (t0) cc_final: 0.7156 (t0) REVERT: I 62 ASP cc_start: 0.8244 (m-30) cc_final: 0.7886 (t0) REVERT: I 67 TYR cc_start: 0.8125 (m-10) cc_final: 0.7694 (m-10) REVERT: I 76 ASP cc_start: 0.7597 (OUTLIER) cc_final: 0.7314 (m-30) REVERT: I 186 LEU cc_start: 0.9378 (mt) cc_final: 0.7782 (mt) REVERT: I 190 GLU cc_start: 0.7997 (tt0) cc_final: 0.7651 (tm-30) REVERT: E 76 ASP cc_start: 0.8161 (m-30) cc_final: 0.7857 (m-30) REVERT: E 77 PHE cc_start: 0.8824 (m-80) cc_final: 0.8510 (m-10) REVERT: E 99 ASN cc_start: 0.8269 (t0) cc_final: 0.7999 (t0) REVERT: E 145 TYR cc_start: 0.9159 (m-80) cc_final: 0.8529 (m-80) REVERT: E 190 GLU cc_start: 0.7869 (tt0) cc_final: 0.7498 (tm-30) REVERT: G 58 ILE cc_start: 0.8747 (mm) cc_final: 0.8535 (mt) REVERT: G 59 ASN cc_start: 0.7597 (t0) cc_final: 0.7387 (t0) REVERT: G 62 ASP cc_start: 0.8251 (m-30) cc_final: 0.7991 (t0) REVERT: G 99 ASN cc_start: 0.8563 (t0) cc_final: 0.8196 (t0) REVERT: G 190 GLU cc_start: 0.7955 (tt0) cc_final: 0.7538 (tm-30) REVERT: F 44 GLN cc_start: 0.7826 (mm-40) cc_final: 0.7145 (mm-40) REVERT: F 60 MET cc_start: 0.8516 (ttt) cc_final: 0.8057 (ttt) REVERT: F 62 ASP cc_start: 0.8151 (m-30) cc_final: 0.7841 (t0) REVERT: F 67 TYR cc_start: 0.7854 (m-10) cc_final: 0.7240 (m-10) REVERT: F 75 MET cc_start: 0.7791 (mtt) cc_final: 0.7448 (mtt) REVERT: F 100 THR cc_start: 0.8915 (m) cc_final: 0.8644 (p) REVERT: F 193 GLN cc_start: 0.8094 (OUTLIER) cc_final: 0.7781 (mp10) REVERT: B 58 ILE cc_start: 0.8774 (mm) cc_final: 0.8478 (mt) REVERT: B 63 TYR cc_start: 0.8572 (m-80) cc_final: 0.8202 (m-80) REVERT: B 84 GLU cc_start: 0.8144 (tp30) cc_final: 0.7816 (tp30) REVERT: B 99 ASN cc_start: 0.8325 (t0) cc_final: 0.8014 (t0) REVERT: B 108 ASP cc_start: 0.7971 (m-30) cc_final: 0.7618 (m-30) REVERT: B 145 TYR cc_start: 0.9131 (m-10) cc_final: 0.8818 (m-80) REVERT: C 67 TYR cc_start: 0.8089 (m-10) cc_final: 0.7709 (m-10) REVERT: C 84 GLU cc_start: 0.8034 (tp30) cc_final: 0.7778 (tp30) REVERT: C 99 ASN cc_start: 0.8447 (t0) cc_final: 0.8139 (t0) REVERT: D 63 TYR cc_start: 0.8599 (m-80) cc_final: 0.8249 (m-80) REVERT: D 64 LYS cc_start: 0.7293 (OUTLIER) cc_final: 0.7032 (ttmm) REVERT: D 99 ASN cc_start: 0.8249 (t0) cc_final: 0.8012 (t0) REVERT: D 108 ASP cc_start: 0.7978 (t0) cc_final: 0.7544 (t70) REVERT: D 118 ASN cc_start: 0.8562 (m-40) cc_final: 0.8308 (m110) REVERT: D 190 GLU cc_start: 0.7763 (tt0) cc_final: 0.7433 (tm-30) REVERT: D 194 TYR cc_start: 0.8205 (t80) cc_final: 0.7915 (t80) REVERT: H 58 ILE cc_start: 0.8735 (mm) cc_final: 0.8435 (mt) REVERT: H 63 TYR cc_start: 0.8666 (m-80) cc_final: 0.8170 (m-80) REVERT: H 83 THR cc_start: 0.8967 (m) cc_final: 0.8743 (t) REVERT: H 190 GLU cc_start: 0.7930 (tt0) cc_final: 0.7501 (tm-30) REVERT: H 194 TYR cc_start: 0.7820 (t80) cc_final: 0.7552 (t80) outliers start: 60 outliers final: 36 residues processed: 516 average time/residue: 0.1100 time to fit residues: 83.8705 Evaluate side-chains 504 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 463 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 46 SER Chi-restraints excluded: chain J residue 80 VAL Chi-restraints excluded: chain J residue 109 SER Chi-restraints excluded: chain A residue 40 GLU Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 108 ASP Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 193 GLN Chi-restraints excluded: chain I residue 76 ASP Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 80 VAL Chi-restraints excluded: chain I residue 150 GLU Chi-restraints excluded: chain E residue 46 SER Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 109 SER Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain G residue 57 ASP Chi-restraints excluded: chain G residue 68 ILE Chi-restraints excluded: chain G residue 109 SER Chi-restraints excluded: chain G residue 154 ILE Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain F residue 64 LYS Chi-restraints excluded: chain F residue 68 ILE Chi-restraints excluded: chain F residue 109 SER Chi-restraints excluded: chain F residue 193 GLN Chi-restraints excluded: chain B residue 64 LYS Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain D residue 64 LYS Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain H residue 66 LYS Chi-restraints excluded: chain H residue 68 ILE Chi-restraints excluded: chain H residue 109 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 80 optimal weight: 0.0570 chunk 126 optimal weight: 2.9990 chunk 160 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 120 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 99 optimal weight: 0.7980 chunk 14 optimal weight: 5.9990 chunk 108 optimal weight: 9.9990 chunk 77 optimal weight: 0.0040 overall best weight: 0.9714 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 61 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.156950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.130057 restraints weight = 18831.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.134254 restraints weight = 11763.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.137062 restraints weight = 8602.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.139318 restraints weight = 6924.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.140849 restraints weight = 5840.543| |-----------------------------------------------------------------------------| r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.3874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 13930 Z= 0.128 Angle : 0.603 8.246 18860 Z= 0.318 Chirality : 0.048 0.144 2100 Planarity : 0.004 0.049 2460 Dihedral : 4.704 18.947 1890 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 2.33 % Allowed : 20.68 % Favored : 76.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.29 (0.21), residues: 1720 helix: -1.32 (0.21), residues: 470 sheet: -2.25 (0.24), residues: 460 loop : -0.97 (0.26), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I 157 TYR 0.020 0.002 TYR G 67 PHE 0.032 0.002 PHE A 77 TRP 0.012 0.002 TRP A 116 HIS 0.003 0.001 HIS H 170 Details of bonding type rmsd covalent geometry : bond 0.00271 (13930) covalent geometry : angle 0.60291 (18860) hydrogen bonds : bond 0.03026 ( 410) hydrogen bonds : angle 5.33316 ( 1140) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 520 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 486 time to evaluate : 0.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 190 GLU cc_start: 0.7722 (tt0) cc_final: 0.7472 (tm-30) REVERT: A 48 GLN cc_start: 0.8704 (mt0) cc_final: 0.8465 (mt0) REVERT: A 59 ASN cc_start: 0.7500 (t0) cc_final: 0.7226 (t0) REVERT: A 67 TYR cc_start: 0.8014 (m-10) cc_final: 0.7735 (m-10) REVERT: A 77 PHE cc_start: 0.8435 (m-80) cc_final: 0.8180 (m-10) REVERT: A 147 VAL cc_start: 0.9210 (m) cc_final: 0.8918 (p) REVERT: A 190 GLU cc_start: 0.7921 (tt0) cc_final: 0.7631 (tm-30) REVERT: A 193 GLN cc_start: 0.7942 (OUTLIER) cc_final: 0.7680 (mp10) REVERT: I 67 TYR cc_start: 0.8083 (m-10) cc_final: 0.7662 (m-10) REVERT: I 169 ARG cc_start: 0.8185 (mmm-85) cc_final: 0.7876 (mmt90) REVERT: I 190 GLU cc_start: 0.7882 (tt0) cc_final: 0.7580 (tm-30) REVERT: E 58 ILE cc_start: 0.8784 (mm) cc_final: 0.8518 (mt) REVERT: E 67 TYR cc_start: 0.7688 (m-10) cc_final: 0.7381 (m-10) REVERT: E 76 ASP cc_start: 0.8008 (m-30) cc_final: 0.7633 (m-30) REVERT: G 58 ILE cc_start: 0.8799 (mm) cc_final: 0.8549 (mt) REVERT: G 63 TYR cc_start: 0.8627 (m-80) cc_final: 0.7982 (m-80) REVERT: G 64 LYS cc_start: 0.7561 (OUTLIER) cc_final: 0.7216 (ttmm) REVERT: G 73 TYR cc_start: 0.8610 (p90) cc_final: 0.8322 (p90) REVERT: G 190 GLU cc_start: 0.7892 (tt0) cc_final: 0.7485 (tm-30) REVERT: F 44 GLN cc_start: 0.7775 (mm-40) cc_final: 0.7295 (mm-40) REVERT: F 60 MET cc_start: 0.8361 (ttt) cc_final: 0.7875 (ttt) REVERT: F 67 TYR cc_start: 0.7938 (m-10) cc_final: 0.7416 (m-10) REVERT: F 100 THR cc_start: 0.8875 (m) cc_final: 0.8650 (p) REVERT: F 108 ASP cc_start: 0.8072 (OUTLIER) cc_final: 0.7453 (m-30) REVERT: F 169 ARG cc_start: 0.8046 (mmm-85) cc_final: 0.7845 (mmt90) REVERT: B 58 ILE cc_start: 0.8747 (mm) cc_final: 0.8412 (mt) REVERT: B 63 TYR cc_start: 0.8259 (m-80) cc_final: 0.8049 (m-80) REVERT: B 64 LYS cc_start: 0.7496 (ttmm) cc_final: 0.7197 (ttmm) REVERT: B 94 ASP cc_start: 0.8079 (m-30) cc_final: 0.7824 (t0) REVERT: B 98 LEU cc_start: 0.8197 (mt) cc_final: 0.7953 (tp) REVERT: B 99 ASN cc_start: 0.8233 (t0) cc_final: 0.7931 (t0) REVERT: B 145 TYR cc_start: 0.8993 (m-10) cc_final: 0.8748 (m-80) REVERT: B 193 GLN cc_start: 0.7660 (mt0) cc_final: 0.7407 (mt0) REVERT: B 194 TYR cc_start: 0.7472 (t80) cc_final: 0.7244 (t80) REVERT: C 58 ILE cc_start: 0.8695 (mm) cc_final: 0.8451 (mt) REVERT: C 67 TYR cc_start: 0.8001 (m-10) cc_final: 0.7631 (m-10) REVERT: D 67 TYR cc_start: 0.7861 (m-10) cc_final: 0.7399 (m-10) REVERT: D 108 ASP cc_start: 0.7546 (t0) cc_final: 0.6857 (m-30) REVERT: D 190 GLU cc_start: 0.7718 (tt0) cc_final: 0.7439 (tm-30) REVERT: H 58 ILE cc_start: 0.8736 (mm) cc_final: 0.8356 (mt) REVERT: H 63 TYR cc_start: 0.8320 (m-80) cc_final: 0.7812 (m-80) REVERT: H 66 LYS cc_start: 0.6376 (mtmm) cc_final: 0.5966 (ptmt) REVERT: H 99 ASN cc_start: 0.8457 (t0) cc_final: 0.8167 (t0) REVERT: H 114 LEU cc_start: 0.9116 (tt) cc_final: 0.8861 (tt) REVERT: H 147 VAL cc_start: 0.9290 (m) cc_final: 0.9048 (p) REVERT: H 186 LEU cc_start: 0.9332 (mt) cc_final: 0.7969 (mt) REVERT: H 190 GLU cc_start: 0.7914 (tt0) cc_final: 0.7484 (tm-30) outliers start: 34 outliers final: 14 residues processed: 494 average time/residue: 0.1125 time to fit residues: 82.1995 Evaluate side-chains 447 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 430 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 46 SER Chi-restraints excluded: chain J residue 109 SER Chi-restraints excluded: chain A residue 40 GLU Chi-restraints excluded: chain A residue 193 GLN Chi-restraints excluded: chain E residue 46 SER Chi-restraints excluded: chain G residue 40 GLU Chi-restraints excluded: chain G residue 64 LYS Chi-restraints excluded: chain G residue 109 SER Chi-restraints excluded: chain F residue 68 ILE Chi-restraints excluded: chain F residue 108 ASP Chi-restraints excluded: chain F residue 109 SER Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain H residue 109 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 168 optimal weight: 9.9990 chunk 82 optimal weight: 3.9990 chunk 79 optimal weight: 5.9990 chunk 6 optimal weight: 7.9990 chunk 106 optimal weight: 6.9990 chunk 1 optimal weight: 5.9990 chunk 94 optimal weight: 20.0000 chunk 140 optimal weight: 4.9990 chunk 75 optimal weight: 8.9990 chunk 130 optimal weight: 9.9990 chunk 7 optimal weight: 8.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 193 GLN J 198 ASN E 198 ASN ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 130 HIS F 59 ASN F 130 HIS B 130 HIS C 48 GLN D 130 HIS H 130 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.145221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.117587 restraints weight = 19370.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.121409 restraints weight = 12319.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.124193 restraints weight = 9159.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.126164 restraints weight = 7424.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.127402 restraints weight = 6377.048| |-----------------------------------------------------------------------------| r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.4097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.054 13930 Z= 0.368 Angle : 0.759 8.810 18860 Z= 0.405 Chirality : 0.055 0.217 2100 Planarity : 0.005 0.041 2460 Dihedral : 5.135 18.882 1890 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 18.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.84 % Favored : 91.16 % Rotamer: Outliers : 4.66 % Allowed : 20.62 % Favored : 74.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.28 (0.21), residues: 1720 helix: -1.33 (0.21), residues: 470 sheet: -1.83 (0.25), residues: 410 loop : -1.31 (0.25), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 169 TYR 0.021 0.002 TYR G 67 PHE 0.050 0.003 PHE E 77 TRP 0.026 0.004 TRP E 116 HIS 0.006 0.002 HIS E 113 Details of bonding type rmsd covalent geometry : bond 0.00841 (13930) covalent geometry : angle 0.75882 (18860) hydrogen bonds : bond 0.04067 ( 410) hydrogen bonds : angle 5.67008 ( 1140) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 551 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 483 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: J 58 ILE cc_start: 0.8770 (mm) cc_final: 0.8489 (mt) REVERT: J 64 LYS cc_start: 0.7558 (ttmm) cc_final: 0.7284 (ttmm) REVERT: J 73 TYR cc_start: 0.8760 (p90) cc_final: 0.8458 (p90) REVERT: J 76 ASP cc_start: 0.8394 (m-30) cc_final: 0.8143 (m-30) REVERT: J 99 ASN cc_start: 0.8473 (t0) cc_final: 0.8255 (t0) REVERT: J 108 ASP cc_start: 0.8169 (m-30) cc_final: 0.7820 (t70) REVERT: A 48 GLN cc_start: 0.8700 (mt0) cc_final: 0.8367 (mt0) REVERT: A 84 GLU cc_start: 0.8399 (tp30) cc_final: 0.7984 (tp30) REVERT: A 147 VAL cc_start: 0.9308 (m) cc_final: 0.8959 (p) REVERT: A 190 GLU cc_start: 0.7987 (tt0) cc_final: 0.7676 (tm-30) REVERT: A 193 GLN cc_start: 0.8324 (OUTLIER) cc_final: 0.7325 (mp10) REVERT: I 67 TYR cc_start: 0.8298 (m-10) cc_final: 0.7848 (m-10) REVERT: I 76 ASP cc_start: 0.7948 (m-30) cc_final: 0.7206 (m-30) REVERT: I 84 GLU cc_start: 0.8141 (tp30) cc_final: 0.7926 (tp30) REVERT: I 99 ASN cc_start: 0.8190 (t0) cc_final: 0.7783 (t0) REVERT: I 190 GLU cc_start: 0.7969 (tt0) cc_final: 0.7699 (tm-30) REVERT: E 63 TYR cc_start: 0.8586 (m-80) cc_final: 0.8311 (m-80) REVERT: E 67 TYR cc_start: 0.8019 (m-10) cc_final: 0.7665 (m-10) REVERT: E 76 ASP cc_start: 0.8349 (m-30) cc_final: 0.7897 (m-30) REVERT: E 84 GLU cc_start: 0.8176 (tp30) cc_final: 0.7969 (tp30) REVERT: E 99 ASN cc_start: 0.8441 (t0) cc_final: 0.8103 (t0) REVERT: E 122 LYS cc_start: 0.8220 (OUTLIER) cc_final: 0.7118 (tptt) REVERT: E 145 TYR cc_start: 0.9131 (m-80) cc_final: 0.8497 (m-80) REVERT: E 190 GLU cc_start: 0.7884 (tt0) cc_final: 0.7550 (tm-30) REVERT: G 58 ILE cc_start: 0.8770 (mm) cc_final: 0.8522 (mt) REVERT: G 190 GLU cc_start: 0.7945 (tt0) cc_final: 0.7587 (tm-30) REVERT: F 44 GLN cc_start: 0.7879 (mm-40) cc_final: 0.7362 (mm-40) REVERT: F 60 MET cc_start: 0.8575 (ttt) cc_final: 0.8076 (ttt) REVERT: F 64 LYS cc_start: 0.7668 (OUTLIER) cc_final: 0.7312 (ttmm) REVERT: F 67 TYR cc_start: 0.8176 (m-10) cc_final: 0.7642 (m-10) REVERT: F 100 THR cc_start: 0.9022 (m) cc_final: 0.8787 (p) REVERT: F 108 ASP cc_start: 0.8136 (OUTLIER) cc_final: 0.7733 (m-30) REVERT: F 109 SER cc_start: 0.8661 (t) cc_final: 0.8357 (m) REVERT: F 193 GLN cc_start: 0.8281 (OUTLIER) cc_final: 0.7825 (mp10) REVERT: B 62 ASP cc_start: 0.7945 (m-30) cc_final: 0.7674 (t0) REVERT: B 63 TYR cc_start: 0.8457 (m-80) cc_final: 0.8003 (m-80) REVERT: B 84 GLU cc_start: 0.8189 (tp30) cc_final: 0.7896 (tp30) REVERT: B 94 ASP cc_start: 0.8336 (m-30) cc_final: 0.7894 (t0) REVERT: B 145 TYR cc_start: 0.9092 (m-10) cc_final: 0.8790 (m-80) REVERT: C 58 ILE cc_start: 0.8683 (mm) cc_final: 0.8454 (mt) REVERT: C 67 TYR cc_start: 0.8101 (m-10) cc_final: 0.7526 (m-10) REVERT: D 64 LYS cc_start: 0.7472 (OUTLIER) cc_final: 0.7099 (ttmm) REVERT: D 67 TYR cc_start: 0.8181 (m-10) cc_final: 0.7708 (m-10) REVERT: D 84 GLU cc_start: 0.8376 (tp30) cc_final: 0.7901 (tp30) REVERT: D 114 LEU cc_start: 0.9167 (tt) cc_final: 0.8874 (tt) REVERT: D 190 GLU cc_start: 0.7739 (tt0) cc_final: 0.7508 (tm-30) REVERT: H 58 ILE cc_start: 0.8787 (mm) cc_final: 0.8461 (mt) REVERT: H 63 TYR cc_start: 0.8522 (m-80) cc_final: 0.8179 (m-80) REVERT: H 76 ASP cc_start: 0.8075 (m-30) cc_final: 0.7765 (m-30) REVERT: H 84 GLU cc_start: 0.8284 (tp30) cc_final: 0.8042 (tp30) REVERT: H 99 ASN cc_start: 0.8441 (t0) cc_final: 0.8164 (t0) REVERT: H 111 TYR cc_start: 0.8880 (m-10) cc_final: 0.8650 (m-80) REVERT: H 147 VAL cc_start: 0.9377 (m) cc_final: 0.9017 (p) REVERT: H 190 GLU cc_start: 0.8009 (tt0) cc_final: 0.7645 (tm-30) outliers start: 68 outliers final: 47 residues processed: 508 average time/residue: 0.1163 time to fit residues: 87.1124 Evaluate side-chains 497 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 444 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 46 SER Chi-restraints excluded: chain J residue 109 SER Chi-restraints excluded: chain J residue 131 ILE Chi-restraints excluded: chain J residue 150 GLU Chi-restraints excluded: chain J residue 167 ILE Chi-restraints excluded: chain A residue 129 MET Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 193 GLN Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain I residue 64 LYS Chi-restraints excluded: chain I residue 80 VAL Chi-restraints excluded: chain I residue 129 MET Chi-restraints excluded: chain I residue 150 GLU Chi-restraints excluded: chain I residue 167 ILE Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 46 SER Chi-restraints excluded: chain E residue 66 LYS Chi-restraints excluded: chain E residue 109 SER Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain E residue 150 GLU Chi-restraints excluded: chain G residue 40 GLU Chi-restraints excluded: chain G residue 64 LYS Chi-restraints excluded: chain G residue 100 THR Chi-restraints excluded: chain G residue 109 SER Chi-restraints excluded: chain G residue 154 ILE Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain F residue 46 SER Chi-restraints excluded: chain F residue 64 LYS Chi-restraints excluded: chain F residue 68 ILE Chi-restraints excluded: chain F residue 108 ASP Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 129 MET Chi-restraints excluded: chain F residue 167 ILE Chi-restraints excluded: chain F residue 193 GLN Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 150 GLU Chi-restraints excluded: chain C residue 40 GLU Chi-restraints excluded: chain C residue 64 LYS Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain D residue 40 GLU Chi-restraints excluded: chain D residue 64 LYS Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain H residue 64 LYS Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 109 SER Chi-restraints excluded: chain H residue 129 MET Chi-restraints excluded: chain H residue 167 ILE Chi-restraints excluded: chain H residue 178 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 41 optimal weight: 1.9990 chunk 160 optimal weight: 6.9990 chunk 155 optimal weight: 7.9990 chunk 114 optimal weight: 0.9980 chunk 94 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 23 optimal weight: 5.9990 chunk 6 optimal weight: 9.9990 chunk 28 optimal weight: 0.9980 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 118 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.152401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.124690 restraints weight = 18908.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.128762 restraints weight = 11833.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.131716 restraints weight = 8690.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.133842 restraints weight = 6976.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.135275 restraints weight = 5925.670| |-----------------------------------------------------------------------------| r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.4521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13930 Z= 0.179 Angle : 0.674 9.396 18860 Z= 0.355 Chirality : 0.050 0.154 2100 Planarity : 0.004 0.042 2460 Dihedral : 4.806 20.988 1890 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 14.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 3.84 % Allowed : 24.11 % Favored : 72.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.03 (0.21), residues: 1720 helix: -0.89 (0.22), residues: 470 sheet: -1.86 (0.25), residues: 410 loop : -1.21 (0.25), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 169 TYR 0.023 0.002 TYR A 67 PHE 0.034 0.002 PHE E 77 TRP 0.015 0.002 TRP J 116 HIS 0.004 0.001 HIS I 170 Details of bonding type rmsd covalent geometry : bond 0.00406 (13930) covalent geometry : angle 0.67391 (18860) hydrogen bonds : bond 0.03318 ( 410) hydrogen bonds : angle 5.43004 ( 1140) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 519 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 463 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 58 ILE cc_start: 0.8778 (mm) cc_final: 0.8466 (mt) REVERT: J 147 VAL cc_start: 0.9192 (m) cc_final: 0.8947 (p) REVERT: A 84 GLU cc_start: 0.8319 (tp30) cc_final: 0.7940 (tp30) REVERT: A 147 VAL cc_start: 0.9280 (m) cc_final: 0.8983 (p) REVERT: A 190 GLU cc_start: 0.7846 (tt0) cc_final: 0.7582 (tm-30) REVERT: A 193 GLN cc_start: 0.8196 (OUTLIER) cc_final: 0.7779 (mp10) REVERT: I 76 ASP cc_start: 0.7999 (m-30) cc_final: 0.7701 (m-30) REVERT: I 84 GLU cc_start: 0.8050 (tp30) cc_final: 0.7770 (tp30) REVERT: I 108 ASP cc_start: 0.8296 (m-30) cc_final: 0.7642 (m-30) REVERT: I 190 GLU cc_start: 0.7851 (tt0) cc_final: 0.7600 (tm-30) REVERT: E 58 ILE cc_start: 0.8788 (mm) cc_final: 0.8421 (mt) REVERT: E 76 ASP cc_start: 0.8155 (m-30) cc_final: 0.7664 (m-30) REVERT: E 84 GLU cc_start: 0.8227 (tp30) cc_final: 0.7973 (tp30) REVERT: E 99 ASN cc_start: 0.8271 (t0) cc_final: 0.7899 (t0) REVERT: E 108 ASP cc_start: 0.8101 (m-30) cc_final: 0.7647 (m-30) REVERT: E 134 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8684 (tt) REVERT: E 190 GLU cc_start: 0.7862 (tt0) cc_final: 0.7481 (tm-30) REVERT: G 58 ILE cc_start: 0.8660 (mm) cc_final: 0.8396 (mt) REVERT: G 63 TYR cc_start: 0.8569 (m-80) cc_final: 0.7964 (m-80) REVERT: G 64 LYS cc_start: 0.7529 (OUTLIER) cc_final: 0.7069 (ttmm) REVERT: F 44 GLN cc_start: 0.7912 (mm-40) cc_final: 0.7457 (mm-40) REVERT: F 60 MET cc_start: 0.8529 (ttt) cc_final: 0.7982 (ttt) REVERT: F 67 TYR cc_start: 0.8136 (m-10) cc_final: 0.7591 (m-10) REVERT: F 84 GLU cc_start: 0.8187 (tp30) cc_final: 0.7823 (tp30) REVERT: F 100 THR cc_start: 0.8851 (m) cc_final: 0.8548 (p) REVERT: F 193 GLN cc_start: 0.8058 (OUTLIER) cc_final: 0.7752 (mp10) REVERT: B 58 ILE cc_start: 0.8739 (mm) cc_final: 0.8458 (mt) REVERT: B 84 GLU cc_start: 0.8133 (tp30) cc_final: 0.7915 (tp30) REVERT: B 145 TYR cc_start: 0.8941 (m-10) cc_final: 0.8614 (m-80) REVERT: C 58 ILE cc_start: 0.8748 (mm) cc_final: 0.8527 (mt) REVERT: C 62 ASP cc_start: 0.7941 (m-30) cc_final: 0.7691 (t0) REVERT: C 63 TYR cc_start: 0.8472 (m-80) cc_final: 0.7979 (m-80) REVERT: C 67 TYR cc_start: 0.8070 (m-10) cc_final: 0.7455 (m-10) REVERT: D 58 ILE cc_start: 0.8822 (mm) cc_final: 0.8530 (mt) REVERT: D 67 TYR cc_start: 0.7931 (m-10) cc_final: 0.7503 (m-10) REVERT: D 84 GLU cc_start: 0.8309 (tp30) cc_final: 0.7881 (tp30) REVERT: D 147 VAL cc_start: 0.9255 (m) cc_final: 0.8991 (p) REVERT: D 190 GLU cc_start: 0.7711 (tt0) cc_final: 0.7335 (tm-30) REVERT: H 58 ILE cc_start: 0.8713 (mm) cc_final: 0.8377 (mt) REVERT: H 63 TYR cc_start: 0.8350 (m-80) cc_final: 0.7891 (m-80) REVERT: H 76 ASP cc_start: 0.7866 (m-30) cc_final: 0.7650 (m-30) REVERT: H 84 GLU cc_start: 0.8244 (tp30) cc_final: 0.8006 (tp30) REVERT: H 190 GLU cc_start: 0.7890 (tt0) cc_final: 0.7602 (tm-30) outliers start: 56 outliers final: 33 residues processed: 486 average time/residue: 0.1130 time to fit residues: 81.6857 Evaluate side-chains 471 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 434 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 40 GLU Chi-restraints excluded: chain J residue 46 SER Chi-restraints excluded: chain J residue 100 THR Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain J residue 109 SER Chi-restraints excluded: chain A residue 40 GLU Chi-restraints excluded: chain A residue 129 MET Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 193 GLN Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain I residue 40 GLU Chi-restraints excluded: chain I residue 129 MET Chi-restraints excluded: chain I residue 186 LEU Chi-restraints excluded: chain E residue 46 SER Chi-restraints excluded: chain E residue 109 SER Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain E residue 134 LEU Chi-restraints excluded: chain E residue 167 ILE Chi-restraints excluded: chain G residue 40 GLU Chi-restraints excluded: chain G residue 64 LYS Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain G residue 100 THR Chi-restraints excluded: chain G residue 109 SER Chi-restraints excluded: chain F residue 46 SER Chi-restraints excluded: chain F residue 193 GLN Chi-restraints excluded: chain B residue 64 LYS Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain C residue 40 GLU Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 131 ILE Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain H residue 109 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 150 optimal weight: 0.9980 chunk 96 optimal weight: 7.9990 chunk 65 optimal weight: 5.9990 chunk 16 optimal weight: 6.9990 chunk 146 optimal weight: 6.9990 chunk 79 optimal weight: 5.9990 chunk 131 optimal weight: 4.9990 chunk 53 optimal weight: 8.9990 chunk 95 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 161 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 61 ASN H 193 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.152726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.125375 restraints weight = 18852.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.129500 restraints weight = 11851.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.132471 restraints weight = 8697.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.134323 restraints weight = 6978.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.135867 restraints weight = 5961.402| |-----------------------------------------------------------------------------| r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.4718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13930 Z= 0.181 Angle : 0.687 9.945 18860 Z= 0.362 Chirality : 0.049 0.152 2100 Planarity : 0.004 0.042 2460 Dihedral : 4.745 20.147 1890 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.60 % Favored : 91.40 % Rotamer: Outliers : 3.97 % Allowed : 24.66 % Favored : 71.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.97 (0.21), residues: 1720 helix: -0.92 (0.22), residues: 490 sheet: -1.85 (0.25), residues: 410 loop : -1.10 (0.25), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG J 169 TYR 0.030 0.003 TYR A 67 PHE 0.057 0.002 PHE J 77 TRP 0.027 0.002 TRP J 116 HIS 0.005 0.001 HIS B 113 Details of bonding type rmsd covalent geometry : bond 0.00410 (13930) covalent geometry : angle 0.68693 (18860) hydrogen bonds : bond 0.03322 ( 410) hydrogen bonds : angle 5.36988 ( 1140) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 520 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 462 time to evaluate : 0.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 58 ILE cc_start: 0.8740 (mm) cc_final: 0.8476 (mt) REVERT: J 147 VAL cc_start: 0.9189 (m) cc_final: 0.8978 (p) REVERT: J 193 GLN cc_start: 0.8292 (mp10) cc_final: 0.7921 (mp10) REVERT: A 84 GLU cc_start: 0.8311 (tp30) cc_final: 0.7955 (tp30) REVERT: A 190 GLU cc_start: 0.7876 (tt0) cc_final: 0.7492 (tm-30) REVERT: A 193 GLN cc_start: 0.8237 (OUTLIER) cc_final: 0.7927 (mp10) REVERT: I 84 GLU cc_start: 0.8056 (tp30) cc_final: 0.7717 (tp30) REVERT: I 108 ASP cc_start: 0.8126 (m-30) cc_final: 0.7496 (m-30) REVERT: I 147 VAL cc_start: 0.9225 (m) cc_final: 0.8940 (p) REVERT: I 190 GLU cc_start: 0.7809 (tt0) cc_final: 0.7555 (tm-30) REVERT: E 58 ILE cc_start: 0.8763 (mm) cc_final: 0.8461 (mt) REVERT: E 76 ASP cc_start: 0.8229 (m-30) cc_final: 0.7903 (m-30) REVERT: E 84 GLU cc_start: 0.8164 (tp30) cc_final: 0.7731 (tp30) REVERT: E 99 ASN cc_start: 0.8221 (t0) cc_final: 0.7892 (t0) REVERT: E 190 GLU cc_start: 0.7922 (tt0) cc_final: 0.7533 (tm-30) REVERT: G 58 ILE cc_start: 0.8634 (mm) cc_final: 0.8365 (mt) REVERT: G 63 TYR cc_start: 0.8546 (m-80) cc_final: 0.8052 (m-80) REVERT: G 64 LYS cc_start: 0.7473 (OUTLIER) cc_final: 0.7036 (ttmm) REVERT: G 114 LEU cc_start: 0.9158 (tt) cc_final: 0.8950 (tt) REVERT: F 44 GLN cc_start: 0.7902 (mm-40) cc_final: 0.7311 (mm-40) REVERT: F 60 MET cc_start: 0.8422 (ttt) cc_final: 0.7997 (ttt) REVERT: F 67 TYR cc_start: 0.8151 (m-10) cc_final: 0.7692 (m-10) REVERT: F 84 GLU cc_start: 0.8070 (tp30) cc_final: 0.7762 (tp30) REVERT: F 100 THR cc_start: 0.8855 (m) cc_final: 0.8470 (p) REVERT: F 193 GLN cc_start: 0.8007 (OUTLIER) cc_final: 0.7723 (mp10) REVERT: B 58 ILE cc_start: 0.8832 (mm) cc_final: 0.8544 (mt) REVERT: B 84 GLU cc_start: 0.8148 (tp30) cc_final: 0.7918 (tp30) REVERT: B 108 ASP cc_start: 0.7951 (m-30) cc_final: 0.7437 (m-30) REVERT: B 145 TYR cc_start: 0.8905 (m-10) cc_final: 0.8655 (m-80) REVERT: C 58 ILE cc_start: 0.8688 (mm) cc_final: 0.8476 (mt) REVERT: C 63 TYR cc_start: 0.8307 (m-80) cc_final: 0.7843 (m-80) REVERT: C 67 TYR cc_start: 0.8045 (m-10) cc_final: 0.7371 (m-10) REVERT: C 190 GLU cc_start: 0.7860 (tt0) cc_final: 0.7533 (tm-30) REVERT: D 58 ILE cc_start: 0.8859 (mm) cc_final: 0.8604 (mt) REVERT: D 62 ASP cc_start: 0.7892 (m-30) cc_final: 0.7680 (t0) REVERT: D 67 TYR cc_start: 0.8041 (m-10) cc_final: 0.7583 (m-10) REVERT: D 84 GLU cc_start: 0.8321 (tp30) cc_final: 0.7931 (tp30) REVERT: D 147 VAL cc_start: 0.9230 (m) cc_final: 0.9005 (p) REVERT: D 190 GLU cc_start: 0.7727 (tt0) cc_final: 0.7346 (tm-30) REVERT: H 58 ILE cc_start: 0.8712 (mm) cc_final: 0.8370 (mt) REVERT: H 63 TYR cc_start: 0.8283 (m-80) cc_final: 0.7849 (m-80) REVERT: H 66 LYS cc_start: 0.6464 (mtmm) cc_final: 0.5909 (ptpt) REVERT: H 76 ASP cc_start: 0.7845 (m-30) cc_final: 0.7612 (m-30) REVERT: H 84 GLU cc_start: 0.8279 (tp30) cc_final: 0.8036 (tp30) REVERT: H 147 VAL cc_start: 0.9339 (m) cc_final: 0.9042 (p) outliers start: 58 outliers final: 45 residues processed: 487 average time/residue: 0.1135 time to fit residues: 81.9626 Evaluate side-chains 490 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 442 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 40 GLU Chi-restraints excluded: chain J residue 46 SER Chi-restraints excluded: chain J residue 100 THR Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain J residue 109 SER Chi-restraints excluded: chain J residue 131 ILE Chi-restraints excluded: chain A residue 129 MET Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 193 GLN Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain I residue 80 VAL Chi-restraints excluded: chain I residue 103 VAL Chi-restraints excluded: chain I residue 129 MET Chi-restraints excluded: chain I residue 167 ILE Chi-restraints excluded: chain I residue 186 LEU Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 46 SER Chi-restraints excluded: chain E residue 109 SER Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain E residue 167 ILE Chi-restraints excluded: chain G residue 40 GLU Chi-restraints excluded: chain G residue 64 LYS Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain G residue 100 THR Chi-restraints excluded: chain G residue 109 SER Chi-restraints excluded: chain G residue 154 ILE Chi-restraints excluded: chain G residue 167 ILE Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 46 SER Chi-restraints excluded: chain F residue 167 ILE Chi-restraints excluded: chain F residue 193 GLN Chi-restraints excluded: chain B residue 40 GLU Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain C residue 40 GLU Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 131 ILE Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain D residue 40 GLU Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain H residue 40 GLU Chi-restraints excluded: chain H residue 109 SER Chi-restraints excluded: chain H residue 122 LYS Chi-restraints excluded: chain H residue 129 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 64 optimal weight: 0.7980 chunk 100 optimal weight: 5.9990 chunk 163 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 53 optimal weight: 10.0000 chunk 81 optimal weight: 2.9990 chunk 18 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 chunk 59 optimal weight: 0.8980 chunk 77 optimal weight: 0.9980 chunk 169 optimal weight: 7.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.154460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.127486 restraints weight = 18694.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.131572 restraints weight = 11831.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.134524 restraints weight = 8693.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.136358 restraints weight = 6993.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.138148 restraints weight = 5978.834| |-----------------------------------------------------------------------------| r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.4902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 13930 Z= 0.167 Angle : 0.693 9.736 18860 Z= 0.361 Chirality : 0.049 0.155 2100 Planarity : 0.004 0.044 2460 Dihedral : 4.726 19.759 1890 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 14.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.60 % Favored : 91.40 % Rotamer: Outliers : 3.77 % Allowed : 24.45 % Favored : 71.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.02 (0.21), residues: 1720 helix: -0.81 (0.22), residues: 490 sheet: -2.42 (0.23), residues: 460 loop : -0.75 (0.25), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 169 TYR 0.023 0.002 TYR I 67 PHE 0.043 0.002 PHE J 77 TRP 0.019 0.002 TRP J 116 HIS 0.005 0.001 HIS B 113 Details of bonding type rmsd covalent geometry : bond 0.00379 (13930) covalent geometry : angle 0.69308 (18860) hydrogen bonds : bond 0.03336 ( 410) hydrogen bonds : angle 5.33601 ( 1140) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 509 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 454 time to evaluate : 0.535 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: J 58 ILE cc_start: 0.8744 (mm) cc_final: 0.8463 (mt) REVERT: A 84 GLU cc_start: 0.8290 (tp30) cc_final: 0.7932 (tp30) REVERT: A 190 GLU cc_start: 0.7872 (tt0) cc_final: 0.7429 (tm-30) REVERT: I 58 ILE cc_start: 0.8804 (mm) cc_final: 0.8525 (mt) REVERT: I 84 GLU cc_start: 0.8014 (tp30) cc_final: 0.7726 (tp30) REVERT: I 108 ASP cc_start: 0.7830 (m-30) cc_final: 0.7414 (m-30) REVERT: I 190 GLU cc_start: 0.7820 (tt0) cc_final: 0.7492 (tm-30) REVERT: E 58 ILE cc_start: 0.8776 (mm) cc_final: 0.8479 (mt) REVERT: E 76 ASP cc_start: 0.8238 (m-30) cc_final: 0.7944 (m-30) REVERT: E 84 GLU cc_start: 0.8107 (tp30) cc_final: 0.7761 (tp30) REVERT: E 99 ASN cc_start: 0.8312 (t0) cc_final: 0.7872 (t0) REVERT: E 145 TYR cc_start: 0.9086 (m-80) cc_final: 0.8505 (m-80) REVERT: G 63 TYR cc_start: 0.8483 (m-80) cc_final: 0.8087 (m-80) REVERT: G 64 LYS cc_start: 0.7488 (OUTLIER) cc_final: 0.7023 (ttmm) REVERT: G 114 LEU cc_start: 0.9134 (tt) cc_final: 0.8917 (tt) REVERT: F 44 GLN cc_start: 0.7877 (mm-40) cc_final: 0.7259 (mm-40) REVERT: F 60 MET cc_start: 0.8382 (ttt) cc_final: 0.7985 (ttt) REVERT: F 67 TYR cc_start: 0.8122 (m-10) cc_final: 0.7811 (m-10) REVERT: F 84 GLU cc_start: 0.8000 (tp30) cc_final: 0.7708 (tp30) REVERT: F 147 VAL cc_start: 0.9305 (m) cc_final: 0.9085 (p) REVERT: F 190 GLU cc_start: 0.7696 (tt0) cc_final: 0.7438 (tm-30) REVERT: B 58 ILE cc_start: 0.8858 (mm) cc_final: 0.8558 (mt) REVERT: B 84 GLU cc_start: 0.8114 (tp30) cc_final: 0.7880 (tp30) REVERT: B 108 ASP cc_start: 0.7952 (m-30) cc_final: 0.7649 (m-30) REVERT: B 145 TYR cc_start: 0.8909 (m-10) cc_final: 0.8637 (m-80) REVERT: C 58 ILE cc_start: 0.8659 (mm) cc_final: 0.8446 (mt) REVERT: C 63 TYR cc_start: 0.8205 (m-80) cc_final: 0.7709 (m-80) REVERT: C 67 TYR cc_start: 0.8000 (m-10) cc_final: 0.7300 (m-10) REVERT: C 190 GLU cc_start: 0.7811 (tt0) cc_final: 0.7501 (tm-30) REVERT: D 58 ILE cc_start: 0.8805 (mm) cc_final: 0.8525 (mt) REVERT: D 67 TYR cc_start: 0.8098 (m-10) cc_final: 0.7661 (m-10) REVERT: D 84 GLU cc_start: 0.8278 (tp30) cc_final: 0.7918 (tp30) REVERT: D 147 VAL cc_start: 0.9218 (m) cc_final: 0.9015 (p) REVERT: D 190 GLU cc_start: 0.7697 (tt0) cc_final: 0.7319 (tm-30) REVERT: H 58 ILE cc_start: 0.8745 (mm) cc_final: 0.8434 (mt) REVERT: H 63 TYR cc_start: 0.8264 (m-80) cc_final: 0.7947 (m-80) REVERT: H 76 ASP cc_start: 0.7856 (m-30) cc_final: 0.7651 (m-30) REVERT: H 84 GLU cc_start: 0.8171 (tp30) cc_final: 0.7851 (tp30) REVERT: H 147 VAL cc_start: 0.9365 (m) cc_final: 0.9077 (p) outliers start: 55 outliers final: 45 residues processed: 480 average time/residue: 0.1151 time to fit residues: 82.2368 Evaluate side-chains 470 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 424 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain J residue 40 GLU Chi-restraints excluded: chain J residue 46 SER Chi-restraints excluded: chain J residue 100 THR Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain J residue 109 SER Chi-restraints excluded: chain J residue 131 ILE Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 129 MET Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain I residue 40 GLU Chi-restraints excluded: chain I residue 103 VAL Chi-restraints excluded: chain I residue 129 MET Chi-restraints excluded: chain I residue 167 ILE Chi-restraints excluded: chain E residue 40 GLU Chi-restraints excluded: chain E residue 46 SER Chi-restraints excluded: chain E residue 66 LYS Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 109 SER Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain E residue 167 ILE Chi-restraints excluded: chain G residue 40 GLU Chi-restraints excluded: chain G residue 64 LYS Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain G residue 100 THR Chi-restraints excluded: chain G residue 108 ASP Chi-restraints excluded: chain G residue 154 ILE Chi-restraints excluded: chain G residue 167 ILE Chi-restraints excluded: chain F residue 129 MET Chi-restraints excluded: chain F residue 167 ILE Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain C residue 40 GLU Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 131 ILE Chi-restraints excluded: chain D residue 40 GLU Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain H residue 40 GLU Chi-restraints excluded: chain H residue 109 SER Chi-restraints excluded: chain H residue 122 LYS Chi-restraints excluded: chain H residue 129 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 5 optimal weight: 10.0000 chunk 44 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 35 optimal weight: 2.9990 chunk 113 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 chunk 142 optimal weight: 10.0000 chunk 75 optimal weight: 10.0000 chunk 9 optimal weight: 9.9990 chunk 160 optimal weight: 5.9990 chunk 164 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 130 HIS ** I 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 130 HIS ** E 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 198 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.146827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.118870 restraints weight = 19116.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.122698 restraints weight = 12417.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.125401 restraints weight = 9332.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.127131 restraints weight = 7653.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.128645 restraints weight = 6636.825| |-----------------------------------------------------------------------------| r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.4896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.057 13930 Z= 0.345 Angle : 0.818 10.313 18860 Z= 0.434 Chirality : 0.054 0.368 2100 Planarity : 0.005 0.046 2460 Dihedral : 5.235 21.583 1890 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 18.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.83 % Favored : 90.17 % Rotamer: Outliers : 4.11 % Allowed : 24.86 % Favored : 71.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.10 (0.21), residues: 1720 helix: -0.99 (0.21), residues: 490 sheet: -1.97 (0.24), residues: 410 loop : -1.19 (0.25), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG J 169 TYR 0.026 0.003 TYR H 67 PHE 0.042 0.003 PHE J 77 TRP 0.022 0.003 TRP J 116 HIS 0.006 0.002 HIS B 113 Details of bonding type rmsd covalent geometry : bond 0.00796 (13930) covalent geometry : angle 0.81801 (18860) hydrogen bonds : bond 0.04109 ( 410) hydrogen bonds : angle 5.63017 ( 1140) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 462 time to evaluate : 0.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 58 ILE cc_start: 0.8830 (mm) cc_final: 0.8577 (mt) REVERT: J 76 ASP cc_start: 0.8593 (m-30) cc_final: 0.8300 (m-30) REVERT: A 48 GLN cc_start: 0.8714 (mt0) cc_final: 0.8426 (mt0) REVERT: A 84 GLU cc_start: 0.8381 (tp30) cc_final: 0.7826 (tp30) REVERT: I 58 ILE cc_start: 0.8863 (mm) cc_final: 0.8640 (mt) REVERT: I 190 GLU cc_start: 0.7929 (tt0) cc_final: 0.7586 (tm-30) REVERT: E 58 ILE cc_start: 0.8814 (mm) cc_final: 0.8539 (mt) REVERT: E 73 TYR cc_start: 0.8843 (p90) cc_final: 0.8641 (p90) REVERT: E 76 ASP cc_start: 0.8471 (m-30) cc_final: 0.8181 (m-30) REVERT: E 99 ASN cc_start: 0.8346 (t0) cc_final: 0.8024 (t0) REVERT: G 58 ILE cc_start: 0.8683 (mm) cc_final: 0.8418 (mt) REVERT: G 63 TYR cc_start: 0.8569 (m-80) cc_final: 0.8076 (m-80) REVERT: G 108 ASP cc_start: 0.8022 (OUTLIER) cc_final: 0.7569 (t70) REVERT: F 44 GLN cc_start: 0.7924 (mm-40) cc_final: 0.7181 (mm-40) REVERT: F 60 MET cc_start: 0.8511 (ttt) cc_final: 0.8072 (ttt) REVERT: F 67 TYR cc_start: 0.8205 (m-10) cc_final: 0.7991 (m-10) REVERT: F 84 GLU cc_start: 0.8144 (tp30) cc_final: 0.7635 (tp30) REVERT: F 147 VAL cc_start: 0.9315 (m) cc_final: 0.9057 (p) REVERT: B 58 ILE cc_start: 0.8900 (mm) cc_final: 0.8592 (mt) REVERT: B 84 GLU cc_start: 0.8223 (tp30) cc_final: 0.7994 (tp30) REVERT: B 108 ASP cc_start: 0.8049 (m-30) cc_final: 0.7654 (t70) REVERT: B 145 TYR cc_start: 0.9019 (m-10) cc_final: 0.8720 (m-80) REVERT: C 63 TYR cc_start: 0.8501 (m-80) cc_final: 0.8085 (m-80) REVERT: C 64 LYS cc_start: 0.7638 (OUTLIER) cc_final: 0.7294 (ttmm) REVERT: C 108 ASP cc_start: 0.8092 (m-30) cc_final: 0.7801 (t70) REVERT: D 58 ILE cc_start: 0.8859 (mm) cc_final: 0.8602 (mt) REVERT: D 67 TYR cc_start: 0.8187 (m-10) cc_final: 0.7809 (m-10) REVERT: D 84 GLU cc_start: 0.8379 (tp30) cc_final: 0.8025 (tp30) REVERT: D 190 GLU cc_start: 0.7792 (tt0) cc_final: 0.7452 (tm-30) REVERT: H 58 ILE cc_start: 0.8784 (mm) cc_final: 0.8469 (mt) REVERT: H 63 TYR cc_start: 0.8396 (m-80) cc_final: 0.8034 (m-80) REVERT: H 76 ASP cc_start: 0.8045 (m-30) cc_final: 0.7792 (m-30) REVERT: H 84 GLU cc_start: 0.8231 (tp30) cc_final: 0.7886 (tp30) REVERT: H 147 VAL cc_start: 0.9422 (m) cc_final: 0.9070 (p) outliers start: 60 outliers final: 49 residues processed: 485 average time/residue: 0.1121 time to fit residues: 80.1576 Evaluate side-chains 491 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 440 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain J residue 40 GLU Chi-restraints excluded: chain J residue 46 SER Chi-restraints excluded: chain J residue 100 THR Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain J residue 109 SER Chi-restraints excluded: chain J residue 131 ILE Chi-restraints excluded: chain J residue 150 GLU Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 40 GLU Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 129 MET Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain I residue 40 GLU Chi-restraints excluded: chain I residue 97 LYS Chi-restraints excluded: chain I residue 100 THR Chi-restraints excluded: chain I residue 103 VAL Chi-restraints excluded: chain I residue 129 MET Chi-restraints excluded: chain I residue 167 ILE Chi-restraints excluded: chain I residue 186 LEU Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 40 GLU Chi-restraints excluded: chain E residue 46 SER Chi-restraints excluded: chain E residue 66 LYS Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 109 SER Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain E residue 167 ILE Chi-restraints excluded: chain G residue 40 GLU Chi-restraints excluded: chain G residue 64 LYS Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain G residue 100 THR Chi-restraints excluded: chain G residue 108 ASP Chi-restraints excluded: chain G residue 167 ILE Chi-restraints excluded: chain F residue 129 MET Chi-restraints excluded: chain F residue 167 ILE Chi-restraints excluded: chain C residue 40 GLU Chi-restraints excluded: chain C residue 64 LYS Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 131 ILE Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain D residue 40 GLU Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain H residue 40 GLU Chi-restraints excluded: chain H residue 109 SER Chi-restraints excluded: chain H residue 129 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 1 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 152 optimal weight: 5.9990 chunk 126 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 118 optimal weight: 0.8980 chunk 150 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 124 optimal weight: 0.6980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 101 GLN D 118 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.163301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.135519 restraints weight = 18441.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.139751 restraints weight = 11799.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.142738 restraints weight = 8741.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.144977 restraints weight = 7063.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.146470 restraints weight = 6003.353| |-----------------------------------------------------------------------------| r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.5236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13930 Z= 0.152 Angle : 0.737 10.424 18860 Z= 0.384 Chirality : 0.050 0.388 2100 Planarity : 0.004 0.042 2460 Dihedral : 4.878 22.156 1890 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 15.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.85 % Favored : 92.15 % Rotamer: Outliers : 3.01 % Allowed : 26.37 % Favored : 70.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.99 (0.21), residues: 1720 helix: -0.59 (0.22), residues: 490 sheet: -2.43 (0.23), residues: 460 loop : -0.85 (0.25), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 169 TYR 0.025 0.002 TYR E 194 PHE 0.029 0.002 PHE J 77 TRP 0.011 0.002 TRP J 116 HIS 0.008 0.001 HIS B 113 Details of bonding type rmsd covalent geometry : bond 0.00340 (13930) covalent geometry : angle 0.73723 (18860) hydrogen bonds : bond 0.03435 ( 410) hydrogen bonds : angle 5.38138 ( 1140) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 418 time to evaluate : 0.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 58 ILE cc_start: 0.8853 (mm) cc_final: 0.8578 (mt) REVERT: A 48 GLN cc_start: 0.8631 (mt0) cc_final: 0.8388 (mt0) REVERT: A 84 GLU cc_start: 0.8310 (tp30) cc_final: 0.7998 (tp30) REVERT: I 73 TYR cc_start: 0.8646 (p90) cc_final: 0.8306 (p90) REVERT: I 84 GLU cc_start: 0.7931 (tp30) cc_final: 0.7516 (tp30) REVERT: E 58 ILE cc_start: 0.8762 (mm) cc_final: 0.8472 (mt) REVERT: E 66 LYS cc_start: 0.6411 (OUTLIER) cc_final: 0.5789 (pttm) REVERT: E 76 ASP cc_start: 0.8265 (m-30) cc_final: 0.7980 (m-30) REVERT: E 84 GLU cc_start: 0.8040 (tp30) cc_final: 0.7317 (tp30) REVERT: E 99 ASN cc_start: 0.8360 (t0) cc_final: 0.7903 (t0) REVERT: E 145 TYR cc_start: 0.9112 (m-80) cc_final: 0.8568 (m-80) REVERT: G 58 ILE cc_start: 0.8713 (mm) cc_final: 0.8464 (mt) REVERT: G 63 TYR cc_start: 0.8237 (m-80) cc_final: 0.7853 (m-80) REVERT: G 84 GLU cc_start: 0.8493 (tp30) cc_final: 0.8184 (tp30) REVERT: F 44 GLN cc_start: 0.7769 (mm-40) cc_final: 0.7136 (mm-40) REVERT: F 60 MET cc_start: 0.8412 (ttt) cc_final: 0.8024 (ttt) REVERT: F 84 GLU cc_start: 0.7993 (tp30) cc_final: 0.7710 (tp30) REVERT: B 58 ILE cc_start: 0.8871 (mm) cc_final: 0.8541 (mt) REVERT: B 145 TYR cc_start: 0.8911 (m-10) cc_final: 0.8636 (m-80) REVERT: C 62 ASP cc_start: 0.7845 (t0) cc_final: 0.7568 (t0) REVERT: C 63 TYR cc_start: 0.8221 (m-80) cc_final: 0.7770 (m-10) REVERT: C 64 LYS cc_start: 0.7527 (OUTLIER) cc_final: 0.7074 (ttmm) REVERT: C 84 GLU cc_start: 0.8315 (tp30) cc_final: 0.7809 (tp30) REVERT: D 58 ILE cc_start: 0.8855 (mm) cc_final: 0.8651 (mt) REVERT: D 67 TYR cc_start: 0.8129 (m-10) cc_final: 0.7730 (m-10) REVERT: D 84 GLU cc_start: 0.8277 (tp30) cc_final: 0.7917 (tp30) REVERT: D 190 GLU cc_start: 0.7752 (tt0) cc_final: 0.7337 (tm-30) REVERT: H 58 ILE cc_start: 0.8760 (mm) cc_final: 0.8441 (mt) REVERT: H 63 TYR cc_start: 0.8142 (m-80) cc_final: 0.7802 (m-80) REVERT: H 84 GLU cc_start: 0.8038 (tp30) cc_final: 0.7749 (tp30) REVERT: H 147 VAL cc_start: 0.9377 (m) cc_final: 0.9077 (p) REVERT: H 169 ARG cc_start: 0.8170 (mmt90) cc_final: 0.7970 (mmm-85) outliers start: 44 outliers final: 35 residues processed: 439 average time/residue: 0.1188 time to fit residues: 76.6593 Evaluate side-chains 435 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 398 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 40 GLU Chi-restraints excluded: chain J residue 46 SER Chi-restraints excluded: chain J residue 100 THR Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain J residue 109 SER Chi-restraints excluded: chain J residue 131 ILE Chi-restraints excluded: chain A residue 129 MET Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain I residue 40 GLU Chi-restraints excluded: chain I residue 97 LYS Chi-restraints excluded: chain I residue 103 VAL Chi-restraints excluded: chain I residue 129 MET Chi-restraints excluded: chain I residue 167 ILE Chi-restraints excluded: chain E residue 46 SER Chi-restraints excluded: chain E residue 66 LYS Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 109 SER Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain E residue 167 ILE Chi-restraints excluded: chain G residue 40 GLU Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain G residue 100 THR Chi-restraints excluded: chain G residue 167 ILE Chi-restraints excluded: chain F residue 129 MET Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain C residue 40 GLU Chi-restraints excluded: chain C residue 64 LYS Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain D residue 40 GLU Chi-restraints excluded: chain H residue 109 SER Chi-restraints excluded: chain H residue 122 LYS Chi-restraints excluded: chain H residue 129 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 160 optimal weight: 8.9990 chunk 41 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 chunk 145 optimal weight: 10.0000 chunk 18 optimal weight: 1.9990 chunk 133 optimal weight: 5.9990 chunk 49 optimal weight: 5.9990 chunk 128 optimal weight: 8.9990 chunk 20 optimal weight: 5.9990 chunk 8 optimal weight: 4.9990 chunk 15 optimal weight: 5.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 101 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.159152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.131023 restraints weight = 18656.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.135130 restraints weight = 12026.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.138045 restraints weight = 8986.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.140130 restraints weight = 7304.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.141590 restraints weight = 6264.941| |-----------------------------------------------------------------------------| r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.5208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 13930 Z= 0.233 Angle : 0.763 10.213 18860 Z= 0.400 Chirality : 0.052 0.389 2100 Planarity : 0.005 0.049 2460 Dihedral : 4.978 22.315 1890 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 16.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.19 % Favored : 90.81 % Rotamer: Outliers : 3.36 % Allowed : 25.89 % Favored : 70.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.38 (0.21), residues: 1720 helix: -0.88 (0.21), residues: 550 sheet: -2.70 (0.23), residues: 440 loop : -1.14 (0.26), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 157 TYR 0.023 0.002 TYR F 67 PHE 0.028 0.003 PHE J 77 TRP 0.012 0.002 TRP J 116 HIS 0.006 0.001 HIS B 113 Details of bonding type rmsd covalent geometry : bond 0.00536 (13930) covalent geometry : angle 0.76268 (18860) hydrogen bonds : bond 0.03697 ( 410) hydrogen bonds : angle 5.42488 ( 1140) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2317.99 seconds wall clock time: 40 minutes 57.23 seconds (2457.23 seconds total)