Starting phenix.real_space_refine on Sat Sep 12 00:18:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6c0w_7326/09_2026/6c0w_7326_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6c0w_7326/09_2026/6c0w_7326.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6c0w_7326/09_2026/6c0w_7326_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6c0w_7326/09_2026/6c0w_7326_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6c0w_7326/09_2026/6c0w_7326.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6c0w_7326/09_2026/6c0w_7326.map" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.011 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: 5 Type Number sf(0) Gaussians P 278 5.49 5 S 16 5.16 5 C 7427 2.51 5 N 2429 2.21 5 O 2972 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13122 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 732 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 2, 'TRANS': 86} Chain: "B" Number of atoms: 634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 634 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "C" Number of atoms: 764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 764 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "D" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "E" Number of atoms: 749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 749 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "F" Number of atoms: 623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 623 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "G" Number of atoms: 771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 771 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "H" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "I" Number of atoms: 2835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 2835 Classifications: {'DNA': 139} Link IDs: {'rna3p': 138} Chain: "J" Number of atoms: 2864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 2864 Classifications: {'DNA': 139} Link IDs: {'rna3p': 138} Chain: "K" Number of atoms: 1712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1712 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 5, 'TRANS': 199} Chain breaks: 1 Time building chain proxies: 2.63, per 1000 atoms: 0.20 Number of scatterers: 13122 At special positions: 0 Unit cell: (100.98, 131.58, 118.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 16 16.00 P 278 15.00 O 2972 8.00 N 2429 7.00 C 7427 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: 0.96 Conformation dependent library (CDL) restraints added in 331.2 milliseconds 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1740 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 10 sheets defined 65.4% alpha, 6.1% beta 138 base pairs and 237 stacking pairs defined. Time for finding SS restraints: 1.68 Creating SS restraints... Processing helix chain 'A' and resid 47 through 55 removed outlier: 3.787A pdb=" N ARG A 52 " --> pdb=" O LEU A 48 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LYS A 53 " --> pdb=" O LYS A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 76 removed outlier: 3.784A pdb=" N VAL A 76 " --> pdb=" O ARG A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 114 Processing helix chain 'A' and resid 122 through 127 removed outlier: 3.801A pdb=" N VAL A 126 " --> pdb=" O PHE A 122 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLN A 127 " --> pdb=" O PRO A 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 122 through 127' Processing helix chain 'B' and resid 32 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.322A pdb=" N ARG B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N GLY B 56 " --> pdb=" O GLU B 52 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N LYS B 59 " --> pdb=" O ARG B 55 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N THR B 71 " --> pdb=" O ARG B 67 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N TYR B 72 " --> pdb=" O ASP B 68 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N THR B 73 " --> pdb=" O ALA B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 removed outlier: 3.743A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 27 through 37 Processing helix chain 'C' and resid 46 through 73 removed outlier: 3.669A pdb=" N TYR C 50 " --> pdb=" O GLY C 46 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ASN C 68 " --> pdb=" O GLU C 64 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ALA C 69 " --> pdb=" O LEU C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.766A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 37 through 49 removed outlier: 3.589A pdb=" N VAL D 41 " --> pdb=" O TYR D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 67 Processing helix chain 'D' and resid 68 through 80 removed outlier: 4.361A pdb=" N SER D 78 " --> pdb=" O ALA D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.656A pdb=" N ILE D 94 " --> pdb=" O THR D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 123 removed outlier: 3.726A pdb=" N THR D 115 " --> pdb=" O VAL D 111 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LYS D 116 " --> pdb=" O SER D 112 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS D 120 " --> pdb=" O LYS D 116 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N SER D 123 " --> pdb=" O THR D 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 55 removed outlier: 3.678A pdb=" N ARG E 52 " --> pdb=" O LEU E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 78 removed outlier: 3.808A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 110 removed outlier: 3.714A pdb=" N LEU E 91 " --> pdb=" O GLN E 87 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LEU E 92 " --> pdb=" O ALA E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 113 No H-bonds generated for 'chain 'E' and resid 111 through 113' Processing helix chain 'E' and resid 122 through 134 removed outlier: 3.710A pdb=" N ARG E 133 " --> pdb=" O ALA E 129 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 41 removed outlier: 3.688A pdb=" N GLY F 41 " --> pdb=" O LEU F 37 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.565A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N ARG F 55 " --> pdb=" O TYR F 51 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N ASN F 64 " --> pdb=" O VAL F 60 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N TYR F 72 " --> pdb=" O ASP F 68 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 removed outlier: 3.675A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 21 removed outlier: 3.707A pdb=" N ALA G 21 " --> pdb=" O ARG G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 27 through 36 Processing helix chain 'G' and resid 46 through 73 removed outlier: 3.936A pdb=" N TYR G 50 " --> pdb=" O GLY G 46 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU G 65 " --> pdb=" O GLU G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.580A pdb=" N LEU G 83 " --> pdb=" O ILE G 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 97 removed outlier: 3.515A pdb=" N LYS G 95 " --> pdb=" O GLU G 91 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 49 removed outlier: 3.589A pdb=" N VAL H 41 " --> pdb=" O TYR H 37 " (cutoff:3.500A) Processing helix chain 'H' and resid 57 through 67 Processing helix chain 'H' and resid 68 through 84 removed outlier: 4.362A pdb=" N SER H 78 " --> pdb=" O ALA H 74 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N HIS H 82 " --> pdb=" O SER H 78 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ASN H 84 " --> pdb=" O LEU H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 removed outlier: 3.657A pdb=" N ILE H 94 " --> pdb=" O THR H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 123 removed outlier: 3.726A pdb=" N THR H 115 " --> pdb=" O VAL H 111 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LYS H 116 " --> pdb=" O SER H 112 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS H 120 " --> pdb=" O LYS H 116 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N SER H 123 " --> pdb=" O THR H 119 " (cutoff:3.500A) Processing helix chain 'K' and resid 4 through 16 removed outlier: 3.528A pdb=" N PHE K 8 " --> pdb=" O THR K 4 " (cutoff:3.500A) Processing helix chain 'K' and resid 20 through 29 removed outlier: 3.726A pdb=" N ASP K 29 " --> pdb=" O LEU K 25 " (cutoff:3.500A) Processing helix chain 'K' and resid 32 through 39 removed outlier: 3.531A pdb=" N VAL K 39 " --> pdb=" O GLN K 35 " (cutoff:3.500A) Processing helix chain 'K' and resid 44 through 59 removed outlier: 3.549A pdb=" N VAL K 48 " --> pdb=" O ARG K 44 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL K 49 " --> pdb=" O LYS K 45 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N GLN K 50 " --> pdb=" O GLU K 46 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLU K 58 " --> pdb=" O HIS K 54 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS K 59 " --> pdb=" O LEU K 55 " (cutoff:3.500A) Processing helix chain 'K' and resid 63 through 75 Processing helix chain 'K' and resid 100 through 116 removed outlier: 3.986A pdb=" N PHE K 104 " --> pdb=" O ASP K 100 " (cutoff:3.500A) Processing helix chain 'K' and resid 171 through 183 Processing helix chain 'K' and resid 197 through 210 removed outlier: 3.983A pdb=" N LEU K 201 " --> pdb=" O TYR K 197 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N GLN K 208 " --> pdb=" O ILE K 204 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 85 through 86 removed outlier: 6.798A pdb=" N ASN A 85 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 120 through 121 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 97 removed outlier: 6.401A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA5, first strand: chain 'C' and resid 100 through 101 Processing sheet with id=AA6, first strand: chain 'E' and resid 85 through 86 removed outlier: 6.926A pdb=" N ASN E 85 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.699A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AA9, first strand: chain 'K' and resid 120 through 122 Processing sheet with id=AB1, first strand: chain 'K' and resid 120 through 122 removed outlier: 4.757A pdb=" N TYR K 151 " --> pdb=" O SER K 164 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N TYR K 155 " --> pdb=" O TYR K 160 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N TYR K 160 " --> pdb=" O TYR K 155 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N LEU K 193 " --> pdb=" O VAL K 85 " (cutoff:3.500A) removed outlier: 8.719A pdb=" N GLN K 87 " --> pdb=" O MET K 191 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N MET K 191 " --> pdb=" O GLN K 87 " (cutoff:3.500A) removed outlier: 8.686A pdb=" N SER K 89 " --> pdb=" O VAL K 189 " (cutoff:3.500A) removed outlier: 8.323A pdb=" N VAL K 189 " --> pdb=" O SER K 89 " (cutoff:3.500A) 400 hydrogen bonds defined for protein. 1185 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 347 hydrogen bonds 670 hydrogen bond angles 0 basepair planarities 138 basepair parallelities 237 stacking parallelities Total time for adding SS restraints: 2.13 Time building geometry restraints manager: 1.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2466 1.33 - 1.45: 4461 1.45 - 1.57: 6426 1.57 - 1.69: 554 1.69 - 1.81: 29 Bond restraints: 13936 Sorted by residual: bond pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " ideal model delta sigma weight residual 1.435 1.497 -0.062 1.30e-02 5.92e+03 2.24e+01 bond pdb=" C3' DT J -61 " pdb=" O3' DT J -61 " ideal model delta sigma weight residual 1.435 1.489 -0.054 1.30e-02 5.92e+03 1.71e+01 bond pdb=" C3' DC J 34 " pdb=" C2' DC J 34 " ideal model delta sigma weight residual 1.516 1.546 -0.030 8.00e-03 1.56e+04 1.41e+01 bond pdb=" C3' DA I 61 " pdb=" C2' DA I 61 " ideal model delta sigma weight residual 1.516 1.545 -0.029 8.00e-03 1.56e+04 1.30e+01 bond pdb=" C3' DG J -5 " pdb=" C2' DG J -5 " ideal model delta sigma weight residual 1.516 1.545 -0.029 8.00e-03 1.56e+04 1.29e+01 ... (remaining 13931 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.81: 18617 1.81 - 3.61: 1281 3.61 - 5.42: 88 5.42 - 7.22: 21 7.22 - 9.03: 9 Bond angle restraints: 20016 Sorted by residual: angle pdb=" O4' DG I -24 " pdb=" C4' DG I -24 " pdb=" C3' DG I -24 " ideal model delta sigma weight residual 106.00 102.85 3.15 6.00e-01 2.78e+00 2.76e+01 angle pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " pdb=" P DT J -16 " ideal model delta sigma weight residual 119.70 125.68 -5.98 1.20e+00 6.94e-01 2.48e+01 angle pdb=" O4' DC J 67 " pdb=" C4' DC J 67 " pdb=" C3' DC J 67 " ideal model delta sigma weight residual 106.00 103.16 2.84 6.00e-01 2.78e+00 2.24e+01 angle pdb=" C ARG K 169 " pdb=" N ARG K 170 " pdb=" CA ARG K 170 " ideal model delta sigma weight residual 121.54 130.57 -9.03 1.91e+00 2.74e-01 2.23e+01 angle pdb=" N3 DT J -50 " pdb=" C4 DT J -50 " pdb=" O4 DT J -50 " ideal model delta sigma weight residual 119.90 122.71 -2.81 6.00e-01 2.78e+00 2.20e+01 ... (remaining 20011 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 6158 35.97 - 71.94: 1421 71.94 - 107.91: 33 107.91 - 143.87: 5 143.87 - 179.84: 3 Dihedral angle restraints: 7620 sinusoidal: 4930 harmonic: 2690 Sorted by residual: dihedral pdb=" CA VAL D 66 " pdb=" C VAL D 66 " pdb=" N ASN D 67 " pdb=" CA ASN D 67 " ideal model delta harmonic sigma weight residual 180.00 153.03 26.97 0 5.00e+00 4.00e-02 2.91e+01 dihedral pdb=" CA VAL H 66 " pdb=" C VAL H 66 " pdb=" N ASN H 67 " pdb=" CA ASN H 67 " ideal model delta harmonic sigma weight residual 180.00 153.05 26.95 0 5.00e+00 4.00e-02 2.91e+01 dihedral pdb=" CA TYR B 98 " pdb=" C TYR B 98 " pdb=" N GLY B 99 " pdb=" CA GLY B 99 " ideal model delta harmonic sigma weight residual -180.00 -157.10 -22.90 0 5.00e+00 4.00e-02 2.10e+01 ... (remaining 7617 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 1849 0.066 - 0.132: 380 0.132 - 0.198: 33 0.198 - 0.264: 6 0.264 - 0.330: 2 Chirality restraints: 2270 Sorted by residual: chirality pdb=" CB VAL H 66 " pdb=" CA VAL H 66 " pdb=" CG1 VAL H 66 " pdb=" CG2 VAL H 66 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.33 2.00e-01 2.50e+01 2.72e+00 chirality pdb=" CB VAL D 66 " pdb=" CA VAL D 66 " pdb=" CG1 VAL D 66 " pdb=" CG2 VAL D 66 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.33 2.00e-01 2.50e+01 2.67e+00 chirality pdb=" C3' DT J -61 " pdb=" C4' DT J -61 " pdb=" O3' DT J -61 " pdb=" C2' DT J -61 " both_signs ideal model delta sigma weight residual False -2.73 -2.52 -0.21 2.00e-01 2.50e+01 1.12e+00 ... (remaining 2267 not shown) Planarity restraints: 1559 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU B 63 " -0.017 2.00e-02 2.50e+03 3.43e-02 1.17e+01 pdb=" C GLU B 63 " 0.059 2.00e-02 2.50e+03 pdb=" O GLU B 63 " -0.022 2.00e-02 2.50e+03 pdb=" N ASN B 64 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS B 31 " 0.051 5.00e-02 4.00e+02 7.67e-02 9.41e+00 pdb=" N PRO B 32 " -0.133 5.00e-02 4.00e+02 pdb=" CA PRO B 32 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO B 32 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL F 57 " -0.014 2.00e-02 2.50e+03 2.79e-02 7.81e+00 pdb=" C VAL F 57 " 0.048 2.00e-02 2.50e+03 pdb=" O VAL F 57 " -0.018 2.00e-02 2.50e+03 pdb=" N LEU F 58 " -0.016 2.00e-02 2.50e+03 ... (remaining 1556 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 403 2.67 - 3.22: 10868 3.22 - 3.78: 23903 3.78 - 4.34: 29972 4.34 - 4.90: 42476 Nonbonded interactions: 107622 Sorted by model distance: nonbonded pdb=" O TYR B 51 " pdb=" NH1 ARG B 55 " model vdw 2.107 3.120 nonbonded pdb=" NH1 ARG F 39 " pdb=" O LYS F 44 " model vdw 2.145 3.120 nonbonded pdb=" OD2 ASP K 70 " pdb=" OH TYR K 151 " model vdw 2.162 3.040 nonbonded pdb=" OH TYR H 42 " pdb=" NZ LYS H 46 " model vdw 2.190 3.120 nonbonded pdb=" OH TYR D 42 " pdb=" NZ LYS D 46 " model vdw 2.190 3.120 ... (remaining 107617 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'E' and resid 46 through 134) } ncs_group { reference = (chain 'B' and resid 24 through 101) selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 15 through 112) selection = (chain 'G' and resid 15 through 112) } ncs_group { reference = 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: 0.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 12.330 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 13936 Z= 0.572 Angle : 0.935 9.028 20016 Z= 0.753 Chirality : 0.053 0.330 2270 Planarity : 0.006 0.077 1559 Dihedral : 27.862 179.844 5880 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % 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: -4.19 (0.20), residues: 905 helix: -2.61 (0.14), residues: 605 sheet: -1.52 (0.80), residues: 38 loop : -2.86 (0.32), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 92 TYR 0.014 0.002 TYR F 88 PHE 0.026 0.002 PHE F 100 TRP 0.033 0.003 TRP K 28 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00700 / 0.57 (13936) covalent geometry : angle 0.93531 / 0.75 (20016) hydrogen bonds : bond 0.14517 / 9.61 ( 743) hydrogen bonds : angle 5.89985 / 3.98 ( 1855) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 385 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 GLN cc_start: 0.8295 (mt0) cc_final: 0.8002 (mt0) REVERT: A 133 ARG cc_start: 0.8017 (ttm170) cc_final: 0.7793 (mtp85) REVERT: B 44 LYS cc_start: 0.8028 (mttt) cc_final: 0.7744 (mttt) REVERT: B 88 TYR cc_start: 0.8530 (m-10) cc_final: 0.8250 (m-10) REVERT: C 23 LEU cc_start: 0.9074 (mt) cc_final: 0.8684 (mp) REVERT: C 79 ILE cc_start: 0.9316 (pt) cc_final: 0.9052 (mt) REVERT: D 105 GLU cc_start: 0.7385 (tp30) cc_final: 0.7169 (tp30) REVERT: E 58 THR cc_start: 0.9151 (p) cc_final: 0.8547 (t) REVERT: E 73 GLU cc_start: 0.7526 (tt0) cc_final: 0.6613 (tt0) REVERT: G 42 ARG cc_start: 0.7681 (mtp-110) cc_final: 0.7029 (mtp85) REVERT: G 111 ILE cc_start: 0.8253 (mt) cc_final: 0.7883 (mt) REVERT: H 36 SER cc_start: 0.8774 (t) cc_final: 0.8453 (t) REVERT: H 52 THR cc_start: 0.9145 (m) cc_final: 0.8923 (m) REVERT: H 101 LEU cc_start: 0.8376 (mm) cc_final: 0.7951 (mt) REVERT: K 5 VAL cc_start: 0.8963 (m) cc_final: 0.8653 (t) REVERT: K 70 ASP cc_start: 0.8060 (t70) cc_final: 0.7578 (t0) REVERT: K 106 ASN cc_start: 0.9100 (m110) cc_final: 0.8650 (m-40) REVERT: K 119 VAL cc_start: 0.9138 (m) cc_final: 0.8936 (t) REVERT: K 135 ILE cc_start: 0.9027 (mp) cc_final: 0.8713 (tt) REVERT: K 150 THR cc_start: 0.9140 (m) cc_final: 0.8936 (m) REVERT: K 158 THR cc_start: 0.7579 (p) cc_final: 0.7283 (p) REVERT: K 191 MET cc_start: 0.6136 (mtt) cc_final: 0.5669 (ttm) outliers start: 0 outliers final: 0 residues processed: 385 average time/residue: 0.1482 time to fit residues: 75.2189 Evaluate side-chains 279 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 279 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 10.0000 chunk 97 optimal weight: 9.9990 chunk 113 optimal weight: 20.0000 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 8.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 8.9990 chunk 100 optimal weight: 9.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 31 HIS C 68 ASN C 89 ASN C 110 ASN G 31 HIS G 38 ASN G 73 ASN G 94 ASN H 47 GLN H 67 ASN ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 75 GLN K 106 ASN K 145 ASN K 146 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.124778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.088393 restraints weight = 26349.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.090533 restraints weight = 15206.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.091539 restraints weight = 10765.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.091912 restraints weight = 9264.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.092048 restraints weight = 8828.382| |-----------------------------------------------------------------------------| r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 13936 Z= 0.228 Angle : 0.789 8.320 20016 Z= 0.442 Chirality : 0.052 0.298 2270 Planarity : 0.005 0.066 1559 Dihedral : 32.337 179.983 4054 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.93 % Allowed : 16.07 % Favored : 80.99 % 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: -2.15 (0.25), residues: 905 helix: -0.84 (0.19), residues: 609 sheet: -1.07 (0.77), residues: 38 loop : -2.63 (0.34), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 35 TYR 0.015 0.002 TYR K 160 PHE 0.012 0.002 PHE B 61 TRP 0.020 0.002 TRP A 47 HIS 0.008 0.001 HIS E 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.23 (13936) covalent geometry : angle 0.78908 / 0.44 (20016) hydrogen bonds : bond 0.07656 / 5.13 ( 743) hydrogen bonds : angle 4.12537 / 2.80 ( 1855) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 300 time to evaluate : 0.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 ARG cc_start: 0.8352 (ttm170) cc_final: 0.8056 (mtp85) REVERT: B 84 MET cc_start: 0.8255 (mmm) cc_final: 0.7905 (mmm) REVERT: B 88 TYR cc_start: 0.8822 (m-10) cc_final: 0.8458 (m-80) REVERT: C 35 ARG cc_start: 0.8398 (mtm110) cc_final: 0.7715 (mtm110) REVERT: D 35 GLU cc_start: 0.8765 (pp20) cc_final: 0.8438 (tm-30) REVERT: D 43 LYS cc_start: 0.8675 (ttpt) cc_final: 0.8376 (ttpt) REVERT: D 51 ASP cc_start: 0.7822 (p0) cc_final: 0.7613 (p0) REVERT: H 76 GLU cc_start: 0.8697 (tm-30) cc_final: 0.8377 (tm-30) REVERT: H 79 ARG cc_start: 0.8068 (mpt-90) cc_final: 0.7828 (ttp-170) REVERT: K 3 GLU cc_start: 0.7889 (tp30) cc_final: 0.7669 (tp30) REVERT: K 5 VAL cc_start: 0.9048 (m) cc_final: 0.8709 (t) REVERT: K 7 GLU cc_start: 0.7423 (mp0) cc_final: 0.6964 (mp0) REVERT: K 44 ARG cc_start: 0.7614 (mtt90) cc_final: 0.7304 (mtt90) REVERT: K 70 ASP cc_start: 0.8667 (t70) cc_final: 0.8271 (t0) REVERT: K 73 TYR cc_start: 0.8891 (t80) cc_final: 0.8604 (t80) REVERT: K 106 ASN cc_start: 0.9371 (m-40) cc_final: 0.8977 (m110) REVERT: K 152 VAL cc_start: 0.9597 (t) cc_final: 0.9275 (m) REVERT: K 191 MET cc_start: 0.6064 (mtt) cc_final: 0.5467 (tmm) outliers start: 23 outliers final: 13 residues processed: 307 average time/residue: 0.1393 time to fit residues: 57.1113 Evaluate side-chains 288 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 275 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 156 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 68 optimal weight: 60.0000 chunk 65 optimal weight: 0.9980 chunk 77 optimal weight: 50.0000 chunk 69 optimal weight: 50.0000 chunk 100 optimal weight: 10.0000 chunk 26 optimal weight: 3.9990 chunk 78 optimal weight: 50.0000 chunk 94 optimal weight: 10.0000 chunk 51 optimal weight: 3.9990 chunk 103 optimal weight: 6.9990 chunk 87 optimal weight: 50.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 85 ASN G 38 ASN H 82 HIS K 77 HIS K 113 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.123997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.087585 restraints weight = 27142.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.089859 restraints weight = 15860.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.091222 restraints weight = 10790.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.091321 restraints weight = 9032.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.091468 restraints weight = 8991.846| |-----------------------------------------------------------------------------| r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.2685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13936 Z= 0.215 Angle : 0.732 8.030 20016 Z= 0.414 Chirality : 0.049 0.314 2270 Planarity : 0.005 0.056 1559 Dihedral : 32.192 179.915 4054 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 5.23 % Allowed : 16.71 % Favored : 78.06 % 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: -1.25 (0.27), residues: 905 helix: -0.12 (0.21), residues: 609 sheet: -0.20 (0.78), residues: 38 loop : -2.48 (0.36), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG K 196 TYR 0.019 0.002 TYR H 83 PHE 0.018 0.002 PHE K 104 TRP 0.013 0.002 TRP A 47 HIS 0.004 0.001 HIS D 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.21 (13936) covalent geometry : angle 0.73154 / 0.41 (20016) hydrogen bonds : bond 0.07035 / 4.77 ( 743) hydrogen bonds : angle 3.67520 / 2.48 ( 1855) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 286 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 ARG cc_start: 0.8408 (ttm170) cc_final: 0.8163 (mtp85) REVERT: B 75 HIS cc_start: 0.8957 (t-90) cc_final: 0.8569 (t-170) REVERT: B 84 MET cc_start: 0.8173 (mmm) cc_final: 0.7733 (mmm) REVERT: B 88 TYR cc_start: 0.8800 (m-10) cc_final: 0.8400 (m-80) REVERT: C 61 GLU cc_start: 0.8085 (tp30) cc_final: 0.7639 (tp30) REVERT: D 43 LYS cc_start: 0.8638 (ttpt) cc_final: 0.8353 (ttpt) REVERT: D 46 LYS cc_start: 0.8959 (ttmm) cc_final: 0.8660 (mmtt) REVERT: D 51 ASP cc_start: 0.7995 (p0) cc_final: 0.7758 (p0) REVERT: D 71 GLU cc_start: 0.8874 (tp30) cc_final: 0.8671 (tp30) REVERT: G 35 ARG cc_start: 0.8052 (tpp80) cc_final: 0.7599 (mtt90) REVERT: H 76 GLU cc_start: 0.8629 (tm-30) cc_final: 0.8324 (tm-30) REVERT: H 101 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7775 (mt) REVERT: K 3 GLU cc_start: 0.8041 (tp30) cc_final: 0.7799 (tp30) REVERT: K 46 GLU cc_start: 0.8257 (tp30) cc_final: 0.8038 (tp30) REVERT: K 70 ASP cc_start: 0.8707 (t70) cc_final: 0.8290 (t0) REVERT: K 73 TYR cc_start: 0.8942 (t80) cc_final: 0.8585 (t80) REVERT: K 86 PHE cc_start: 0.8545 (m-80) cc_final: 0.8288 (m-80) REVERT: K 175 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8838 (tt) REVERT: K 191 MET cc_start: 0.5895 (mtt) cc_final: 0.5176 (tmm) outliers start: 41 outliers final: 26 residues processed: 304 average time/residue: 0.1444 time to fit residues: 58.5049 Evaluate side-chains 296 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 268 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain K residue 156 SER Chi-restraints excluded: chain K residue 158 THR Chi-restraints excluded: chain K residue 175 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 28 optimal weight: 3.9990 chunk 34 optimal weight: 10.0000 chunk 50 optimal weight: 6.9990 chunk 81 optimal weight: 50.0000 chunk 88 optimal weight: 50.0000 chunk 14 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 chunk 89 optimal weight: 50.0000 chunk 72 optimal weight: 50.0000 chunk 46 optimal weight: 1.9990 chunk 67 optimal weight: 6.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 127 GLN H 67 ASN H 82 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.126454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.089223 restraints weight = 26862.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.091531 restraints weight = 15471.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.092517 restraints weight = 10944.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.092843 restraints weight = 9439.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.092958 restraints weight = 9052.995| |-----------------------------------------------------------------------------| r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13936 Z= 0.171 Angle : 0.696 8.482 20016 Z= 0.396 Chirality : 0.048 0.319 2270 Planarity : 0.005 0.051 1559 Dihedral : 32.064 179.393 4054 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 5.23 % Allowed : 18.88 % Favored : 75.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.28), residues: 905 helix: 0.34 (0.21), residues: 607 sheet: 0.10 (0.79), residues: 38 loop : -2.43 (0.36), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 92 TYR 0.035 0.002 TYR H 83 PHE 0.015 0.001 PHE K 108 TRP 0.011 0.001 TRP K 28 HIS 0.003 0.001 HIS K 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.17 (13936) covalent geometry : angle 0.69623 / 0.40 (20016) hydrogen bonds : bond 0.06615 / 4.48 ( 743) hydrogen bonds : angle 3.37044 / 2.27 ( 1855) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 290 time to evaluate : 0.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 LYS cc_start: 0.8586 (ttmt) cc_final: 0.8383 (ttmm) REVERT: A 133 ARG cc_start: 0.8305 (ttm170) cc_final: 0.8054 (mtp85) REVERT: B 75 HIS cc_start: 0.8839 (t-90) cc_final: 0.8590 (t-170) REVERT: B 84 MET cc_start: 0.8096 (mmm) cc_final: 0.7701 (mmm) REVERT: B 88 TYR cc_start: 0.8794 (m-10) cc_final: 0.8438 (m-80) REVERT: C 61 GLU cc_start: 0.8070 (tp30) cc_final: 0.7667 (tp30) REVERT: D 38 SER cc_start: 0.9149 (p) cc_final: 0.8947 (t) REVERT: D 43 LYS cc_start: 0.8655 (ttpt) cc_final: 0.8351 (ttpt) REVERT: D 51 ASP cc_start: 0.7914 (p0) cc_final: 0.7690 (p0) REVERT: F 29 ILE cc_start: 0.9018 (mm) cc_final: 0.8800 (mp) REVERT: G 39 TYR cc_start: 0.9000 (m-10) cc_final: 0.8584 (m-80) REVERT: G 61 GLU cc_start: 0.8708 (tm-30) cc_final: 0.8422 (tm-30) REVERT: G 92 GLU cc_start: 0.7320 (mp0) cc_final: 0.7107 (pm20) REVERT: H 101 LEU cc_start: 0.8309 (OUTLIER) cc_final: 0.7871 (mt) REVERT: K 5 VAL cc_start: 0.8942 (m) cc_final: 0.8608 (t) REVERT: K 37 GLN cc_start: 0.8756 (tt0) cc_final: 0.8438 (mm-40) REVERT: K 46 GLU cc_start: 0.8306 (tp30) cc_final: 0.8063 (tp30) REVERT: K 70 ASP cc_start: 0.8541 (t70) cc_final: 0.8159 (t0) REVERT: K 73 TYR cc_start: 0.8744 (t80) cc_final: 0.8429 (t80) REVERT: K 85 VAL cc_start: 0.6964 (p) cc_final: 0.6653 (p) REVERT: K 86 PHE cc_start: 0.8505 (m-80) cc_final: 0.8271 (m-80) REVERT: K 152 VAL cc_start: 0.9573 (t) cc_final: 0.9340 (m) REVERT: K 160 TYR cc_start: 0.8030 (m-80) cc_final: 0.7682 (m-10) REVERT: K 175 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8802 (tt) REVERT: K 191 MET cc_start: 0.5907 (mtt) cc_final: 0.5296 (tmm) outliers start: 41 outliers final: 24 residues processed: 306 average time/residue: 0.1329 time to fit residues: 55.0936 Evaluate side-chains 302 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 276 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 127 GLN Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain K residue 119 VAL Chi-restraints excluded: chain K residue 156 SER Chi-restraints excluded: chain K residue 163 THR Chi-restraints excluded: chain K residue 175 LEU Chi-restraints excluded: chain K residue 179 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 100 optimal weight: 10.0000 chunk 38 optimal weight: 1.9990 chunk 76 optimal weight: 50.0000 chunk 57 optimal weight: 6.9990 chunk 105 optimal weight: 9.9990 chunk 44 optimal weight: 7.9990 chunk 111 optimal weight: 20.0000 chunk 37 optimal weight: 0.6980 chunk 82 optimal weight: 50.0000 chunk 85 optimal weight: 50.0000 chunk 9 optimal weight: 0.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 38 ASN H 67 ASN H 82 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.126127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.088908 restraints weight = 26998.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.091178 restraints weight = 15726.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.092133 restraints weight = 11095.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.092471 restraints weight = 9614.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.092570 restraints weight = 9112.595| |-----------------------------------------------------------------------------| r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.3134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13936 Z= 0.177 Angle : 0.696 9.535 20016 Z= 0.394 Chirality : 0.047 0.315 2270 Planarity : 0.004 0.050 1559 Dihedral : 31.984 179.348 4054 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 5.23 % Allowed : 20.79 % Favored : 73.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.28), residues: 905 helix: 0.54 (0.21), residues: 607 sheet: 0.39 (0.82), residues: 38 loop : -2.17 (0.37), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 92 TYR 0.027 0.002 TYR H 83 PHE 0.018 0.001 PHE K 104 TRP 0.009 0.001 TRP K 28 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.18 (13936) covalent geometry : angle 0.69575 / 0.39 (20016) hydrogen bonds : bond 0.06529 / 4.41 ( 743) hydrogen bonds : angle 3.31144 / 2.23 ( 1855) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 272 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ARG cc_start: 0.8590 (mpp80) cc_final: 0.8138 (mtm-85) REVERT: A 133 ARG cc_start: 0.8310 (ttm170) cc_final: 0.8047 (mtp85) REVERT: B 84 MET cc_start: 0.8121 (mmm) cc_final: 0.7695 (mmm) REVERT: B 88 TYR cc_start: 0.8808 (m-10) cc_final: 0.8370 (m-80) REVERT: C 61 GLU cc_start: 0.8211 (tp30) cc_final: 0.7767 (tp30) REVERT: D 43 LYS cc_start: 0.8675 (ttpt) cc_final: 0.8380 (ttpt) REVERT: D 51 ASP cc_start: 0.7970 (p0) cc_final: 0.7763 (p0) REVERT: E 127 GLN cc_start: 0.8115 (OUTLIER) cc_final: 0.7863 (mm-40) REVERT: F 29 ILE cc_start: 0.9079 (mm) cc_final: 0.8836 (mp) REVERT: G 39 TYR cc_start: 0.9054 (m-10) cc_final: 0.8477 (m-80) REVERT: G 61 GLU cc_start: 0.8810 (tm-30) cc_final: 0.8576 (tm-30) REVERT: G 92 GLU cc_start: 0.7334 (mp0) cc_final: 0.7130 (pm20) REVERT: H 59 MET cc_start: 0.8126 (tpp) cc_final: 0.7912 (tpp) REVERT: H 101 LEU cc_start: 0.8334 (OUTLIER) cc_final: 0.7854 (mt) REVERT: K 5 VAL cc_start: 0.8903 (m) cc_final: 0.8681 (t) REVERT: K 37 GLN cc_start: 0.8729 (tt0) cc_final: 0.8424 (mm-40) REVERT: K 46 GLU cc_start: 0.8386 (tp30) cc_final: 0.8122 (tp30) REVERT: K 70 ASP cc_start: 0.8578 (t70) cc_final: 0.8247 (t0) REVERT: K 85 VAL cc_start: 0.6920 (p) cc_final: 0.6697 (p) REVERT: K 152 VAL cc_start: 0.9584 (t) cc_final: 0.9315 (m) REVERT: K 162 PHE cc_start: 0.8325 (m-10) cc_final: 0.8124 (m-10) REVERT: K 175 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8459 (tt) REVERT: K 191 MET cc_start: 0.6028 (mtt) cc_final: 0.5164 (tmm) outliers start: 41 outliers final: 29 residues processed: 290 average time/residue: 0.1308 time to fit residues: 51.6191 Evaluate side-chains 295 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 263 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 127 GLN Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain K residue 119 VAL Chi-restraints excluded: chain K residue 156 SER Chi-restraints excluded: chain K residue 158 THR Chi-restraints excluded: chain K residue 175 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 32 optimal weight: 7.9990 chunk 51 optimal weight: 7.9990 chunk 105 optimal weight: 30.0000 chunk 113 optimal weight: 6.9990 chunk 70 optimal weight: 50.0000 chunk 62 optimal weight: 6.9990 chunk 9 optimal weight: 5.9990 chunk 38 optimal weight: 8.9990 chunk 66 optimal weight: 5.9990 chunk 40 optimal weight: 8.9990 chunk 53 optimal weight: 1.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 115 HIS C 38 ASN D 63 ASN E 85 ASN E 127 GLN H 82 HIS K 75 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.124953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.087603 restraints weight = 26842.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.089709 restraints weight = 15858.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.090745 restraints weight = 11260.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.091087 restraints weight = 9600.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.091197 restraints weight = 9172.931| |-----------------------------------------------------------------------------| r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.3282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13936 Z= 0.216 Angle : 0.715 7.586 20016 Z= 0.402 Chirality : 0.048 0.314 2270 Planarity : 0.004 0.053 1559 Dihedral : 31.981 179.797 4054 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 5.87 % Allowed : 19.77 % Favored : 74.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.28), residues: 905 helix: 0.68 (0.21), residues: 605 sheet: 0.27 (0.82), residues: 38 loop : -2.10 (0.37), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 92 TYR 0.030 0.003 TYR C 39 PHE 0.013 0.001 PHE B 100 TRP 0.009 0.001 TRP K 28 HIS 0.010 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.22 (13936) covalent geometry : angle 0.71460 / 0.40 (20016) hydrogen bonds : bond 0.06666 / 4.52 ( 743) hydrogen bonds : angle 3.36458 / 2.27 ( 1855) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 267 time to evaluate : 0.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 ARG cc_start: 0.8373 (ttm170) cc_final: 0.8084 (mtp85) REVERT: B 49 LEU cc_start: 0.8205 (mt) cc_final: 0.7977 (mm) REVERT: B 52 GLU cc_start: 0.8428 (mm-30) cc_final: 0.8182 (mm-30) REVERT: B 84 MET cc_start: 0.8139 (mmm) cc_final: 0.7692 (mmm) REVERT: B 88 TYR cc_start: 0.8815 (m-10) cc_final: 0.8363 (m-80) REVERT: C 61 GLU cc_start: 0.8228 (tp30) cc_final: 0.7288 (tp30) REVERT: C 92 GLU cc_start: 0.7475 (pm20) cc_final: 0.7217 (pm20) REVERT: D 43 LYS cc_start: 0.8667 (ttpt) cc_final: 0.8362 (ttpt) REVERT: F 29 ILE cc_start: 0.9085 (mm) cc_final: 0.8841 (mp) REVERT: F 84 MET cc_start: 0.7955 (tpp) cc_final: 0.7707 (tpp) REVERT: G 61 GLU cc_start: 0.8875 (tm-30) cc_final: 0.8661 (tm-30) REVERT: G 84 GLN cc_start: 0.9156 (tp40) cc_final: 0.8387 (tt0) REVERT: G 92 GLU cc_start: 0.7386 (mp0) cc_final: 0.7138 (pm20) REVERT: H 71 GLU cc_start: 0.8673 (tm-30) cc_final: 0.8390 (tm-30) REVERT: H 91 SER cc_start: 0.8900 (p) cc_final: 0.8415 (t) REVERT: H 101 LEU cc_start: 0.8343 (OUTLIER) cc_final: 0.7888 (mt) REVERT: K 5 VAL cc_start: 0.8964 (m) cc_final: 0.8655 (t) REVERT: K 37 GLN cc_start: 0.8729 (tt0) cc_final: 0.8503 (mm-40) REVERT: K 46 GLU cc_start: 0.8427 (tp30) cc_final: 0.8186 (tp30) REVERT: K 70 ASP cc_start: 0.8656 (t70) cc_final: 0.8300 (t0) REVERT: K 152 VAL cc_start: 0.9612 (t) cc_final: 0.9316 (m) REVERT: K 191 MET cc_start: 0.6079 (mtt) cc_final: 0.5170 (tmm) outliers start: 46 outliers final: 31 residues processed: 293 average time/residue: 0.1296 time to fit residues: 51.4637 Evaluate side-chains 296 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 264 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain K residue 25 LEU Chi-restraints excluded: chain K residue 119 VAL Chi-restraints excluded: chain K residue 156 SER Chi-restraints excluded: chain K residue 189 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 0 optimal weight: 10.0000 chunk 38 optimal weight: 4.9990 chunk 112 optimal weight: 30.0000 chunk 102 optimal weight: 4.9990 chunk 100 optimal weight: 20.0000 chunk 31 optimal weight: 2.9990 chunk 92 optimal weight: 50.0000 chunk 17 optimal weight: 8.9990 chunk 48 optimal weight: 0.0470 chunk 80 optimal weight: 50.0000 chunk 106 optimal weight: 30.0000 overall best weight: 4.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 38 ASN E 85 ASN H 67 ASN H 82 HIS K 113 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.125354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.088080 restraints weight = 26827.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.089940 restraints weight = 15807.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.090993 restraints weight = 11383.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.091411 restraints weight = 9812.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.091466 restraints weight = 9303.312| |-----------------------------------------------------------------------------| r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.3382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13936 Z= 0.190 Angle : 0.704 8.236 20016 Z= 0.398 Chirality : 0.048 0.318 2270 Planarity : 0.004 0.051 1559 Dihedral : 31.938 179.923 4054 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 5.36 % Allowed : 21.81 % Favored : 72.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.28), residues: 905 helix: 0.76 (0.21), residues: 608 sheet: 0.26 (0.83), residues: 38 loop : -2.03 (0.37), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 92 TYR 0.030 0.002 TYR K 160 PHE 0.019 0.001 PHE K 104 TRP 0.008 0.001 TRP K 28 HIS 0.008 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.19 (13936) covalent geometry : angle 0.70439 / 0.40 (20016) hydrogen bonds : bond 0.06555 / 4.43 ( 743) hydrogen bonds : angle 3.26992 / 2.20 ( 1855) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 270 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ARG cc_start: 0.8642 (mpp80) cc_final: 0.8113 (mtm-85) REVERT: A 133 ARG cc_start: 0.8329 (ttm170) cc_final: 0.8067 (mtp85) REVERT: B 49 LEU cc_start: 0.8181 (mt) cc_final: 0.7969 (mm) REVERT: B 84 MET cc_start: 0.8054 (mmm) cc_final: 0.7684 (mmm) REVERT: B 88 TYR cc_start: 0.8777 (m-10) cc_final: 0.8327 (m-80) REVERT: C 61 GLU cc_start: 0.8157 (tp30) cc_final: 0.7705 (tp30) REVERT: D 43 LYS cc_start: 0.8704 (ttpt) cc_final: 0.8381 (ttpt) REVERT: F 29 ILE cc_start: 0.9092 (mm) cc_final: 0.8859 (mp) REVERT: G 39 TYR cc_start: 0.9044 (m-10) cc_final: 0.8592 (m-80) REVERT: G 61 GLU cc_start: 0.8916 (tm-30) cc_final: 0.8692 (tm-30) REVERT: G 84 GLN cc_start: 0.9139 (tp40) cc_final: 0.8347 (tt0) REVERT: G 92 GLU cc_start: 0.7362 (mp0) cc_final: 0.7151 (pm20) REVERT: H 91 SER cc_start: 0.8895 (p) cc_final: 0.8401 (t) REVERT: H 101 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.7872 (mt) REVERT: H 108 LYS cc_start: 0.8247 (ptpp) cc_final: 0.7889 (ptpp) REVERT: K 37 GLN cc_start: 0.8736 (tt0) cc_final: 0.8478 (mm-40) REVERT: K 70 ASP cc_start: 0.8631 (t70) cc_final: 0.8272 (t0) REVERT: K 152 VAL cc_start: 0.9617 (t) cc_final: 0.9310 (m) REVERT: K 191 MET cc_start: 0.6051 (mtt) cc_final: 0.5129 (tmm) REVERT: K 196 ARG cc_start: 0.7315 (ttm-80) cc_final: 0.6869 (ttm170) outliers start: 42 outliers final: 33 residues processed: 288 average time/residue: 0.1349 time to fit residues: 52.3902 Evaluate side-chains 299 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 265 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain K residue 25 LEU Chi-restraints excluded: chain K residue 119 VAL Chi-restraints excluded: chain K residue 175 LEU Chi-restraints excluded: chain K residue 189 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 109 optimal weight: 7.9990 chunk 75 optimal weight: 50.0000 chunk 60 optimal weight: 7.9990 chunk 55 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 22 optimal weight: 6.9990 chunk 62 optimal weight: 0.9990 chunk 95 optimal weight: 10.0000 chunk 102 optimal weight: 7.9990 chunk 36 optimal weight: 0.2980 chunk 78 optimal weight: 40.0000 overall best weight: 3.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 38 ASN E 85 ASN H 82 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.126036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.087888 restraints weight = 26674.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.090148 restraints weight = 15907.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.091585 restraints weight = 11722.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.092439 restraints weight = 9880.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.092918 restraints weight = 9009.459| |-----------------------------------------------------------------------------| r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.3509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13936 Z= 0.171 Angle : 0.695 9.282 20016 Z= 0.394 Chirality : 0.047 0.316 2270 Planarity : 0.004 0.047 1559 Dihedral : 31.869 179.668 4054 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 4.85 % Allowed : 22.32 % Favored : 72.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.28), residues: 905 helix: 0.92 (0.21), residues: 607 sheet: 0.41 (0.85), residues: 38 loop : -2.08 (0.37), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 92 TYR 0.029 0.003 TYR K 160 PHE 0.018 0.001 PHE K 104 TRP 0.008 0.001 TRP K 83 HIS 0.007 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.17 (13936) covalent geometry : angle 0.69498 / 0.39 (20016) hydrogen bonds : bond 0.06372 / 4.29 ( 743) hydrogen bonds : angle 3.14876 / 2.11 ( 1855) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 270 time to evaluate : 0.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ARG cc_start: 0.8597 (mpp80) cc_final: 0.8099 (mtm-85) REVERT: A 133 ARG cc_start: 0.8302 (ttm170) cc_final: 0.8028 (mtp85) REVERT: B 84 MET cc_start: 0.8023 (mmm) cc_final: 0.7648 (mmm) REVERT: B 88 TYR cc_start: 0.8788 (m-10) cc_final: 0.8294 (m-80) REVERT: C 61 GLU cc_start: 0.8130 (tp30) cc_final: 0.7699 (tp30) REVERT: D 35 GLU cc_start: 0.8873 (pp20) cc_final: 0.8502 (tm-30) REVERT: D 43 LYS cc_start: 0.8725 (ttpt) cc_final: 0.8379 (ttpt) REVERT: F 29 ILE cc_start: 0.9104 (mm) cc_final: 0.8880 (mp) REVERT: G 39 TYR cc_start: 0.9059 (m-10) cc_final: 0.8501 (m-80) REVERT: G 84 GLN cc_start: 0.9119 (tp40) cc_final: 0.8330 (tt0) REVERT: H 101 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.7942 (mt) REVERT: K 37 GLN cc_start: 0.8685 (tt0) cc_final: 0.8476 (mm-40) REVERT: K 70 ASP cc_start: 0.8684 (t70) cc_final: 0.8322 (t0) REVERT: K 123 PHE cc_start: 0.8080 (m-80) cc_final: 0.7830 (m-80) REVERT: K 152 VAL cc_start: 0.9619 (t) cc_final: 0.9255 (m) REVERT: K 191 MET cc_start: 0.6218 (mtt) cc_final: 0.5236 (tmm) REVERT: K 196 ARG cc_start: 0.7369 (ttm-80) cc_final: 0.6926 (ttm170) outliers start: 38 outliers final: 30 residues processed: 288 average time/residue: 0.1450 time to fit residues: 56.8729 Evaluate side-chains 287 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 256 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 128 LEU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain K residue 25 LEU Chi-restraints excluded: chain K residue 119 VAL Chi-restraints excluded: chain K residue 189 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 26 optimal weight: 7.9990 chunk 53 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 90 optimal weight: 50.0000 chunk 12 optimal weight: 4.9990 chunk 68 optimal weight: 60.0000 chunk 29 optimal weight: 9.9990 chunk 80 optimal weight: 50.0000 chunk 82 optimal weight: 50.0000 chunk 62 optimal weight: 0.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 38 ASN E 85 ASN H 67 ASN H 82 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.126562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.088255 restraints weight = 27007.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.090580 restraints weight = 16076.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.092058 restraints weight = 11766.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.092946 restraints weight = 9877.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.093309 restraints weight = 8985.775| |-----------------------------------------------------------------------------| r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.3602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 13936 Z= 0.163 Angle : 0.701 10.973 20016 Z= 0.396 Chirality : 0.047 0.316 2270 Planarity : 0.004 0.050 1559 Dihedral : 31.822 179.601 4054 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 4.46 % Allowed : 24.74 % Favored : 70.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.28), residues: 905 helix: 0.95 (0.21), residues: 608 sheet: 0.46 (0.87), residues: 38 loop : -2.03 (0.38), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 92 TYR 0.029 0.002 TYR K 160 PHE 0.017 0.001 PHE K 104 TRP 0.051 0.002 TRP A 47 HIS 0.007 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.16 (13936) covalent geometry : angle 0.70074 / 0.40 (20016) hydrogen bonds : bond 0.06327 / 4.25 ( 743) hydrogen bonds : angle 3.14760 / 2.10 ( 1855) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 274 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ARG cc_start: 0.8614 (mpp80) cc_final: 0.8045 (mtm-85) REVERT: A 133 ARG cc_start: 0.8299 (ttm170) cc_final: 0.8020 (mtp85) REVERT: B 84 MET cc_start: 0.7964 (mmm) cc_final: 0.7611 (mmm) REVERT: B 88 TYR cc_start: 0.8786 (m-10) cc_final: 0.8302 (m-80) REVERT: C 61 GLU cc_start: 0.8134 (tp30) cc_final: 0.7565 (tp30) REVERT: C 94 ASN cc_start: 0.9174 (t0) cc_final: 0.8971 (t0) REVERT: D 35 GLU cc_start: 0.8848 (pp20) cc_final: 0.8515 (tm-30) REVERT: D 43 LYS cc_start: 0.8741 (ttpt) cc_final: 0.8377 (ttpt) REVERT: F 29 ILE cc_start: 0.9096 (mm) cc_final: 0.8888 (mp) REVERT: G 39 TYR cc_start: 0.9086 (m-10) cc_final: 0.8504 (m-80) REVERT: G 84 GLN cc_start: 0.9125 (tp40) cc_final: 0.8332 (tt0) REVERT: H 101 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.7985 (mt) REVERT: K 5 VAL cc_start: 0.8733 (m) cc_final: 0.8496 (t) REVERT: K 37 GLN cc_start: 0.8672 (tt0) cc_final: 0.8400 (mm-40) REVERT: K 70 ASP cc_start: 0.8682 (t70) cc_final: 0.8297 (t0) REVERT: K 122 SER cc_start: 0.8341 (m) cc_final: 0.7960 (p) REVERT: K 152 VAL cc_start: 0.9603 (t) cc_final: 0.9302 (m) REVERT: K 191 MET cc_start: 0.6241 (mtt) cc_final: 0.5183 (tmm) outliers start: 35 outliers final: 29 residues processed: 289 average time/residue: 0.1358 time to fit residues: 53.8328 Evaluate side-chains 298 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 268 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 128 LEU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain K residue 119 VAL Chi-restraints excluded: chain K residue 175 LEU Chi-restraints excluded: chain K residue 189 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 104 optimal weight: 20.0000 chunk 72 optimal weight: 40.0000 chunk 88 optimal weight: 50.0000 chunk 67 optimal weight: 10.0000 chunk 20 optimal weight: 20.0000 chunk 106 optimal weight: 0.0870 chunk 94 optimal weight: 7.9990 chunk 57 optimal weight: 0.9990 chunk 26 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 overall best weight: 2.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 38 ASN E 85 ASN H 82 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.127305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.089083 restraints weight = 26870.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.091389 restraints weight = 15946.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.092910 restraints weight = 11695.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.093789 restraints weight = 9790.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.094301 restraints weight = 8902.081| |-----------------------------------------------------------------------------| r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.3754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 13936 Z= 0.153 Angle : 0.691 11.104 20016 Z= 0.392 Chirality : 0.047 0.314 2270 Planarity : 0.004 0.053 1559 Dihedral : 31.758 179.468 4054 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 4.21 % Allowed : 25.13 % Favored : 70.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.29), residues: 905 helix: 1.05 (0.21), residues: 610 sheet: 0.72 (0.87), residues: 38 loop : -1.99 (0.38), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG F 92 TYR 0.026 0.002 TYR K 154 PHE 0.034 0.002 PHE K 206 TRP 0.031 0.002 TRP A 47 HIS 0.007 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.15 (13936) covalent geometry : angle 0.69122 / 0.39 (20016) hydrogen bonds : bond 0.06190 / 4.16 ( 743) hydrogen bonds : angle 3.05519 / 2.05 ( 1855) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 273 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ARG cc_start: 0.8580 (mpp80) cc_final: 0.8016 (mtm-85) REVERT: A 133 ARG cc_start: 0.8276 (ttm170) cc_final: 0.7995 (mtp85) REVERT: B 84 MET cc_start: 0.7910 (mmm) cc_final: 0.7576 (mmm) REVERT: B 88 TYR cc_start: 0.8769 (m-10) cc_final: 0.8296 (m-80) REVERT: C 41 GLU cc_start: 0.8348 (mt-10) cc_final: 0.8136 (mp0) REVERT: C 61 GLU cc_start: 0.8100 (tp30) cc_final: 0.7585 (tp30) REVERT: C 94 ASN cc_start: 0.9147 (t0) cc_final: 0.8896 (t0) REVERT: D 43 LYS cc_start: 0.8769 (ttpt) cc_final: 0.8472 (ttpt) REVERT: D 105 GLU cc_start: 0.7148 (tp30) cc_final: 0.6740 (tp30) REVERT: G 39 TYR cc_start: 0.9052 (m-10) cc_final: 0.8773 (m-80) REVERT: G 77 ARG cc_start: 0.7777 (ttm-80) cc_final: 0.7345 (mtp85) REVERT: G 84 GLN cc_start: 0.9112 (tp40) cc_final: 0.8301 (tt0) REVERT: H 101 LEU cc_start: 0.8367 (OUTLIER) cc_final: 0.7961 (mt) REVERT: K 5 VAL cc_start: 0.8664 (m) cc_final: 0.8402 (t) REVERT: K 37 GLN cc_start: 0.8660 (tt0) cc_final: 0.8418 (mm-40) REVERT: K 70 ASP cc_start: 0.8659 (t70) cc_final: 0.8314 (t0) REVERT: K 74 MET cc_start: 0.8475 (tpt) cc_final: 0.8274 (tpt) REVERT: K 122 SER cc_start: 0.8240 (m) cc_final: 0.7897 (p) REVERT: K 123 PHE cc_start: 0.8031 (m-80) cc_final: 0.7751 (m-80) REVERT: K 152 VAL cc_start: 0.9589 (t) cc_final: 0.9317 (m) REVERT: K 185 HIS cc_start: 0.8614 (m90) cc_final: 0.7903 (m-70) REVERT: K 191 MET cc_start: 0.6241 (mtt) cc_final: 0.5421 (ttm) REVERT: K 196 ARG cc_start: 0.7468 (ttm-80) cc_final: 0.6929 (ttm170) outliers start: 33 outliers final: 28 residues processed: 285 average time/residue: 0.1426 time to fit residues: 55.2713 Evaluate side-chains 297 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 268 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 128 LEU Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain K residue 119 VAL Chi-restraints excluded: chain K residue 175 LEU Chi-restraints excluded: chain K residue 189 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 104 optimal weight: 30.0000 chunk 100 optimal weight: 5.9990 chunk 99 optimal weight: 10.0000 chunk 82 optimal weight: 50.0000 chunk 69 optimal weight: 50.0000 chunk 31 optimal weight: 5.9990 chunk 71 optimal weight: 50.0000 chunk 52 optimal weight: 0.0970 chunk 20 optimal weight: 8.9990 chunk 39 optimal weight: 10.0000 chunk 98 optimal weight: 7.9990 overall best weight: 5.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 38 ASN E 85 ASN H 82 HIS H 84 ASN K 118 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.125012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.086658 restraints weight = 26999.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.088854 restraints weight = 16305.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.090296 restraints weight = 12100.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.091155 restraints weight = 10190.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.091502 restraints weight = 9279.469| |-----------------------------------------------------------------------------| r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.3797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 13936 Z= 0.223 Angle : 0.736 10.408 20016 Z= 0.411 Chirality : 0.048 0.310 2270 Planarity : 0.005 0.058 1559 Dihedral : 31.829 179.983 4054 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 4.46 % Allowed : 24.87 % Favored : 70.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.29), residues: 905 helix: 1.00 (0.21), residues: 607 sheet: 0.77 (0.86), residues: 38 loop : -1.84 (0.39), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 92 TYR 0.040 0.003 TYR K 160 PHE 0.019 0.002 PHE K 206 TRP 0.027 0.002 TRP A 47 HIS 0.006 0.001 HIS H 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00459 / 0.22 (13936) covalent geometry : angle 0.73597 / 0.41 (20016) hydrogen bonds : bond 0.06581 / 4.44 ( 743) hydrogen bonds : angle 3.29685 / 2.21 ( 1855) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1949.30 seconds wall clock time: 34 minutes 24.54 seconds (2064.54 seconds total)