Starting phenix.real_space_refine on Tue Nov 18 08:22:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6c0w_7326/11_2025/6c0w_7326_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6c0w_7326/11_2025/6c0w_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6c0w_7326/11_2025/6c0w_7326.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6c0w_7326/11_2025/6c0w_7326.map" model { file = "/net/cci-nas-00/data/ceres_data/6c0w_7326/11_2025/6c0w_7326_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6c0w_7326/11_2025/6c0w_7326_neut.cif" } 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-2.0-5881/lib/python3.9/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: 3.08, per 1000 atoms: 0.23 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: 1.03 Conformation dependent library (CDL) restraints added in 398.3 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: 2.23 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: 2.64 Time building geometry restraints manager: 1.39 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 1.422 1.497 -0.075 3.00e-02 1.11e+03 6.17e+00 bond pdb=" C3' DT J -61 " pdb=" O3' DT J -61 " ideal model delta sigma weight residual 1.422 1.489 -0.067 3.00e-02 1.11e+03 4.96e+00 bond pdb=" C3' DG J 20 " pdb=" O3' DG J 20 " ideal model delta sigma weight residual 1.422 1.480 -0.058 3.00e-02 1.11e+03 3.73e+00 bond pdb=" C3' DA J -38 " pdb=" O3' DA J -38 " ideal model delta sigma weight residual 1.422 1.467 -0.045 3.00e-02 1.11e+03 2.24e+00 bond pdb=" C3' DC I 4 " pdb=" O3' DC I 4 " ideal model delta sigma weight residual 1.422 1.465 -0.043 3.00e-02 1.11e+03 2.01e+00 ... (remaining 13931 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.81: 19125 1.81 - 3.61: 798 3.61 - 5.42: 67 5.42 - 7.22: 17 7.22 - 9.03: 9 Bond angle restraints: 20016 Sorted by residual: 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=" C3' DT J -17 " pdb=" O3' DT J -17 " pdb=" P DT J -16 " ideal model delta sigma weight residual 120.20 125.68 -5.48 1.50e+00 4.44e-01 1.34e+01 angle pdb=" C3' DT J -61 " pdb=" O3' DT J -61 " pdb=" P DA J -60 " ideal model delta sigma weight residual 120.20 125.31 -5.11 1.50e+00 4.44e-01 1.16e+01 angle pdb=" N GLY B 99 " pdb=" CA GLY B 99 " pdb=" C GLY B 99 " ideal model delta sigma weight residual 113.18 121.03 -7.85 2.37e+00 1.78e-01 1.10e+01 angle pdb=" N GLY H 104 " pdb=" CA GLY H 104 " pdb=" C GLY H 104 " ideal model delta sigma weight residual 113.18 120.87 -7.69 2.37e+00 1.78e-01 1.05e+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: 1965 0.066 - 0.132: 269 0.132 - 0.198: 34 0.198 - 0.264: 0 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=" P DT J -16 " pdb=" OP1 DT J -16 " pdb=" OP2 DT J -16 " pdb=" O5' DT J -16 " both_signs ideal model delta sigma weight residual True 2.35 -2.54 -0.19 2.00e-01 2.50e+01 9.08e-01 ... (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: 0.160 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: 0.190 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.960 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: 0.010 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 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 : 0.006 0.075 13936 Z= 0.260 Angle : 0.810 9.028 20016 Z= 0.473 Chirality : 0.047 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 covalent geometry : bond 0.00580 (13936) covalent geometry : angle 0.80981 (20016) hydrogen bonds : bond 0.14517 ( 743) hydrogen bonds : angle 5.89985 ( 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 : 0.363 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: 0.8248 (m-10) REVERT: C 23 LEU cc_start: 0.9074 (mt) cc_final: 0.8687 (mp) REVERT: C 79 ILE cc_start: 0.9316 (pt) cc_final: 0.9052 (mt) REVERT: D 105 GLU cc_start: 0.7384 (tp30) cc_final: 0.7169 (tp30) REVERT: E 58 THR cc_start: 0.9151 (p) cc_final: 0.8546 (t) REVERT: E 73 GLU cc_start: 0.7526 (tt0) cc_final: 0.6612 (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: 0.8454 (t) REVERT: H 52 THR cc_start: 0.9145 (m) cc_final: 0.8924 (m) REVERT: H 101 LEU cc_start: 0.8376 (mm) cc_final: 0.7949 (mt) REVERT: K 5 VAL cc_start: 0.8963 (m) cc_final: 0.8654 (t) REVERT: K 70 ASP cc_start: 0.8059 (t70) cc_final: 0.7579 (t0) REVERT: K 106 ASN cc_start: 0.9100 (m110) cc_final: 0.8649 (m-40) REVERT: K 119 VAL cc_start: 0.9138 (m) cc_final: 0.8937 (t) REVERT: K 135 ILE cc_start: 0.9027 (mp) cc_final: 0.8712 (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: 0.7284 (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: 0.1773 time to fit residues: 88.4080 Evaluate side-chains 278 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 278 time to evaluate : 0.319 ------------------------------------------------------------------------------- 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: 0.9990 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: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 77 HIS K 79 HIS K 106 ASN K 145 ASN K 146 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.126080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.088354 restraints weight = 26532.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.090730 restraints weight = 15691.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.092272 restraints weight = 11436.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.093183 restraints weight = 9555.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.093653 restraints weight = 8673.261| |-----------------------------------------------------------------------------| r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 13936 Z= 0.218 Angle : 0.665 7.280 20016 Z= 0.383 Chirality : 0.038 0.186 2270 Planarity : 0.005 0.060 1559 Dihedral : 31.733 178.153 4054 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 3.06 % Allowed : 16.20 % Favored : 80.74 % 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: -1.90 (0.25), residues: 905 helix: -0.64 (0.19), residues: 609 sheet: -0.80 (0.77), residues: 38 loop : -2.61 (0.33), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 42 TYR 0.014 0.002 TYR C 57 PHE 0.012 0.002 PHE K 108 TRP 0.017 0.002 TRP K 28 HIS 0.006 0.001 HIS C 31 Details of bonding type rmsd covalent geometry : bond 0.00483 (13936) covalent geometry : angle 0.66496 (20016) hydrogen bonds : bond 0.06303 ( 743) hydrogen bonds : angle 3.65694 ( 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 342 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 318 time to evaluate : 0.360 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 56 LYS cc_start: 0.8567 (ttmt) cc_final: 0.8289 (ttmm) REVERT: A 133 ARG cc_start: 0.8358 (ttm170) cc_final: 0.8061 (mtp85) REVERT: B 84 MET cc_start: 0.8081 (mmm) cc_final: 0.7612 (mmm) REVERT: B 88 TYR cc_start: 0.8739 (m-10) cc_final: 0.8369 (m-80) REVERT: C 61 GLU cc_start: 0.7983 (tp30) cc_final: 0.7778 (tp30) REVERT: D 43 LYS cc_start: 0.8731 (ttpt) cc_final: 0.8467 (ttpt) REVERT: D 51 ASP cc_start: 0.7778 (p0) cc_final: 0.7572 (p0) REVERT: F 29 ILE cc_start: 0.8940 (mm) cc_final: 0.8688 (mp) REVERT: F 58 LEU cc_start: 0.9085 (tp) cc_final: 0.8885 (tt) REVERT: G 39 TYR cc_start: 0.9042 (m-10) cc_final: 0.8650 (m-80) REVERT: K 5 VAL cc_start: 0.9045 (m) cc_final: 0.8686 (t) REVERT: K 7 GLU cc_start: 0.7854 (mp0) cc_final: 0.7563 (mp0) REVERT: K 70 ASP cc_start: 0.8715 (t70) cc_final: 0.8362 (t0) REVERT: K 73 TYR cc_start: 0.8946 (t80) cc_final: 0.8544 (t80) REVERT: K 86 PHE cc_start: 0.8637 (m-80) cc_final: 0.8318 (m-80) REVERT: K 108 PHE cc_start: 0.8701 (t80) cc_final: 0.8488 (t80) REVERT: K 152 VAL cc_start: 0.9612 (t) cc_final: 0.9310 (m) REVERT: K 162 PHE cc_start: 0.8373 (m-10) cc_final: 0.8162 (m-10) REVERT: K 191 MET cc_start: 0.6074 (mtt) cc_final: 0.5336 (tmm) outliers start: 24 outliers final: 15 residues processed: 326 average time/residue: 0.1673 time to fit residues: 71.4631 Evaluate side-chains 293 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 278 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 74 ILE 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 34 LEU Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 108 ASP Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 79 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 68 optimal weight: 30.0000 chunk 65 optimal weight: 2.9990 chunk 77 optimal weight: 10.0000 chunk 69 optimal weight: 20.0000 chunk 100 optimal weight: 8.9990 chunk 26 optimal weight: 0.0070 chunk 78 optimal weight: 10.0000 chunk 94 optimal weight: 9.9990 chunk 51 optimal weight: 1.9990 chunk 103 optimal weight: 10.0000 chunk 87 optimal weight: 10.0000 overall best weight: 4.8006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 63 ASN H 67 ASN H 82 HIS K 113 GLN K 118 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.124023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.087162 restraints weight = 26884.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.089461 restraints weight = 15281.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.090376 restraints weight = 10549.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.090581 restraints weight = 9164.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.090738 restraints weight = 9136.222| |-----------------------------------------------------------------------------| r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.3140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 13936 Z= 0.222 Angle : 0.651 7.807 20016 Z= 0.375 Chirality : 0.038 0.149 2270 Planarity : 0.004 0.056 1559 Dihedral : 31.658 178.450 4054 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 5.10 % Allowed : 18.24 % Favored : 76.66 % 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: -0.83 (0.27), residues: 905 helix: 0.17 (0.21), residues: 607 sheet: -0.25 (0.76), residues: 38 loop : -2.20 (0.36), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 92 TYR 0.020 0.002 TYR H 83 PHE 0.020 0.002 PHE K 108 TRP 0.014 0.001 TRP K 28 HIS 0.008 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00496 (13936) covalent geometry : angle 0.65082 (20016) hydrogen bonds : bond 0.06186 ( 743) hydrogen bonds : angle 3.36738 ( 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 332 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 292 time to evaluate : 0.381 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 80 ARG cc_start: 0.8356 (mpp80) cc_final: 0.8084 (mpp80) REVERT: B 84 MET cc_start: 0.8124 (mmm) cc_final: 0.7690 (mmm) REVERT: B 88 TYR cc_start: 0.8754 (m-10) cc_final: 0.8363 (m-80) REVERT: D 38 SER cc_start: 0.9183 (p) cc_final: 0.8810 (t) REVERT: D 43 LYS cc_start: 0.8701 (ttpt) cc_final: 0.8346 (ttpt) REVERT: H 71 GLU cc_start: 0.8698 (tm-30) cc_final: 0.8492 (tm-30) REVERT: H 91 SER cc_start: 0.8905 (p) cc_final: 0.8437 (t) REVERT: H 101 LEU cc_start: 0.8174 (OUTLIER) cc_final: 0.7645 (mt) REVERT: K 5 VAL cc_start: 0.8936 (m) cc_final: 0.8564 (t) REVERT: K 18 MET cc_start: 0.8452 (mmm) cc_final: 0.8023 (mtm) REVERT: K 70 ASP cc_start: 0.8714 (t70) cc_final: 0.8329 (t0) REVERT: K 86 PHE cc_start: 0.8617 (m-80) cc_final: 0.8291 (m-80) REVERT: K 123 PHE cc_start: 0.8046 (m-80) cc_final: 0.7725 (m-80) REVERT: K 152 VAL cc_start: 0.9606 (t) cc_final: 0.9299 (m) REVERT: K 191 MET cc_start: 0.5993 (mtt) cc_final: 0.5018 (tmm) outliers start: 40 outliers final: 25 residues processed: 310 average time/residue: 0.1497 time to fit residues: 62.2614 Evaluate side-chains 288 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 262 time to evaluate : 0.377 ------------------------------------------------------------------------------- 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 82 VAL Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 54 VAL 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 D residue 52 THR Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 55 SER 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 D residue 115 THR Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 101 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 28 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 81 optimal weight: 20.0000 chunk 88 optimal weight: 10.0000 chunk 14 optimal weight: 2.9990 chunk 104 optimal weight: 20.0000 chunk 89 optimal weight: 10.0000 chunk 72 optimal weight: 10.0000 chunk 46 optimal weight: 3.9990 chunk 67 optimal weight: 9.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 85 ASN H 82 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.125883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.088919 restraints weight = 26897.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.091283 restraints weight = 15265.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.092196 restraints weight = 10674.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.092549 restraints weight = 9165.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.092704 restraints weight = 8803.227| |-----------------------------------------------------------------------------| r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.3466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13936 Z= 0.193 Angle : 0.628 8.913 20016 Z= 0.362 Chirality : 0.037 0.150 2270 Planarity : 0.004 0.051 1559 Dihedral : 31.512 178.810 4054 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 4.59 % Allowed : 21.30 % Favored : 74.11 % 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: -0.25 (0.28), residues: 905 helix: 0.61 (0.21), residues: 611 sheet: 0.31 (0.82), residues: 38 loop : -2.07 (0.37), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 92 TYR 0.027 0.002 TYR H 83 PHE 0.013 0.001 PHE K 104 TRP 0.011 0.001 TRP K 28 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00430 (13936) covalent geometry : angle 0.62802 (20016) hydrogen bonds : bond 0.05871 ( 743) hydrogen bonds : angle 3.12974 ( 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 323 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 287 time to evaluate : 0.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 84 MET cc_start: 0.8051 (mmm) cc_final: 0.7592 (mmm) REVERT: B 88 TYR cc_start: 0.8799 (m-10) cc_final: 0.8338 (m-80) REVERT: C 61 GLU cc_start: 0.7972 (tp30) cc_final: 0.7069 (tp30) REVERT: C 94 ASN cc_start: 0.9264 (t0) cc_final: 0.9024 (t0) REVERT: D 43 LYS cc_start: 0.8793 (ttpt) cc_final: 0.8431 (ttpt) REVERT: D 105 GLU cc_start: 0.7480 (tp30) cc_final: 0.7279 (tp30) REVERT: E 85 ASN cc_start: 0.8700 (m-40) cc_final: 0.8351 (m-40) REVERT: G 39 TYR cc_start: 0.9132 (m-10) cc_final: 0.8671 (m-80) REVERT: G 41 GLU cc_start: 0.6957 (tm-30) cc_final: 0.6753 (tm-30) REVERT: H 91 SER cc_start: 0.8871 (p) cc_final: 0.8429 (t) REVERT: H 101 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.7829 (mt) REVERT: K 5 VAL cc_start: 0.8774 (m) cc_final: 0.8561 (t) REVERT: K 18 MET cc_start: 0.8264 (mmm) cc_final: 0.7995 (mtm) REVERT: K 70 ASP cc_start: 0.8596 (t70) cc_final: 0.8154 (t0) REVERT: K 86 PHE cc_start: 0.8602 (m-80) cc_final: 0.8341 (m-80) REVERT: K 123 PHE cc_start: 0.8008 (m-80) cc_final: 0.7700 (m-80) REVERT: K 152 VAL cc_start: 0.9586 (t) cc_final: 0.9271 (m) REVERT: K 170 ARG cc_start: 0.8447 (ptm160) cc_final: 0.7890 (ttm170) REVERT: K 185 HIS cc_start: 0.8412 (m90) cc_final: 0.7956 (m-70) REVERT: K 191 MET cc_start: 0.6061 (mtt) cc_final: 0.5131 (tmm) REVERT: K 196 ARG cc_start: 0.7495 (ttm-80) cc_final: 0.7095 (ttm170) outliers start: 36 outliers final: 28 residues processed: 301 average time/residue: 0.1343 time to fit residues: 55.2509 Evaluate side-chains 289 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 260 time to evaluate : 0.299 ------------------------------------------------------------------------------- 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 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 62 ILE Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain F residue 70 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 62 ILE Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain K residue 163 THR Chi-restraints excluded: chain K residue 175 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 100 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 76 optimal weight: 10.0000 chunk 57 optimal weight: 1.9990 chunk 105 optimal weight: 7.9990 chunk 44 optimal weight: 4.9990 chunk 111 optimal weight: 30.0000 chunk 37 optimal weight: 2.9990 chunk 82 optimal weight: 10.0000 chunk 85 optimal weight: 9.9990 chunk 9 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 HIS H 82 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.126476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.089481 restraints weight = 26843.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.091554 restraints weight = 15433.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.092670 restraints weight = 10800.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.093138 restraints weight = 9220.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.093237 restraints weight = 8761.104| |-----------------------------------------------------------------------------| r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.3706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13936 Z= 0.178 Angle : 0.614 7.364 20016 Z= 0.356 Chirality : 0.036 0.150 2270 Planarity : 0.004 0.046 1559 Dihedral : 31.393 178.798 4054 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 5.48 % Allowed : 21.94 % Favored : 72.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.03 (0.28), residues: 905 helix: 0.85 (0.21), residues: 616 sheet: 0.42 (0.83), residues: 38 loop : -2.08 (0.37), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 92 TYR 0.029 0.002 TYR H 83 PHE 0.018 0.001 PHE K 108 TRP 0.008 0.001 TRP K 28 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00394 (13936) covalent geometry : angle 0.61420 (20016) hydrogen bonds : bond 0.05775 ( 743) hydrogen bonds : angle 3.02182 ( 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 334 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 291 time to evaluate : 0.250 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: 0.8112 (mtm110) cc_final: 0.7638 (mtm-85) REVERT: B 84 MET cc_start: 0.8075 (mmm) cc_final: 0.7666 (mmm) REVERT: B 88 TYR cc_start: 0.8783 (m-10) cc_final: 0.8314 (m-80) REVERT: C 61 GLU cc_start: 0.7938 (tp30) cc_final: 0.7657 (tp30) REVERT: C 94 ASN cc_start: 0.9263 (t0) cc_final: 0.9019 (t0) REVERT: D 43 LYS cc_start: 0.8757 (ttpt) cc_final: 0.8430 (ttpt) REVERT: E 85 ASN cc_start: 0.8624 (m-40) cc_final: 0.8242 (m-40) REVERT: G 39 TYR cc_start: 0.9133 (m-10) cc_final: 0.8623 (m-80) REVERT: G 84 GLN cc_start: 0.9173 (tp40) cc_final: 0.8340 (tt0) REVERT: H 86 ARG cc_start: 0.8755 (tpp80) cc_final: 0.8429 (tpp80) REVERT: H 91 SER cc_start: 0.8852 (p) cc_final: 0.8409 (t) REVERT: H 101 LEU cc_start: 0.8379 (OUTLIER) cc_final: 0.7877 (mt) REVERT: K 5 VAL cc_start: 0.8719 (m) cc_final: 0.8421 (t) REVERT: K 33 GLU cc_start: 0.8369 (pm20) cc_final: 0.7808 (mm-30) REVERT: K 37 GLN cc_start: 0.8132 (mt0) cc_final: 0.7532 (mp10) REVERT: K 70 ASP cc_start: 0.8608 (t70) cc_final: 0.8226 (t0) REVERT: K 85 VAL cc_start: 0.7017 (p) cc_final: 0.6805 (p) REVERT: K 86 PHE cc_start: 0.8550 (m-80) cc_final: 0.8297 (m-80) REVERT: K 123 PHE cc_start: 0.7983 (m-80) cc_final: 0.7716 (m-80) REVERT: K 152 VAL cc_start: 0.9583 (t) cc_final: 0.9273 (m) REVERT: K 162 PHE cc_start: 0.8256 (m-10) cc_final: 0.8022 (m-10) REVERT: K 191 MET cc_start: 0.6145 (mtt) cc_final: 0.5227 (tmm) REVERT: K 196 ARG cc_start: 0.7435 (ttm-80) cc_final: 0.7040 (ttm170) outliers start: 43 outliers final: 32 residues processed: 311 average time/residue: 0.1453 time to fit residues: 60.6524 Evaluate side-chains 299 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 266 time to evaluate : 0.369 ------------------------------------------------------------------------------- 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 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 65 LEU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 55 SER 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 119 VAL Chi-restraints excluded: chain F residue 70 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 58 LEU Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain K residue 163 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: 0.9990 chunk 105 optimal weight: 6.9990 chunk 113 optimal weight: 1.9990 chunk 70 optimal weight: 10.0000 chunk 62 optimal weight: 0.8980 chunk 9 optimal weight: 7.9990 chunk 38 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 82 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.128779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.092210 restraints weight = 26702.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.094609 restraints weight = 15032.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.095627 restraints weight = 10444.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.096021 restraints weight = 8979.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.096132 restraints weight = 8597.979| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.4014 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= 0.151 Angle : 0.597 8.711 20016 Z= 0.345 Chirality : 0.036 0.216 2270 Planarity : 0.004 0.037 1559 Dihedral : 31.197 179.293 4054 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 3.32 % Allowed : 24.36 % Favored : 72.32 % 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: 0.39 (0.28), residues: 905 helix: 1.11 (0.21), residues: 607 sheet: 0.65 (0.86), residues: 38 loop : -1.83 (0.36), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 92 TYR 0.018 0.002 TYR H 83 PHE 0.019 0.001 PHE K 108 TRP 0.007 0.001 TRP K 83 HIS 0.007 0.001 HIS H 82 Details of bonding type rmsd covalent geometry : bond 0.00327 (13936) covalent geometry : angle 0.59695 (20016) hydrogen bonds : bond 0.05501 ( 743) hydrogen bonds : angle 2.89119 ( 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 318 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 292 time to evaluate : 0.271 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: 0.8204 (mtm110) cc_final: 0.7481 (mtm180) REVERT: B 84 MET cc_start: 0.7957 (mmm) cc_final: 0.7533 (mmm) REVERT: B 88 TYR cc_start: 0.8770 (m-10) cc_final: 0.8307 (m-80) REVERT: C 61 GLU cc_start: 0.8019 (tp30) cc_final: 0.7554 (tp30) REVERT: C 74 LYS cc_start: 0.8684 (mtmt) cc_final: 0.8424 (mtmm) REVERT: C 94 ASN cc_start: 0.9209 (t0) cc_final: 0.8956 (t0) REVERT: D 43 LYS cc_start: 0.8692 (ttpt) cc_final: 0.8338 (ttpt) REVERT: E 58 THR cc_start: 0.9147 (p) cc_final: 0.8663 (t) REVERT: F 84 MET cc_start: 0.8152 (tpp) cc_final: 0.7934 (tpp) REVERT: G 39 TYR cc_start: 0.9094 (m-10) cc_final: 0.8533 (m-80) REVERT: G 84 GLN cc_start: 0.9116 (tp40) cc_final: 0.8289 (tt0) REVERT: H 101 LEU cc_start: 0.8240 (mm) cc_final: 0.7879 (mt) REVERT: K 5 VAL cc_start: 0.8615 (m) cc_final: 0.8301 (t) REVERT: K 70 ASP cc_start: 0.8666 (t70) cc_final: 0.8262 (t0) REVERT: K 85 VAL cc_start: 0.6868 (p) cc_final: 0.6590 (p) REVERT: K 122 SER cc_start: 0.8231 (m) cc_final: 0.7846 (p) REVERT: K 152 VAL cc_start: 0.9589 (t) cc_final: 0.9285 (m) REVERT: K 162 PHE cc_start: 0.8255 (m-10) cc_final: 0.8036 (m-10) REVERT: K 185 HIS cc_start: 0.8590 (m90) cc_final: 0.7831 (m-70) REVERT: K 191 MET cc_start: 0.6144 (mtt) cc_final: 0.5395 (ttm) outliers start: 26 outliers final: 19 residues processed: 299 average time/residue: 0.1463 time to fit residues: 59.1615 Evaluate side-chains 292 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 273 time to evaluate : 0.388 ------------------------------------------------------------------------------- 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 26 ILE Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 55 SER 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 G residue 58 LEU Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain K residue 63 ILE Chi-restraints excluded: chain K residue 163 THR Chi-restraints excluded: chain K residue 175 LEU 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: 20.0000 chunk 102 optimal weight: 8.9990 chunk 100 optimal weight: 8.9990 chunk 31 optimal weight: 5.9990 chunk 92 optimal weight: 10.0000 chunk 17 optimal weight: 3.9990 chunk 48 optimal weight: 6.9990 chunk 80 optimal weight: 20.0000 chunk 106 optimal weight: 20.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 82 HIS K 185 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.124292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.086994 restraints weight = 27030.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.089243 restraints weight = 15885.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.090188 restraints weight = 11107.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.090573 restraints weight = 9598.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.090723 restraints weight = 9397.421| |-----------------------------------------------------------------------------| r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.4007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 13936 Z= 0.262 Angle : 0.687 8.932 20016 Z= 0.389 Chirality : 0.039 0.160 2270 Planarity : 0.004 0.035 1559 Dihedral : 31.454 176.660 4054 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 4.85 % Allowed : 23.98 % Favored : 71.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.15 (0.28), residues: 905 helix: 0.85 (0.21), residues: 615 sheet: 0.87 (0.89), residues: 38 loop : -1.84 (0.38), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 35 TYR 0.023 0.002 TYR K 160 PHE 0.019 0.002 PHE A 67 TRP 0.010 0.001 TRP K 28 HIS 0.003 0.001 HIS H 82 Details of bonding type rmsd covalent geometry : bond 0.00588 (13936) covalent geometry : angle 0.68719 (20016) hydrogen bonds : bond 0.06396 ( 743) hydrogen bonds : angle 3.34768 ( 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 296 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 258 time to evaluate : 0.392 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: B 84 MET cc_start: 0.8041 (mmm) cc_final: 0.7614 (mmm) REVERT: B 88 TYR cc_start: 0.8784 (m-10) cc_final: 0.8230 (m-80) REVERT: C 61 GLU cc_start: 0.8085 (tp30) cc_final: 0.7826 (tp30) REVERT: C 74 LYS cc_start: 0.8677 (mtmt) cc_final: 0.8407 (mtmm) REVERT: C 94 ASN cc_start: 0.9348 (t0) cc_final: 0.9069 (t0) REVERT: D 43 LYS cc_start: 0.8824 (ttpt) cc_final: 0.8449 (ttpt) REVERT: F 84 MET cc_start: 0.8047 (tpp) cc_final: 0.7799 (tpp) REVERT: G 84 GLN cc_start: 0.9181 (tp40) cc_final: 0.8398 (tt0) REVERT: H 62 MET cc_start: 0.9095 (mmm) cc_final: 0.8878 (tpp) REVERT: H 86 ARG cc_start: 0.8861 (tpp80) cc_final: 0.8626 (tpp80) REVERT: H 101 LEU cc_start: 0.8407 (OUTLIER) cc_final: 0.7935 (mt) REVERT: K 70 ASP cc_start: 0.8696 (t70) cc_final: 0.8235 (t0) REVERT: K 123 PHE cc_start: 0.8074 (m-80) cc_final: 0.7765 (m-80) REVERT: K 170 ARG cc_start: 0.8285 (ttp-170) cc_final: 0.7868 (ttm170) REVERT: K 185 HIS cc_start: 0.8640 (m-70) cc_final: 0.7837 (m-70) REVERT: K 191 MET cc_start: 0.6085 (mtt) cc_final: 0.5355 (tpt) outliers start: 38 outliers final: 30 residues processed: 276 average time/residue: 0.1427 time to fit residues: 53.1662 Evaluate side-chains 277 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 246 time to evaluate : 0.341 ------------------------------------------------------------------------------- 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 A residue 104 HIS Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 30 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 D residue 55 SER 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 E residue 119 VAL 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 H residue 54 ILE Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 82 HIS Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain K residue 40 ASN Chi-restraints excluded: chain K residue 63 ILE Chi-restraints excluded: chain K residue 150 THR Chi-restraints excluded: chain K residue 158 THR Chi-restraints excluded: chain K residue 163 THR Chi-restraints excluded: chain K residue 175 LEU 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: 10.0000 chunk 60 optimal weight: 3.9990 chunk 55 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 22 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 95 optimal weight: 0.5980 chunk 102 optimal weight: 10.0000 chunk 36 optimal weight: 6.9990 chunk 78 optimal weight: 10.0000 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 85 ASN H 82 HIS ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 187 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.127218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.090391 restraints weight = 26409.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.092686 restraints weight = 14837.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.093698 restraints weight = 10363.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.094216 restraints weight = 8850.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.094357 restraints weight = 8616.738| |-----------------------------------------------------------------------------| r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.4120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13936 Z= 0.170 Angle : 0.629 10.376 20016 Z= 0.361 Chirality : 0.036 0.160 2270 Planarity : 0.004 0.047 1559 Dihedral : 31.243 178.743 4054 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 3.32 % Allowed : 27.68 % Favored : 69.01 % 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: 0.50 (0.29), residues: 905 helix: 1.08 (0.21), residues: 610 sheet: 0.98 (0.90), residues: 38 loop : -1.55 (0.39), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 92 TYR 0.026 0.002 TYR K 160 PHE 0.011 0.001 PHE K 104 TRP 0.006 0.001 TRP K 28 HIS 0.013 0.001 HIS H 82 Details of bonding type rmsd covalent geometry : bond 0.00378 (13936) covalent geometry : angle 0.62927 (20016) hydrogen bonds : bond 0.05692 ( 743) hydrogen bonds : angle 2.99284 ( 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 298 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 272 time to evaluate : 0.372 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: 0.8265 (mtm110) cc_final: 0.7556 (mtm180) REVERT: B 84 MET cc_start: 0.7938 (mmm) cc_final: 0.7530 (mmm) REVERT: B 88 TYR cc_start: 0.8731 (m-10) cc_final: 0.8251 (m-80) REVERT: C 61 GLU cc_start: 0.7980 (tp30) cc_final: 0.7679 (tp30) REVERT: C 74 LYS cc_start: 0.8705 (mtmt) cc_final: 0.8418 (mtmm) REVERT: C 92 GLU cc_start: 0.7724 (pm20) cc_final: 0.7350 (pm20) REVERT: C 94 ASN cc_start: 0.9284 (t0) cc_final: 0.9015 (t0) REVERT: D 43 LYS cc_start: 0.8737 (ttpt) cc_final: 0.8353 (ttpt) REVERT: E 58 THR cc_start: 0.9109 (p) cc_final: 0.8628 (t) REVERT: F 84 MET cc_start: 0.8059 (tpp) cc_final: 0.7838 (tpp) REVERT: G 84 GLN cc_start: 0.9083 (tp40) cc_final: 0.8174 (tt0) REVERT: H 62 MET cc_start: 0.9068 (mmm) cc_final: 0.8812 (tpp) REVERT: H 86 ARG cc_start: 0.8770 (tpp80) cc_final: 0.8500 (tpp80) REVERT: H 91 SER cc_start: 0.8892 (p) cc_final: 0.8529 (t) REVERT: H 101 LEU cc_start: 0.8318 (OUTLIER) cc_final: 0.7896 (mt) REVERT: K 5 VAL cc_start: 0.8559 (m) cc_final: 0.8267 (t) REVERT: K 70 ASP cc_start: 0.8690 (t70) cc_final: 0.8269 (t0) REVERT: K 106 ASN cc_start: 0.9396 (m-40) cc_final: 0.8857 (m110) REVERT: K 122 SER cc_start: 0.8051 (m) cc_final: 0.7763 (p) REVERT: K 123 PHE cc_start: 0.7960 (m-80) cc_final: 0.7653 (m-80) REVERT: K 152 VAL cc_start: 0.9577 (t) cc_final: 0.9253 (m) REVERT: K 185 HIS cc_start: 0.8637 (m-70) cc_final: 0.7912 (m-70) REVERT: K 191 MET cc_start: 0.6042 (mtt) cc_final: 0.5276 (tpt) REVERT: K 196 ARG cc_start: 0.7308 (ttm-80) cc_final: 0.7021 (ptm160) outliers start: 26 outliers final: 19 residues processed: 285 average time/residue: 0.1476 time to fit residues: 56.8015 Evaluate side-chains 280 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 260 time to evaluate : 0.358 ------------------------------------------------------------------------------- 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 60 VAL 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 D residue 55 SER 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 119 VAL Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain K residue 63 ILE Chi-restraints excluded: chain K residue 163 THR Chi-restraints excluded: chain K residue 175 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 26 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 27 optimal weight: 7.9990 chunk 38 optimal weight: 10.0000 chunk 90 optimal weight: 10.0000 chunk 12 optimal weight: 4.9990 chunk 68 optimal weight: 30.0000 chunk 29 optimal weight: 3.9990 chunk 80 optimal weight: 20.0000 chunk 82 optimal weight: 10.0000 chunk 62 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 85 ASN H 82 HIS ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 187 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.126690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.089528 restraints weight = 26805.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.091765 restraints weight = 15356.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.092864 restraints weight = 10739.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.093145 restraints weight = 9281.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.093225 restraints weight = 8834.719| |-----------------------------------------------------------------------------| r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.4195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13936 Z= 0.190 Angle : 0.645 9.451 20016 Z= 0.368 Chirality : 0.038 0.317 2270 Planarity : 0.004 0.054 1559 Dihedral : 31.234 178.002 4054 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 3.32 % Allowed : 28.70 % Favored : 67.98 % 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: 0.53 (0.28), residues: 905 helix: 1.11 (0.21), residues: 611 sheet: 1.01 (0.90), residues: 38 loop : -1.59 (0.38), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 92 TYR 0.016 0.002 TYR G 39 PHE 0.011 0.001 PHE A 67 TRP 0.008 0.001 TRP K 28 HIS 0.002 0.001 HIS A 115 Details of bonding type rmsd covalent geometry : bond 0.00427 (13936) covalent geometry : angle 0.64504 (20016) hydrogen bonds : bond 0.05818 ( 743) hydrogen bonds : angle 3.08233 ( 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 284 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 258 time to evaluate : 0.365 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: 0.8265 (mtm110) cc_final: 0.7702 (mtm-85) REVERT: B 84 MET cc_start: 0.7940 (mmm) cc_final: 0.7549 (mmm) REVERT: B 88 TYR cc_start: 0.8761 (m-10) cc_final: 0.8259 (m-80) REVERT: C 61 GLU cc_start: 0.8075 (tp30) cc_final: 0.7756 (tp30) REVERT: C 94 ASN cc_start: 0.9309 (t0) cc_final: 0.9032 (t0) REVERT: D 43 LYS cc_start: 0.8747 (ttpt) cc_final: 0.8354 (ttpt) REVERT: D 105 GLU cc_start: 0.7148 (tp30) cc_final: 0.6930 (tp30) REVERT: E 58 THR cc_start: 0.9173 (p) cc_final: 0.8675 (t) REVERT: E 127 GLN cc_start: 0.8230 (mt0) cc_final: 0.7845 (mm-40) REVERT: F 84 MET cc_start: 0.8102 (tpp) cc_final: 0.7894 (tpp) REVERT: G 84 GLN cc_start: 0.9080 (tp40) cc_final: 0.8181 (tt0) REVERT: H 62 MET cc_start: 0.9083 (mmm) cc_final: 0.8840 (tpp) REVERT: H 86 ARG cc_start: 0.8812 (tpp80) cc_final: 0.8574 (tpp80) REVERT: H 101 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.7957 (mt) REVERT: K 5 VAL cc_start: 0.8655 (m) cc_final: 0.8352 (t) REVERT: K 70 ASP cc_start: 0.8671 (t70) cc_final: 0.8241 (t0) REVERT: K 106 ASN cc_start: 0.9372 (m-40) cc_final: 0.8828 (m110) REVERT: K 122 SER cc_start: 0.8027 (m) cc_final: 0.7760 (p) REVERT: K 123 PHE cc_start: 0.7939 (m-80) cc_final: 0.7683 (m-80) REVERT: K 170 ARG cc_start: 0.8278 (ttp-170) cc_final: 0.7809 (ttm170) REVERT: K 185 HIS cc_start: 0.8705 (m-70) cc_final: 0.8014 (m-70) REVERT: K 191 MET cc_start: 0.6011 (mtt) cc_final: 0.5201 (tpt) REVERT: K 196 ARG cc_start: 0.7347 (ttm-80) cc_final: 0.7067 (ptm160) outliers start: 26 outliers final: 23 residues processed: 271 average time/residue: 0.1407 time to fit residues: 51.8720 Evaluate side-chains 282 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 258 time to evaluate : 0.367 ------------------------------------------------------------------------------- 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 60 VAL 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 111 ILE Chi-restraints excluded: chain D residue 55 SER 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 E residue 119 VAL Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain K residue 63 ILE Chi-restraints excluded: chain K residue 163 THR Chi-restraints excluded: chain K residue 175 LEU Chi-restraints excluded: chain K residue 187 GLN 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: 10.0000 chunk 88 optimal weight: 10.0000 chunk 67 optimal weight: 10.0000 chunk 20 optimal weight: 6.9990 chunk 106 optimal weight: 0.0870 chunk 94 optimal weight: 7.9990 chunk 57 optimal weight: 10.0000 chunk 26 optimal weight: 7.9990 chunk 18 optimal weight: 6.9990 chunk 50 optimal weight: 2.9990 overall best weight: 5.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN E 85 ASN H 82 HIS ** K 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.125499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.088247 restraints weight = 26751.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.090065 restraints weight = 15786.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.091206 restraints weight = 11187.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.091724 restraints weight = 9567.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.091920 restraints weight = 9186.197| |-----------------------------------------------------------------------------| r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.4213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 13936 Z= 0.227 Angle : 0.678 10.703 20016 Z= 0.385 Chirality : 0.039 0.338 2270 Planarity : 0.004 0.060 1559 Dihedral : 31.297 177.523 4054 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 3.44 % Allowed : 27.81 % Favored : 68.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.28), residues: 905 helix: 1.08 (0.21), residues: 611 sheet: 0.95 (0.90), residues: 38 loop : -1.53 (0.38), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 92 TYR 0.032 0.002 TYR K 160 PHE 0.014 0.001 PHE A 67 TRP 0.009 0.001 TRP K 28 HIS 0.007 0.001 HIS H 82 Details of bonding type rmsd covalent geometry : bond 0.00511 (13936) covalent geometry : angle 0.67794 (20016) hydrogen bonds : bond 0.06076 ( 743) hydrogen bonds : angle 3.23093 ( 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 275 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 248 time to evaluate : 0.295 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 80 ARG cc_start: 0.8219 (mtm110) cc_final: 0.7598 (mtm-85) REVERT: B 84 MET cc_start: 0.7963 (mmm) cc_final: 0.7562 (mmm) REVERT: B 88 TYR cc_start: 0.8774 (m-10) cc_final: 0.8259 (m-80) REVERT: C 61 GLU cc_start: 0.8116 (tp30) cc_final: 0.7867 (tp30) REVERT: C 94 ASN cc_start: 0.9315 (t0) cc_final: 0.9040 (t0) REVERT: D 43 LYS cc_start: 0.8774 (ttpt) cc_final: 0.8375 (ttpt) REVERT: D 105 GLU cc_start: 0.7171 (tp30) cc_final: 0.6943 (tp30) REVERT: E 58 THR cc_start: 0.9205 (p) cc_final: 0.8670 (t) REVERT: G 84 GLN cc_start: 0.9123 (tp40) cc_final: 0.8265 (tt0) REVERT: H 62 MET cc_start: 0.9081 (mmm) cc_final: 0.8870 (tpp) REVERT: H 91 SER cc_start: 0.8929 (p) cc_final: 0.8395 (t) REVERT: H 101 LEU cc_start: 0.8403 (OUTLIER) cc_final: 0.7964 (mt) REVERT: K 70 ASP cc_start: 0.8713 (t70) cc_final: 0.8233 (t0) REVERT: K 101 MET cc_start: 0.7265 (mmm) cc_final: 0.7053 (mmm) REVERT: K 106 ASN cc_start: 0.9355 (m-40) cc_final: 0.8808 (m110) REVERT: K 122 SER cc_start: 0.7983 (m) cc_final: 0.7728 (p) REVERT: K 123 PHE cc_start: 0.7990 (m-80) cc_final: 0.7704 (m-80) REVERT: K 170 ARG cc_start: 0.8284 (ttp-170) cc_final: 0.7818 (ttm170) REVERT: K 185 HIS cc_start: 0.8692 (m-70) cc_final: 0.7998 (m-70) REVERT: K 191 MET cc_start: 0.5995 (mtt) cc_final: 0.5184 (tpt) REVERT: K 196 ARG cc_start: 0.7250 (ttm-80) cc_final: 0.7028 (ptm160) outliers start: 27 outliers final: 25 residues processed: 260 average time/residue: 0.1395 time to fit residues: 49.4380 Evaluate side-chains 274 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 248 time to evaluate : 0.371 ------------------------------------------------------------------------------- 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 104 HIS 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 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 111 ILE Chi-restraints excluded: chain D residue 55 SER 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 E residue 119 VAL Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain K residue 63 ILE Chi-restraints excluded: chain K residue 163 THR Chi-restraints excluded: chain K residue 175 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 104 optimal weight: 9.9990 chunk 100 optimal weight: 1.9990 chunk 99 optimal weight: 7.9990 chunk 82 optimal weight: 10.0000 chunk 69 optimal weight: 20.0000 chunk 31 optimal weight: 2.9990 chunk 71 optimal weight: 10.0000 chunk 52 optimal weight: 0.8980 chunk 20 optimal weight: 20.0000 chunk 39 optimal weight: 0.9990 chunk 98 optimal weight: 3.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 82 HIS K 187 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.128294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.091195 restraints weight = 26509.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.093144 restraints weight = 15321.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.094159 restraints weight = 10920.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.094385 restraints weight = 9307.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.094528 restraints weight = 9294.063| |-----------------------------------------------------------------------------| r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.4324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 13936 Z= 0.165 Angle : 0.644 11.129 20016 Z= 0.367 Chirality : 0.037 0.338 2270 Planarity : 0.004 0.054 1559 Dihedral : 31.132 178.777 4054 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 3.32 % Allowed : 28.44 % Favored : 68.24 % 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: 0.70 (0.28), residues: 905 helix: 1.26 (0.21), residues: 607 sheet: 0.89 (0.89), residues: 38 loop : -1.48 (0.38), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 92 TYR 0.032 0.002 TYR K 160 PHE 0.011 0.001 PHE K 104 TRP 0.008 0.001 TRP A 86 HIS 0.011 0.001 HIS H 82 Details of bonding type rmsd covalent geometry : bond 0.00367 (13936) covalent geometry : angle 0.64383 (20016) hydrogen bonds : bond 0.05633 ( 743) hydrogen bonds : angle 3.00475 ( 1855) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1985.25 seconds wall clock time: 34 minutes 58.98 seconds (2098.98 seconds total)