Starting phenix.real_space_refine on Thu Sep 18 02:48:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yni_39424/09_2025/8yni_39424.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yni_39424/09_2025/8yni_39424.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8yni_39424/09_2025/8yni_39424.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yni_39424/09_2025/8yni_39424.map" model { file = "/net/cci-nas-00/data/ceres_data/8yni_39424/09_2025/8yni_39424.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yni_39424/09_2025/8yni_39424.cif" } resolution = 3.66 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.041 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 74 5.16 5 C 8571 2.51 5 N 2335 2.21 5 O 2549 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13529 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 1502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1502 Classifications: {'peptide': 181} Link IDs: {'PTRANS': 3, 'TRANS': 177} Chain: "B" Number of atoms: 1510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1510 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 3, 'TRANS': 178} Chain: "C" Number of atoms: 1510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1510 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 3, 'TRANS': 178} Chain: "H" Number of atoms: 1380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1380 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 4, 'TRANS': 164} Chain breaks: 2 Chain: "I" Number of atoms: 1386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1386 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 4, 'TRANS': 165} Chain breaks: 1 Chain: "J" Number of atoms: 1392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1392 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 4, 'TRANS': 166} Chain breaks: 1 Chain: "K" Number of atoms: 1424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1424 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 4, 'TRANS': 170} Chain: "L" Number of atoms: 667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 667 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 2, 'TRANS': 81} Chain: "R" Number of atoms: 667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 667 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 2, 'TRANS': 81} Chain: "Q" Number of atoms: 667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 667 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 2, 'TRANS': 81} Chain: "G" Number of atoms: 1424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1424 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 4, 'TRANS': 170} Time building chain proxies: 3.49, per 1000 atoms: 0.26 Number of scatterers: 13529 At special positions: 0 Unit cell: (115.92, 104.16, 143.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 74 16.00 O 2549 8.00 N 2335 7.00 C 8571 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: 1.18 Conformation dependent library (CDL) restraints added in 592.2 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 3254 Ramachandran restraints generated. 1627 Oldfield, 0 Emsley, 1627 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3202 Finding SS restraints... Secondary structure from input PDB file: 115 helices and 0 sheets defined 77.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 3 through 12 removed outlier: 3.576A pdb=" N LEU A 7 " --> pdb=" O PHE A 3 " (cutoff:3.500A) Processing helix chain 'A' and resid 15 through 26 Processing helix chain 'A' and resid 31 through 36 removed outlier: 3.582A pdb=" N GLU A 36 " --> pdb=" O GLN A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 51 removed outlier: 3.514A pdb=" N LEU A 44 " --> pdb=" O ASP A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 69 removed outlier: 3.534A pdb=" N ILE A 69 " --> pdb=" O LEU A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 78 Processing helix chain 'A' and resid 82 through 91 Processing helix chain 'A' and resid 92 through 96 removed outlier: 3.996A pdb=" N ALA A 96 " --> pdb=" O PRO A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 111 removed outlier: 3.580A pdb=" N VAL A 103 " --> pdb=" O SER A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 122 Processing helix chain 'A' and resid 129 through 134 Processing helix chain 'A' and resid 138 through 149 Processing helix chain 'A' and resid 157 through 168 Processing helix chain 'A' and resid 169 through 182 removed outlier: 3.529A pdb=" N LYS A 173 " --> pdb=" O LYS A 169 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ILE A 174 " --> pdb=" O SER A 170 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N SER A 182 " --> pdb=" O TYR A 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 12 Processing helix chain 'B' and resid 15 through 26 Processing helix chain 'B' and resid 40 through 51 removed outlier: 3.574A pdb=" N LEU B 44 " --> pdb=" O ASP B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 69 removed outlier: 3.570A pdb=" N GLU B 64 " --> pdb=" O SER B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 78 removed outlier: 3.757A pdb=" N LEU B 75 " --> pdb=" O ARG B 71 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE B 76 " --> pdb=" O LEU B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 92 Processing helix chain 'B' and resid 99 through 111 removed outlier: 3.616A pdb=" N VAL B 103 " --> pdb=" O SER B 99 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU B 111 " --> pdb=" O GLN B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 123 Processing helix chain 'B' and resid 124 through 129 Processing helix chain 'B' and resid 138 through 149 removed outlier: 3.579A pdb=" N ARG B 149 " --> pdb=" O GLU B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 168 removed outlier: 4.089A pdb=" N GLN B 166 " --> pdb=" O ARG B 162 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ILE B 167 " --> pdb=" O VAL B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 182 removed outlier: 3.539A pdb=" N SER B 182 " --> pdb=" O TYR B 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 12 Processing helix chain 'C' and resid 15 through 26 Processing helix chain 'C' and resid 31 through 36 Processing helix chain 'C' and resid 40 through 51 Processing helix chain 'C' and resid 59 through 69 removed outlier: 3.540A pdb=" N ILE C 69 " --> pdb=" O LEU C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 78 Processing helix chain 'C' and resid 82 through 92 removed outlier: 3.744A pdb=" N THR C 92 " --> pdb=" O ARG C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 110 Processing helix chain 'C' and resid 113 through 124 removed outlier: 3.622A pdb=" N LEU C 124 " --> pdb=" O PHE C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 129 removed outlier: 3.871A pdb=" N ILE C 128 " --> pdb=" O LEU C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 149 Processing helix chain 'C' and resid 157 through 168 Processing helix chain 'C' and resid 169 through 182 Processing helix chain 'H' and resid 4 through 11 removed outlier: 3.757A pdb=" N GLN H 8 " --> pdb=" O GLU H 4 " (cutoff:3.500A) Processing helix chain 'H' and resid 14 through 26 Processing helix chain 'H' and resid 36 through 47 Processing helix chain 'H' and resid 51 through 63 Processing helix chain 'H' and resid 64 through 71 removed outlier: 3.563A pdb=" N LEU H 68 " --> pdb=" O ARG H 64 " (cutoff:3.500A) Processing helix chain 'H' and resid 75 through 84 removed outlier: 3.876A pdb=" N LEU H 84 " --> pdb=" O GLU H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 91 through 102 Processing helix chain 'H' and resid 105 through 117 Processing helix chain 'H' and resid 118 through 120 No H-bonds generated for 'chain 'H' and resid 118 through 120' Processing helix chain 'H' and resid 130 through 142 removed outlier: 3.736A pdb=" N VAL H 136 " --> pdb=" O LEU H 132 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N GLU H 137 " --> pdb=" O ASP H 133 " (cutoff:3.500A) Processing helix chain 'H' and resid 149 through 158 removed outlier: 3.551A pdb=" N ASN H 158 " --> pdb=" O LYS H 154 " (cutoff:3.500A) Processing helix chain 'H' and resid 161 through 175 removed outlier: 3.671A pdb=" N LYS H 165 " --> pdb=" O ARG H 161 " (cutoff:3.500A) Processing helix chain 'I' and resid 2 through 13 removed outlier: 3.930A pdb=" N ILE I 6 " --> pdb=" O SER I 2 " (cutoff:3.500A) Processing helix chain 'I' and resid 14 through 25 Processing helix chain 'I' and resid 26 through 30 removed outlier: 3.958A pdb=" N ILE I 30 " --> pdb=" O ASP I 27 " (cutoff:3.500A) Processing helix chain 'I' and resid 36 through 47 Processing helix chain 'I' and resid 51 through 62 Processing helix chain 'I' and resid 64 through 71 Processing helix chain 'I' and resid 75 through 86 Processing helix chain 'I' and resid 91 through 104 removed outlier: 3.809A pdb=" N VAL I 95 " --> pdb=" O SER I 91 " (cutoff:3.500A) Processing helix chain 'I' and resid 105 through 117 removed outlier: 3.623A pdb=" N VAL I 109 " --> pdb=" O ASP I 105 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N SER I 110 " --> pdb=" O LYS I 106 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER I 111 " --> pdb=" O SER I 107 " (cutoff:3.500A) Processing helix chain 'I' and resid 130 through 141 Processing helix chain 'I' and resid 149 through 159 removed outlier: 3.541A pdb=" N CYS I 155 " --> pdb=" O LEU I 151 " (cutoff:3.500A) Processing helix chain 'I' and resid 162 through 175 removed outlier: 3.809A pdb=" N THR I 166 " --> pdb=" O ILE I 162 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LYS I 167 " --> pdb=" O ASP I 163 " (cutoff:3.500A) Processing helix chain 'J' and resid 2 through 13 removed outlier: 3.968A pdb=" N ILE J 6 " --> pdb=" O SER J 2 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 25 removed outlier: 3.613A pdb=" N MET J 20 " --> pdb=" O ASP J 16 " (cutoff:3.500A) Processing helix chain 'J' and resid 37 through 48 Processing helix chain 'J' and resid 51 through 63 Processing helix chain 'J' and resid 64 through 71 removed outlier: 3.801A pdb=" N LEU J 68 " --> pdb=" O ARG J 64 " (cutoff:3.500A) Processing helix chain 'J' and resid 75 through 86 removed outlier: 3.725A pdb=" N VAL J 79 " --> pdb=" O ASP J 75 " (cutoff:3.500A) Processing helix chain 'J' and resid 91 through 104 removed outlier: 3.844A pdb=" N ASP J 103 " --> pdb=" O GLU J 99 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU J 104 " --> pdb=" O ILE J 100 " (cutoff:3.500A) Processing helix chain 'J' and resid 105 through 117 Processing helix chain 'J' and resid 130 through 141 Processing helix chain 'J' and resid 149 through 158 removed outlier: 3.557A pdb=" N LYS J 157 " --> pdb=" O GLU J 153 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASN J 158 " --> pdb=" O LYS J 154 " (cutoff:3.500A) Processing helix chain 'J' and resid 162 through 175 Processing helix chain 'K' and resid 2 through 12 removed outlier: 3.758A pdb=" N ILE K 6 " --> pdb=" O SER K 2 " (cutoff:3.500A) Processing helix chain 'K' and resid 14 through 25 removed outlier: 3.515A pdb=" N LYS K 18 " --> pdb=" O ASP K 14 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N GLU K 19 " --> pdb=" O THR K 15 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N MET K 20 " --> pdb=" O ASP K 16 " (cutoff:3.500A) Processing helix chain 'K' and resid 36 through 48 Processing helix chain 'K' and resid 51 through 63 Processing helix chain 'K' and resid 64 through 71 removed outlier: 3.567A pdb=" N LEU K 68 " --> pdb=" O ARG K 64 " (cutoff:3.500A) Processing helix chain 'K' and resid 75 through 86 Processing helix chain 'K' and resid 91 through 102 Processing helix chain 'K' and resid 105 through 116 removed outlier: 3.888A pdb=" N VAL K 109 " --> pdb=" O ASP K 105 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N SER K 110 " --> pdb=" O LYS K 106 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N SER K 111 " --> pdb=" O SER K 107 " (cutoff:3.500A) Processing helix chain 'K' and resid 130 through 141 Processing helix chain 'K' and resid 149 through 159 Processing helix chain 'K' and resid 162 through 175 Processing helix chain 'L' and resid 2 through 13 Processing helix chain 'L' and resid 16 through 27 Processing helix chain 'L' and resid 32 through 38 removed outlier: 3.764A pdb=" N ARG L 38 " --> pdb=" O ARG L 34 " (cutoff:3.500A) Processing helix chain 'L' and resid 41 through 52 removed outlier: 3.867A pdb=" N GLN L 52 " --> pdb=" O MET L 48 " (cutoff:3.500A) Processing helix chain 'L' and resid 60 through 69 Processing helix chain 'L' and resid 72 through 83 removed outlier: 4.062A pdb=" N GLU L 83 " --> pdb=" O VAL L 79 " (cutoff:3.500A) Processing helix chain 'R' and resid 2 through 14 Processing helix chain 'R' and resid 16 through 27 Processing helix chain 'R' and resid 32 through 39 removed outlier: 3.541A pdb=" N ARG R 38 " --> pdb=" O ARG R 34 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL R 39 " --> pdb=" O LYS R 35 " (cutoff:3.500A) Processing helix chain 'R' and resid 41 through 52 Processing helix chain 'R' and resid 60 through 70 Processing helix chain 'R' and resid 72 through 84 removed outlier: 3.537A pdb=" N LEU R 76 " --> pdb=" O ARG R 72 " (cutoff:3.500A) Processing helix chain 'Q' and resid 2 through 14 removed outlier: 3.531A pdb=" N SER Q 14 " --> pdb=" O SER Q 10 " (cutoff:3.500A) Processing helix chain 'Q' and resid 16 through 28 Processing helix chain 'Q' and resid 33 through 37 Processing helix chain 'Q' and resid 41 through 52 removed outlier: 3.667A pdb=" N GLU Q 51 " --> pdb=" O SER Q 47 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLN Q 52 " --> pdb=" O MET Q 48 " (cutoff:3.500A) Processing helix chain 'Q' and resid 60 through 70 Processing helix chain 'Q' and resid 72 through 84 Processing helix chain 'G' and resid 2 through 12 removed outlier: 3.855A pdb=" N ILE G 6 " --> pdb=" O SER G 2 " (cutoff:3.500A) Processing helix chain 'G' and resid 14 through 25 removed outlier: 3.812A pdb=" N GLU G 19 " --> pdb=" O THR G 15 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N MET G 20 " --> pdb=" O ASP G 16 " (cutoff:3.500A) Processing helix chain 'G' and resid 36 through 48 Processing helix chain 'G' and resid 51 through 63 removed outlier: 4.121A pdb=" N ALA G 56 " --> pdb=" O VAL G 52 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N GLU G 57 " --> pdb=" O GLY G 53 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LEU G 58 " --> pdb=" O ASP G 54 " (cutoff:3.500A) Processing helix chain 'G' and resid 64 through 71 removed outlier: 4.064A pdb=" N LEU G 68 " --> pdb=" O ARG G 64 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS G 69 " --> pdb=" O PHE G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 75 through 86 Processing helix chain 'G' and resid 91 through 102 removed outlier: 3.577A pdb=" N VAL G 95 " --> pdb=" O SER G 91 " (cutoff:3.500A) Processing helix chain 'G' and resid 105 through 116 removed outlier: 3.755A pdb=" N SER G 111 " --> pdb=" O SER G 107 " (cutoff:3.500A) Processing helix chain 'G' and resid 123 through 127 removed outlier: 3.615A pdb=" N SER G 126 " --> pdb=" O GLY G 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 130 through 141 removed outlier: 3.663A pdb=" N LEU G 141 " --> pdb=" O GLU G 137 " (cutoff:3.500A) Processing helix chain 'G' and resid 149 through 159 removed outlier: 3.628A pdb=" N ILE G 159 " --> pdb=" O CYS G 155 " (cutoff:3.500A) Processing helix chain 'G' and resid 161 through 175 removed outlier: 3.764A pdb=" N LYS G 165 " --> pdb=" O ARG G 161 " (cutoff:3.500A) 744 hydrogen bonds defined for protein. 2217 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.02 Time building geometry restraints manager: 1.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4552 1.34 - 1.46: 1951 1.46 - 1.58: 7037 1.58 - 1.69: 0 1.69 - 1.81: 129 Bond restraints: 13669 Sorted by residual: bond pdb=" N VAL Q 39 " pdb=" CA VAL Q 39 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.24e-02 6.50e+03 8.47e+00 bond pdb=" N ARG L 30 " pdb=" CA ARG L 30 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.33e-02 5.65e+03 6.31e+00 bond pdb=" N LYS C 51 " pdb=" CA LYS C 51 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.32e-02 5.74e+03 6.03e+00 bond pdb=" N GLU Q 37 " pdb=" CA GLU Q 37 " ideal model delta sigma weight residual 1.456 1.486 -0.030 1.33e-02 5.65e+03 5.04e+00 bond pdb=" N TYR C 29 " pdb=" CA TYR C 29 " ideal model delta sigma weight residual 1.456 1.481 -0.026 1.32e-02 5.74e+03 3.83e+00 ... (remaining 13664 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.63: 18129 1.63 - 3.26: 158 3.26 - 4.89: 24 4.89 - 6.52: 3 6.52 - 8.16: 1 Bond angle restraints: 18315 Sorted by residual: angle pdb=" N TYR C 29 " pdb=" CA TYR C 29 " pdb=" CB TYR C 29 " ideal model delta sigma weight residual 110.49 102.33 8.16 1.48e+00 4.57e-01 3.04e+01 angle pdb=" N LYS C 51 " pdb=" CA LYS C 51 " pdb=" C LYS C 51 " ideal model delta sigma weight residual 113.02 108.19 4.83 1.20e+00 6.94e-01 1.62e+01 angle pdb=" C LYS C 51 " pdb=" CA LYS C 51 " pdb=" CB LYS C 51 " ideal model delta sigma weight residual 110.37 116.48 -6.11 1.78e+00 3.16e-01 1.18e+01 angle pdb=" C GLU C 50 " pdb=" N LYS C 51 " pdb=" CA LYS C 51 " ideal model delta sigma weight residual 122.56 116.76 5.80 1.72e+00 3.38e-01 1.14e+01 angle pdb=" N ILE G 159 " pdb=" CA ILE G 159 " pdb=" C ILE G 159 " ideal model delta sigma weight residual 112.29 109.22 3.07 9.40e-01 1.13e+00 1.07e+01 ... (remaining 18310 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 7705 17.82 - 35.65: 824 35.65 - 53.47: 106 53.47 - 71.29: 12 71.29 - 89.11: 11 Dihedral angle restraints: 8658 sinusoidal: 3776 harmonic: 4882 Sorted by residual: dihedral pdb=" N TYR C 29 " pdb=" C TYR C 29 " pdb=" CA TYR C 29 " pdb=" CB TYR C 29 " ideal model delta harmonic sigma weight residual 122.80 113.65 9.15 0 2.50e+00 1.60e-01 1.34e+01 dihedral pdb=" CB GLU C 116 " pdb=" CG GLU C 116 " pdb=" CD GLU C 116 " pdb=" OE1 GLU C 116 " ideal model delta sinusoidal sigma weight residual 0.00 -84.79 84.79 1 3.00e+01 1.11e-03 9.70e+00 dihedral pdb=" CB MET K 97 " pdb=" CG MET K 97 " pdb=" SD MET K 97 " pdb=" CE MET K 97 " ideal model delta sinusoidal sigma weight residual 60.00 118.08 -58.08 3 1.50e+01 4.44e-03 9.46e+00 ... (remaining 8655 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1608 0.038 - 0.076: 446 0.076 - 0.114: 73 0.114 - 0.152: 8 0.152 - 0.190: 2 Chirality restraints: 2137 Sorted by residual: chirality pdb=" CA TYR C 29 " pdb=" N TYR C 29 " pdb=" C TYR C 29 " pdb=" CB TYR C 29 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.00e-01 chirality pdb=" CB VAL C 150 " pdb=" CA VAL C 150 " pdb=" CG1 VAL C 150 " pdb=" CG2 VAL C 150 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 7.01e-01 chirality pdb=" CA GLU Q 37 " pdb=" N GLU Q 37 " pdb=" C GLU Q 37 " pdb=" CB GLU Q 37 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.43e-01 ... (remaining 2134 not shown) Planarity restraints: 2331 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG L 30 " -0.225 9.50e-02 1.11e+02 1.01e-01 6.24e+00 pdb=" NE ARG L 30 " 0.013 2.00e-02 2.50e+03 pdb=" CZ ARG L 30 " 0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG L 30 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG L 30 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL H 33 " -0.020 5.00e-02 4.00e+02 3.07e-02 1.51e+00 pdb=" N PRO H 34 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO H 34 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO H 34 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA H 145 " 0.020 5.00e-02 4.00e+02 3.01e-02 1.45e+00 pdb=" N PRO H 146 " -0.052 5.00e-02 4.00e+02 pdb=" CA PRO H 146 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO H 146 " 0.017 5.00e-02 4.00e+02 ... (remaining 2328 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1211 2.74 - 3.28: 13630 3.28 - 3.82: 21321 3.82 - 4.36: 23510 4.36 - 4.90: 40505 Nonbonded interactions: 100177 Sorted by model distance: nonbonded pdb=" OH TYR B 29 " pdb=" O GLN B 97 " model vdw 2.202 3.040 nonbonded pdb=" OE2 GLU L 22 " pdb=" NE2 HIS R 9 " model vdw 2.209 3.120 nonbonded pdb=" OE2 GLU R 22 " pdb=" NE2 HIS Q 9 " model vdw 2.271 3.120 nonbonded pdb=" OH TYR B 8 " pdb=" OE2 GLU B 12 " model vdw 2.276 3.040 nonbonded pdb=" O ASP K 163 " pdb=" OG1 THR K 166 " model vdw 2.287 3.040 ... (remaining 100172 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 2 through 182) selection = (chain 'C' and resid 2 through 182) } ncs_group { reference = (chain 'G' and (resid 2 through 28 or resid 31 through 121 or resid 128 through \ 175)) selection = (chain 'H' and (resid 2 through 121 or resid 128 through 175)) selection = (chain 'I' and (resid 2 through 28 or resid 31 through 175)) selection = (chain 'J' and (resid 2 through 28 or resid 31 through 121 or resid 128 through \ 175)) selection = (chain 'K' and (resid 2 through 28 or resid 31 through 121 or resid 128 through \ 175)) } ncs_group { reference = chain 'L' selection = chain 'Q' selection = chain 'R' } 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: 2.570 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: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.540 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 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 : 0.002 0.036 13669 Z= 0.102 Angle : 0.419 8.156 18315 Z= 0.239 Chirality : 0.034 0.190 2137 Planarity : 0.003 0.101 2331 Dihedral : 13.963 89.115 5456 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.62 (0.22), residues: 1627 helix: 1.82 (0.16), residues: 1210 sheet: None (None), residues: 0 loop : -1.16 (0.29), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 61 TYR 0.006 0.001 TYR C 178 PHE 0.009 0.001 PHE A 120 HIS 0.002 0.000 HIS H 160 Details of bonding type rmsd covalent geometry : bond 0.00193 (13669) covalent geometry : angle 0.41891 (18315) hydrogen bonds : bond 0.14655 ( 744) hydrogen bonds : angle 4.30651 ( 2217) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3254 Ramachandran restraints generated. 1627 Oldfield, 0 Emsley, 1627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3254 Ramachandran restraints generated. 1627 Oldfield, 0 Emsley, 1627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 395 time to evaluate : 0.598 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: symmetry clash REVERT: A 50 GLU cc_start: 0.8419 (mm-30) cc_final: 0.8211 (tp30) REVERT: A 64 GLU cc_start: 0.8582 (tm-30) cc_final: 0.8160 (tm-30) REVERT: A 101 TYR cc_start: 0.7680 (t80) cc_final: 0.7057 (t80) REVERT: A 107 GLN cc_start: 0.9198 (mt0) cc_final: 0.8725 (tm-30) REVERT: B 91 GLN cc_start: 0.8257 (mm-40) cc_final: 0.7876 (tm-30) REVERT: B 141 ASP cc_start: 0.8629 (t70) cc_final: 0.8130 (t0) REVERT: B 178 TYR cc_start: 0.9089 (t80) cc_final: 0.8832 (t80) REVERT: C 138 ASN cc_start: 0.8861 (p0) cc_final: 0.7979 (p0) REVERT: H 25 CYS cc_start: 0.8390 (m) cc_final: 0.8166 (t) REVERT: H 97 MET cc_start: 0.8939 (mmm) cc_final: 0.8693 (mmp) REVERT: H 99 GLU cc_start: 0.8413 (tm-30) cc_final: 0.8193 (tm-30) REVERT: I 8 GLN cc_start: 0.8792 (mt0) cc_final: 0.8580 (pt0) REVERT: I 17 GLU cc_start: 0.9157 (mm-30) cc_final: 0.8871 (mp0) REVERT: J 148 GLN cc_start: 0.8317 (mt0) cc_final: 0.8102 (mt0) REVERT: K 39 ASP cc_start: 0.8275 (m-30) cc_final: 0.8013 (m-30) REVERT: K 102 GLU cc_start: 0.8303 (mm-30) cc_final: 0.7841 (tm-30) REVERT: K 103 ASP cc_start: 0.8522 (m-30) cc_final: 0.8252 (t0) REVERT: K 106 LYS cc_start: 0.9337 (mttt) cc_final: 0.9122 (mtpp) REVERT: K 116 MET cc_start: 0.8812 (mtm) cc_final: 0.8611 (mtp) REVERT: K 139 GLU cc_start: 0.8917 (tt0) cc_final: 0.8553 (tm-30) REVERT: L 1 MET cc_start: 0.8313 (ptt) cc_final: 0.8045 (mmm) REVERT: L 54 ASP cc_start: 0.8284 (p0) cc_final: 0.7866 (p0) REVERT: L 64 ARG cc_start: 0.9138 (mtt180) cc_final: 0.8712 (mtt180) REVERT: L 83 GLU cc_start: 0.8273 (pm20) cc_final: 0.8003 (pm20) REVERT: R 3 PRO cc_start: 0.9454 (Cg_exo) cc_final: 0.8916 (Cg_endo) REVERT: R 19 GLU cc_start: 0.8922 (mt-10) cc_final: 0.8598 (mt-10) REVERT: R 35 LYS cc_start: 0.8804 (mttt) cc_final: 0.8286 (mtmm) REVERT: R 38 ARG cc_start: 0.8335 (ptp-110) cc_final: 0.8088 (ptp-170) REVERT: R 44 ASP cc_start: 0.9099 (m-30) cc_final: 0.8840 (p0) REVERT: R 51 GLU cc_start: 0.8049 (tp30) cc_final: 0.7749 (tp30) REVERT: R 64 ARG cc_start: 0.9276 (mtp180) cc_final: 0.9012 (mtm180) REVERT: Q 1 MET cc_start: 0.8420 (mtt) cc_final: 0.8058 (mmt) REVERT: Q 15 LEU cc_start: 0.9424 (mt) cc_final: 0.9044 (mp) REVERT: Q 19 GLU cc_start: 0.8928 (mt-10) cc_final: 0.8240 (mt-10) REVERT: Q 30 ARG cc_start: 0.8021 (mmt-90) cc_final: 0.7795 (mmt90) REVERT: Q 35 LYS cc_start: 0.9058 (mmtm) cc_final: 0.8658 (mmtm) REVERT: Q 46 PHE cc_start: 0.9620 (m-10) cc_final: 0.9413 (m-80) REVERT: Q 74 ASP cc_start: 0.8972 (p0) cc_final: 0.8351 (p0) REVERT: G 1 MET cc_start: 0.6336 (ttp) cc_final: 0.5767 (tmm) REVERT: G 119 TYR cc_start: 0.7979 (m-80) cc_final: 0.7679 (m-10) outliers start: 0 outliers final: 0 residues processed: 395 average time/residue: 0.1296 time to fit residues: 70.7735 Evaluate side-chains 219 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 219 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 0.3980 chunk 149 optimal weight: 5.9990 overall best weight: 1.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 166 GLN C 125 GLN I 160 HIS J 88 HIS L 53 ASN G 82 HIS G 86 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.086737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.062987 restraints weight = 45813.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.065363 restraints weight = 23612.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.066949 restraints weight = 15643.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.068001 restraints weight = 11954.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.068648 restraints weight = 10023.213| |-----------------------------------------------------------------------------| r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.2555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13669 Z= 0.154 Angle : 0.596 8.091 18315 Z= 0.304 Chirality : 0.038 0.193 2137 Planarity : 0.004 0.032 2331 Dihedral : 3.495 13.469 1809 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.62 % Allowed : 11.97 % Favored : 86.42 % 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 aren not related in a simple way. whole: 1.44 (0.22), residues: 1627 helix: 1.65 (0.16), residues: 1225 sheet: None (None), residues: 0 loop : -1.20 (0.29), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG Q 77 TYR 0.011 0.001 TYR B 106 PHE 0.019 0.001 PHE I 114 HIS 0.010 0.001 HIS G 7 Details of bonding type rmsd covalent geometry : bond 0.00359 (13669) covalent geometry : angle 0.59557 (18315) hydrogen bonds : bond 0.04006 ( 744) hydrogen bonds : angle 3.97279 ( 2217) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3254 Ramachandran restraints generated. 1627 Oldfield, 0 Emsley, 1627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3254 Ramachandran restraints generated. 1627 Oldfield, 0 Emsley, 1627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 242 time to evaluate : 0.538 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: symmetry clash REVERT: A 39 LYS cc_start: 0.9482 (mttt) cc_final: 0.9173 (mmtm) REVERT: A 50 GLU cc_start: 0.8432 (mm-30) cc_final: 0.8152 (tp30) REVERT: A 64 GLU cc_start: 0.8659 (tm-30) cc_final: 0.8171 (tm-30) REVERT: A 86 MET cc_start: 0.8584 (OUTLIER) cc_final: 0.8341 (tpt) REVERT: A 107 GLN cc_start: 0.9224 (mt0) cc_final: 0.8936 (tt0) REVERT: B 86 MET cc_start: 0.8397 (tpp) cc_final: 0.8168 (tpp) REVERT: B 141 ASP cc_start: 0.8776 (t70) cc_final: 0.8273 (t0) REVERT: B 146 MET cc_start: 0.8790 (mtm) cc_final: 0.8589 (mtm) REVERT: H 19 GLU cc_start: 0.8826 (mt-10) cc_final: 0.8319 (mp0) REVERT: H 25 CYS cc_start: 0.8397 (m) cc_final: 0.8147 (t) REVERT: I 8 GLN cc_start: 0.8718 (mt0) cc_final: 0.8499 (pt0) REVERT: I 17 GLU cc_start: 0.9111 (mm-30) cc_final: 0.8809 (mp0) REVERT: I 36 ASN cc_start: 0.8510 (t0) cc_final: 0.8182 (t0) REVERT: I 174 SER cc_start: 0.9174 (t) cc_final: 0.8947 (p) REVERT: J 99 GLU cc_start: 0.9187 (tp30) cc_final: 0.8809 (tm-30) REVERT: J 116 MET cc_start: 0.8209 (mmt) cc_final: 0.8000 (mmt) REVERT: K 39 ASP cc_start: 0.8471 (m-30) cc_final: 0.8109 (m-30) REVERT: K 102 GLU cc_start: 0.8576 (mm-30) cc_final: 0.8018 (tp30) REVERT: K 103 ASP cc_start: 0.8748 (m-30) cc_final: 0.8265 (t0) REVERT: K 139 GLU cc_start: 0.9032 (tt0) cc_final: 0.8634 (tm-30) REVERT: L 1 MET cc_start: 0.8607 (ptt) cc_final: 0.8265 (mmm) REVERT: L 22 GLU cc_start: 0.8950 (mt-10) cc_final: 0.8730 (mt-10) REVERT: L 51 GLU cc_start: 0.7985 (mm-30) cc_final: 0.7544 (mm-30) REVERT: L 64 ARG cc_start: 0.9204 (mtt180) cc_final: 0.8906 (mtt180) REVERT: R 19 GLU cc_start: 0.9037 (mt-10) cc_final: 0.8660 (mt-10) REVERT: R 38 ARG cc_start: 0.8467 (ptp-110) cc_final: 0.8150 (ptp-170) REVERT: R 64 ARG cc_start: 0.9196 (mtp180) cc_final: 0.8991 (mtm180) REVERT: Q 1 MET cc_start: 0.8525 (mtt) cc_final: 0.8173 (mmt) REVERT: Q 37 GLU cc_start: 0.6967 (mm-30) cc_final: 0.6719 (mm-30) REVERT: Q 46 PHE cc_start: 0.9617 (m-10) cc_final: 0.9392 (m-80) REVERT: G 1 MET cc_start: 0.6260 (ttp) cc_final: 0.5711 (tmm) REVERT: G 4 GLU cc_start: 0.8278 (tm-30) cc_final: 0.8044 (mm-30) REVERT: G 119 TYR cc_start: 0.8111 (m-80) cc_final: 0.7723 (m-10) outliers start: 25 outliers final: 13 residues processed: 260 average time/residue: 0.1214 time to fit residues: 45.0527 Evaluate side-chains 215 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 201 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 MET Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 164 CYS Chi-restraints excluded: chain C residue 10 ILE Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 110 SER Chi-restraints excluded: chain H residue 158 ASN Chi-restraints excluded: chain J residue 74 MET Chi-restraints excluded: chain K residue 30 ILE Chi-restraints excluded: chain K residue 68 LEU Chi-restraints excluded: chain K residue 120 MET Chi-restraints excluded: chain Q residue 22 GLU Chi-restraints excluded: chain G residue 27 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 78 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 11 optimal weight: 9.9990 chunk 114 optimal weight: 3.9990 chunk 99 optimal weight: 4.9990 chunk 161 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 129 optimal weight: 0.0050 chunk 23 optimal weight: 0.0970 chunk 152 optimal weight: 6.9990 overall best weight: 1.0198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 88 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.087623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.063970 restraints weight = 46357.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.066420 restraints weight = 23081.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.068051 restraints weight = 15036.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.069140 restraints weight = 11396.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.069851 restraints weight = 9501.800| |-----------------------------------------------------------------------------| r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.2970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13669 Z= 0.113 Angle : 0.537 11.796 18315 Z= 0.273 Chirality : 0.036 0.163 2137 Planarity : 0.003 0.026 2331 Dihedral : 3.463 13.290 1809 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.49 % Allowed : 14.17 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.35 (0.21), residues: 1627 helix: 1.58 (0.15), residues: 1237 sheet: None (None), residues: 0 loop : -1.31 (0.29), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG Q 71 TYR 0.020 0.001 TYR K 93 PHE 0.014 0.001 PHE A 181 HIS 0.004 0.000 HIS L 9 Details of bonding type rmsd covalent geometry : bond 0.00254 (13669) covalent geometry : angle 0.53718 (18315) hydrogen bonds : bond 0.03259 ( 744) hydrogen bonds : angle 3.72397 ( 2217) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3254 Ramachandran restraints generated. 1627 Oldfield, 0 Emsley, 1627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3254 Ramachandran restraints generated. 1627 Oldfield, 0 Emsley, 1627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 225 time to evaluate : 0.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 LYS cc_start: 0.9483 (mttt) cc_final: 0.9190 (mmtm) REVERT: A 64 GLU cc_start: 0.8620 (tm-30) cc_final: 0.8155 (tm-30) REVERT: A 81 THR cc_start: 0.8856 (m) cc_final: 0.8576 (m) REVERT: A 101 TYR cc_start: 0.7710 (t80) cc_final: 0.7470 (t80) REVERT: B 124 LEU cc_start: 0.8770 (tp) cc_final: 0.8502 (tp) REVERT: B 141 ASP cc_start: 0.8737 (t70) cc_final: 0.8201 (t0) REVERT: B 146 MET cc_start: 0.8686 (mtm) cc_final: 0.8418 (mtm) REVERT: H 19 GLU cc_start: 0.8867 (mt-10) cc_final: 0.8463 (mt-10) REVERT: H 25 CYS cc_start: 0.8366 (m) cc_final: 0.8124 (t) REVERT: H 99 GLU cc_start: 0.8429 (tm-30) cc_final: 0.7977 (tm-30) REVERT: I 8 GLN cc_start: 0.8729 (mt0) cc_final: 0.8516 (pt0) REVERT: I 17 GLU cc_start: 0.9081 (mm-30) cc_final: 0.8775 (mp0) REVERT: I 36 ASN cc_start: 0.8560 (t0) cc_final: 0.8226 (t0) REVERT: I 174 SER cc_start: 0.9211 (t) cc_final: 0.8983 (p) REVERT: J 99 GLU cc_start: 0.9186 (tp30) cc_final: 0.8803 (tm-30) REVERT: K 39 ASP cc_start: 0.8499 (m-30) cc_final: 0.8132 (m-30) REVERT: K 102 GLU cc_start: 0.8528 (mm-30) cc_final: 0.8005 (tp30) REVERT: K 103 ASP cc_start: 0.8725 (m-30) cc_final: 0.8236 (t0) REVERT: L 1 MET cc_start: 0.8629 (ptt) cc_final: 0.8256 (mmm) REVERT: L 22 GLU cc_start: 0.8935 (mt-10) cc_final: 0.8692 (mt-10) REVERT: L 51 GLU cc_start: 0.8039 (mm-30) cc_final: 0.7473 (mm-30) REVERT: L 64 ARG cc_start: 0.9242 (mtt180) cc_final: 0.9031 (mtm110) REVERT: R 19 GLU cc_start: 0.8949 (mt-10) cc_final: 0.8610 (mt-10) REVERT: R 38 ARG cc_start: 0.8491 (ptp-110) cc_final: 0.8153 (ptp-170) REVERT: R 64 ARG cc_start: 0.9229 (mtp180) cc_final: 0.8942 (mtm180) REVERT: Q 1 MET cc_start: 0.8415 (mtt) cc_final: 0.8075 (mmt) REVERT: Q 37 GLU cc_start: 0.7116 (mm-30) cc_final: 0.6832 (mm-30) REVERT: Q 46 PHE cc_start: 0.9642 (m-10) cc_final: 0.9408 (m-80) REVERT: Q 64 ARG cc_start: 0.9312 (ptp-170) cc_final: 0.8806 (mtt90) REVERT: G 4 GLU cc_start: 0.8273 (tm-30) cc_final: 0.7975 (mp0) REVERT: G 74 MET cc_start: 0.8031 (mmm) cc_final: 0.7691 (ttt) REVERT: G 119 TYR cc_start: 0.8131 (m-80) cc_final: 0.7765 (m-10) outliers start: 23 outliers final: 15 residues processed: 242 average time/residue: 0.1236 time to fit residues: 42.4199 Evaluate side-chains 219 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 204 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 164 CYS Chi-restraints excluded: chain C residue 10 ILE Chi-restraints excluded: chain C residue 16 SER Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 158 ASN Chi-restraints excluded: chain I residue 13 LEU Chi-restraints excluded: chain K residue 120 MET Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain Q residue 22 GLU Chi-restraints excluded: chain G residue 6 ILE Chi-restraints excluded: chain G residue 27 ASP Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 91 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 140 optimal weight: 4.9990 chunk 55 optimal weight: 8.9990 chunk 9 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 25 optimal weight: 0.0010 chunk 100 optimal weight: 0.0170 chunk 112 optimal weight: 0.8980 chunk 160 optimal weight: 0.9990 chunk 134 optimal weight: 0.0570 chunk 127 optimal weight: 6.9990 overall best weight: 0.3942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 86 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.088239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.064887 restraints weight = 45375.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.067249 restraints weight = 23378.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.068846 restraints weight = 15460.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.069897 restraints weight = 11785.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.070536 restraints weight = 9879.926| |-----------------------------------------------------------------------------| r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.3254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 13669 Z= 0.099 Angle : 0.522 10.691 18315 Z= 0.267 Chirality : 0.035 0.168 2137 Planarity : 0.003 0.026 2331 Dihedral : 3.406 15.882 1809 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.68 % Allowed : 14.88 % Favored : 83.44 % 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 aren not related in a simple way. whole: 1.40 (0.22), residues: 1627 helix: 1.60 (0.15), residues: 1239 sheet: None (None), residues: 0 loop : -1.23 (0.29), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 77 TYR 0.019 0.001 TYR J 93 PHE 0.012 0.001 PHE A 181 HIS 0.003 0.000 HIS L 9 Details of bonding type rmsd covalent geometry : bond 0.00212 (13669) covalent geometry : angle 0.52248 (18315) hydrogen bonds : bond 0.02726 ( 744) hydrogen bonds : angle 3.52263 ( 2217) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3254 Ramachandran restraints generated. 1627 Oldfield, 0 Emsley, 1627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3254 Ramachandran restraints generated. 1627 Oldfield, 0 Emsley, 1627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 226 time to evaluate : 0.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 LYS cc_start: 0.9438 (mttt) cc_final: 0.9145 (mmtm) REVERT: A 64 GLU cc_start: 0.8641 (tm-30) cc_final: 0.8087 (tm-30) REVERT: A 110 GLU cc_start: 0.8857 (tp30) cc_final: 0.8626 (tp30) REVERT: B 106 TYR cc_start: 0.8801 (t80) cc_final: 0.8088 (t80) REVERT: B 141 ASP cc_start: 0.8646 (t70) cc_final: 0.8108 (t0) REVERT: B 146 MET cc_start: 0.8773 (mtm) cc_final: 0.8550 (mtm) REVERT: C 35 GLN cc_start: 0.8443 (tt0) cc_final: 0.8210 (tt0) REVERT: C 101 TYR cc_start: 0.8058 (t80) cc_final: 0.7722 (t80) REVERT: H 19 GLU cc_start: 0.8871 (mt-10) cc_final: 0.8656 (mt-10) REVERT: H 25 CYS cc_start: 0.8348 (m) cc_final: 0.8104 (t) REVERT: H 99 GLU cc_start: 0.8485 (tm-30) cc_final: 0.8248 (tm-30) REVERT: I 8 GLN cc_start: 0.8707 (mt0) cc_final: 0.8499 (pt0) REVERT: I 17 GLU cc_start: 0.9012 (mm-30) cc_final: 0.8795 (mp0) REVERT: I 36 ASN cc_start: 0.8494 (t0) cc_final: 0.8175 (t0) REVERT: J 99 GLU cc_start: 0.9136 (tp30) cc_final: 0.8826 (tm-30) REVERT: J 116 MET cc_start: 0.8693 (mmt) cc_final: 0.8388 (mmt) REVERT: K 39 ASP cc_start: 0.8447 (m-30) cc_final: 0.8083 (m-30) REVERT: K 102 GLU cc_start: 0.8368 (mm-30) cc_final: 0.7920 (tp30) REVERT: K 103 ASP cc_start: 0.8616 (m-30) cc_final: 0.8194 (t0) REVERT: L 1 MET cc_start: 0.8585 (ptt) cc_final: 0.8269 (mmm) REVERT: L 22 GLU cc_start: 0.8909 (mt-10) cc_final: 0.8662 (mt-10) REVERT: L 51 GLU cc_start: 0.8044 (mm-30) cc_final: 0.7432 (mm-30) REVERT: L 64 ARG cc_start: 0.9234 (mtt180) cc_final: 0.8752 (mtt-85) REVERT: L 69 SER cc_start: 0.8957 (m) cc_final: 0.8679 (p) REVERT: R 19 GLU cc_start: 0.8860 (mt-10) cc_final: 0.8649 (mt-10) REVERT: R 37 GLU cc_start: 0.8583 (tm-30) cc_final: 0.8363 (tm-30) REVERT: R 64 ARG cc_start: 0.9291 (mtp180) cc_final: 0.8955 (mtm180) REVERT: Q 1 MET cc_start: 0.8332 (mtt) cc_final: 0.7987 (mmt) REVERT: Q 37 GLU cc_start: 0.7232 (mm-30) cc_final: 0.6995 (mm-30) REVERT: Q 46 PHE cc_start: 0.9667 (m-10) cc_final: 0.9455 (m-80) REVERT: Q 64 ARG cc_start: 0.9296 (ptp-170) cc_final: 0.8979 (mtt90) REVERT: G 4 GLU cc_start: 0.8271 (tm-30) cc_final: 0.7906 (mp0) REVERT: G 44 LEU cc_start: 0.9312 (OUTLIER) cc_final: 0.9014 (mm) REVERT: G 119 TYR cc_start: 0.8118 (m-80) cc_final: 0.7845 (m-10) outliers start: 26 outliers final: 19 residues processed: 245 average time/residue: 0.1363 time to fit residues: 47.5420 Evaluate side-chains 229 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 209 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 164 CYS Chi-restraints excluded: chain C residue 10 ILE Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 110 SER Chi-restraints excluded: chain H residue 141 LEU Chi-restraints excluded: chain H residue 158 ASN Chi-restraints excluded: chain I residue 13 LEU Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain K residue 25 CYS Chi-restraints excluded: chain K residue 120 MET Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain Q residue 22 GLU Chi-restraints excluded: chain G residue 6 ILE Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 27 ASP Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 91 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 81 optimal weight: 0.0670 chunk 14 optimal weight: 0.0270 chunk 149 optimal weight: 7.9990 chunk 152 optimal weight: 5.9990 chunk 103 optimal weight: 3.9990 chunk 31 optimal weight: 10.0000 chunk 161 optimal weight: 7.9990 chunk 70 optimal weight: 0.0060 chunk 10 optimal weight: 3.9990 chunk 105 optimal weight: 7.9990 chunk 67 optimal weight: 1.9990 overall best weight: 1.2196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 88 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.087110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.063767 restraints weight = 45736.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.066074 restraints weight = 23626.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.067628 restraints weight = 15650.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.068669 restraints weight = 11962.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.069358 restraints weight = 10015.006| |-----------------------------------------------------------------------------| r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.3433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13669 Z= 0.115 Angle : 0.543 9.690 18315 Z= 0.275 Chirality : 0.036 0.190 2137 Planarity : 0.003 0.033 2331 Dihedral : 3.427 20.450 1809 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.20 % Allowed : 15.65 % Favored : 82.15 % 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 aren not related in a simple way. whole: 1.49 (0.22), residues: 1627 helix: 1.68 (0.16), residues: 1236 sheet: None (None), residues: 0 loop : -1.24 (0.29), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG Q 77 TYR 0.018 0.001 TYR A 106 PHE 0.016 0.001 PHE A 181 HIS 0.007 0.001 HIS Q 9 Details of bonding type rmsd covalent geometry : bond 0.00263 (13669) covalent geometry : angle 0.54313 (18315) hydrogen bonds : bond 0.02877 ( 744) hydrogen bonds : angle 3.58067 ( 2217) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3254 Ramachandran restraints generated. 1627 Oldfield, 0 Emsley, 1627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3254 Ramachandran restraints generated. 1627 Oldfield, 0 Emsley, 1627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 220 time to evaluate : 0.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 LYS cc_start: 0.9442 (mttt) cc_final: 0.9142 (mmtm) REVERT: A 64 GLU cc_start: 0.8646 (tm-30) cc_final: 0.8234 (tm-30) REVERT: A 110 GLU cc_start: 0.8924 (tp30) cc_final: 0.8698 (tp30) REVERT: B 106 TYR cc_start: 0.8789 (t80) cc_final: 0.8573 (t80) REVERT: B 141 ASP cc_start: 0.8666 (t70) cc_final: 0.8114 (t0) REVERT: C 101 TYR cc_start: 0.8177 (t80) cc_final: 0.7809 (t80) REVERT: H 19 GLU cc_start: 0.8862 (mt-10) cc_final: 0.8431 (mt-10) REVERT: H 25 CYS cc_start: 0.8405 (m) cc_final: 0.8158 (t) REVERT: I 8 GLN cc_start: 0.8722 (mt0) cc_final: 0.8506 (pt0) REVERT: I 17 GLU cc_start: 0.9037 (mm-30) cc_final: 0.8767 (mp0) REVERT: I 36 ASN cc_start: 0.8528 (t0) cc_final: 0.8213 (t0) REVERT: I 97 MET cc_start: 0.9187 (mmp) cc_final: 0.8975 (mmm) REVERT: J 99 GLU cc_start: 0.9145 (tp30) cc_final: 0.8833 (tm-30) REVERT: J 116 MET cc_start: 0.8799 (mmt) cc_final: 0.8368 (mmt) REVERT: K 10 GLU cc_start: 0.8749 (tm-30) cc_final: 0.8513 (tm-30) REVERT: K 39 ASP cc_start: 0.8466 (m-30) cc_final: 0.8092 (m-30) REVERT: K 102 GLU cc_start: 0.8371 (mm-30) cc_final: 0.7846 (tp30) REVERT: K 103 ASP cc_start: 0.8621 (m-30) cc_final: 0.8209 (t0) REVERT: L 1 MET cc_start: 0.8619 (ptt) cc_final: 0.8316 (mmp) REVERT: L 22 GLU cc_start: 0.8936 (mt-10) cc_final: 0.8667 (mt-10) REVERT: L 51 GLU cc_start: 0.8083 (mm-30) cc_final: 0.7506 (mm-30) REVERT: L 69 SER cc_start: 0.8984 (m) cc_final: 0.8704 (p) REVERT: R 1 MET cc_start: 0.9041 (tmm) cc_final: 0.8825 (ppp) REVERT: R 19 GLU cc_start: 0.8900 (mt-10) cc_final: 0.8509 (mt-10) REVERT: R 64 ARG cc_start: 0.9308 (mtp180) cc_final: 0.8982 (mtm180) REVERT: Q 1 MET cc_start: 0.8327 (mtt) cc_final: 0.7980 (mmt) REVERT: Q 37 GLU cc_start: 0.7099 (mm-30) cc_final: 0.6822 (mm-30) REVERT: Q 38 ARG cc_start: 0.7392 (ttp80) cc_final: 0.7007 (tpt90) REVERT: Q 46 PHE cc_start: 0.9672 (m-10) cc_final: 0.9463 (m-80) REVERT: G 4 GLU cc_start: 0.8274 (tm-30) cc_final: 0.7861 (mp0) REVERT: G 44 LEU cc_start: 0.9308 (OUTLIER) cc_final: 0.9006 (mm) REVERT: G 119 TYR cc_start: 0.8125 (m-80) cc_final: 0.7753 (m-10) REVERT: G 156 LEU cc_start: 0.9168 (mt) cc_final: 0.8943 (pp) outliers start: 34 outliers final: 25 residues processed: 242 average time/residue: 0.1373 time to fit residues: 47.2074 Evaluate side-chains 232 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 206 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 164 CYS Chi-restraints excluded: chain B residue 181 PHE Chi-restraints excluded: chain C residue 10 ILE Chi-restraints excluded: chain C residue 16 SER Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 110 SER Chi-restraints excluded: chain H residue 141 LEU Chi-restraints excluded: chain H residue 158 ASN Chi-restraints excluded: chain I residue 13 LEU Chi-restraints excluded: chain I residue 74 MET Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 120 MET Chi-restraints excluded: chain K residue 25 CYS Chi-restraints excluded: chain K residue 112 LEU Chi-restraints excluded: chain K residue 120 MET Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain R residue 59 HIS Chi-restraints excluded: chain Q residue 22 GLU Chi-restraints excluded: chain Q residue 50 LEU Chi-restraints excluded: chain G residue 6 ILE Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 27 ASP Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 91 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 75 optimal weight: 1.9990 chunk 109 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 116 optimal weight: 7.9990 chunk 151 optimal weight: 0.7980 chunk 77 optimal weight: 0.8980 chunk 87 optimal weight: 0.9980 chunk 71 optimal weight: 0.9980 chunk 152 optimal weight: 3.9990 chunk 79 optimal weight: 0.6980 chunk 25 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 36 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.087575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.064270 restraints weight = 45414.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.066557 restraints weight = 23774.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.068096 restraints weight = 15852.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.069129 restraints weight = 12180.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.069824 restraints weight = 10222.033| |-----------------------------------------------------------------------------| r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.3575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 13669 Z= 0.104 Angle : 0.545 10.179 18315 Z= 0.276 Chirality : 0.036 0.172 2137 Planarity : 0.003 0.052 2331 Dihedral : 3.441 20.130 1809 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.88 % Allowed : 17.21 % Favored : 80.92 % 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 aren not related in a simple way. whole: 1.43 (0.22), residues: 1627 helix: 1.65 (0.16), residues: 1234 sheet: None (None), residues: 0 loop : -1.31 (0.28), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG Q 78 TYR 0.019 0.001 TYR A 106 PHE 0.015 0.001 PHE A 181 HIS 0.003 0.000 HIS L 9 Details of bonding type rmsd covalent geometry : bond 0.00234 (13669) covalent geometry : angle 0.54500 (18315) hydrogen bonds : bond 0.02689 ( 744) hydrogen bonds : angle 3.50686 ( 2217) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3254 Ramachandran restraints generated. 1627 Oldfield, 0 Emsley, 1627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3254 Ramachandran restraints generated. 1627 Oldfield, 0 Emsley, 1627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 224 time to evaluate : 0.643 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 39 LYS cc_start: 0.9437 (mttt) cc_final: 0.9149 (mmtm) REVERT: A 64 GLU cc_start: 0.8618 (tm-30) cc_final: 0.8173 (tm-30) REVERT: B 106 TYR cc_start: 0.8820 (t80) cc_final: 0.8089 (t80) REVERT: B 141 ASP cc_start: 0.8630 (t70) cc_final: 0.8098 (t0) REVERT: B 146 MET cc_start: 0.8685 (mtm) cc_final: 0.8394 (mtm) REVERT: C 101 TYR cc_start: 0.8131 (t80) cc_final: 0.7769 (t80) REVERT: H 19 GLU cc_start: 0.8865 (mt-10) cc_final: 0.8391 (mt-10) REVERT: H 25 CYS cc_start: 0.8370 (m) cc_final: 0.8142 (t) REVERT: I 8 GLN cc_start: 0.8713 (mt0) cc_final: 0.8505 (pt0) REVERT: I 17 GLU cc_start: 0.9008 (mm-30) cc_final: 0.8750 (mp0) REVERT: I 36 ASN cc_start: 0.8446 (t0) cc_final: 0.8174 (t0) REVERT: J 99 GLU cc_start: 0.9138 (tp30) cc_final: 0.8858 (tm-30) REVERT: J 116 MET cc_start: 0.8774 (mmt) cc_final: 0.8374 (mmt) REVERT: K 10 GLU cc_start: 0.8771 (tm-30) cc_final: 0.8535 (tm-30) REVERT: K 39 ASP cc_start: 0.8461 (m-30) cc_final: 0.8091 (m-30) REVERT: K 102 GLU cc_start: 0.8325 (mm-30) cc_final: 0.7934 (tp30) REVERT: K 103 ASP cc_start: 0.8592 (m-30) cc_final: 0.8214 (t0) REVERT: K 151 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8696 (tt) REVERT: L 22 GLU cc_start: 0.8940 (mt-10) cc_final: 0.8662 (mt-10) REVERT: L 51 GLU cc_start: 0.8120 (mm-30) cc_final: 0.7538 (mm-30) REVERT: L 64 ARG cc_start: 0.9158 (mtm110) cc_final: 0.8894 (mtp85) REVERT: L 69 SER cc_start: 0.8946 (m) cc_final: 0.8642 (p) REVERT: L 71 ARG cc_start: 0.9066 (mtm-85) cc_final: 0.8694 (ptp90) REVERT: R 19 GLU cc_start: 0.8861 (mt-10) cc_final: 0.8455 (mt-10) REVERT: R 64 ARG cc_start: 0.9296 (mtp180) cc_final: 0.8790 (ptp-170) REVERT: Q 1 MET cc_start: 0.8276 (mtt) cc_final: 0.7954 (mmt) REVERT: Q 37 GLU cc_start: 0.7172 (mm-30) cc_final: 0.6889 (mm-30) REVERT: Q 38 ARG cc_start: 0.7487 (ttp80) cc_final: 0.7100 (tpt90) REVERT: Q 46 PHE cc_start: 0.9670 (m-10) cc_final: 0.9467 (m-80) REVERT: Q 64 ARG cc_start: 0.9197 (ttm170) cc_final: 0.8789 (ttm-80) REVERT: G 4 GLU cc_start: 0.8309 (tm-30) cc_final: 0.7855 (mp0) REVERT: G 44 LEU cc_start: 0.9308 (OUTLIER) cc_final: 0.9012 (mm) REVERT: G 119 TYR cc_start: 0.8059 (m-80) cc_final: 0.7781 (m-10) REVERT: G 156 LEU cc_start: 0.9204 (mt) cc_final: 0.8969 (pp) outliers start: 29 outliers final: 24 residues processed: 244 average time/residue: 0.1383 time to fit residues: 47.8379 Evaluate side-chains 236 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 210 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 164 CYS Chi-restraints excluded: chain C residue 10 ILE Chi-restraints excluded: chain C residue 16 SER Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 110 SER Chi-restraints excluded: chain H residue 141 LEU Chi-restraints excluded: chain H residue 158 ASN Chi-restraints excluded: chain I residue 13 LEU Chi-restraints excluded: chain I residue 74 MET Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 120 MET Chi-restraints excluded: chain K residue 25 CYS Chi-restraints excluded: chain K residue 112 LEU Chi-restraints excluded: chain K residue 120 MET Chi-restraints excluded: chain K residue 151 LEU Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain R residue 59 HIS Chi-restraints excluded: chain Q residue 22 GLU Chi-restraints excluded: chain Q residue 50 LEU Chi-restraints excluded: chain G residue 6 ILE Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 27 ASP Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 91 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 24 optimal weight: 0.0470 chunk 81 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 70 optimal weight: 0.9990 chunk 33 optimal weight: 7.9990 chunk 152 optimal weight: 9.9990 chunk 129 optimal weight: 0.9990 overall best weight: 0.8082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 107 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.087660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.064446 restraints weight = 45331.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.066700 restraints weight = 23653.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.068205 restraints weight = 15832.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.069243 restraints weight = 12201.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.069940 restraints weight = 10222.918| |-----------------------------------------------------------------------------| r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.3728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 13669 Z= 0.106 Angle : 0.571 15.659 18315 Z= 0.285 Chirality : 0.036 0.173 2137 Planarity : 0.003 0.039 2331 Dihedral : 3.475 23.826 1809 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.81 % Allowed : 17.92 % Favored : 80.27 % 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 aren not related in a simple way. whole: 1.44 (0.22), residues: 1627 helix: 1.65 (0.16), residues: 1246 sheet: None (None), residues: 0 loop : -1.38 (0.29), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG Q 78 TYR 0.019 0.001 TYR J 93 PHE 0.013 0.001 PHE A 181 HIS 0.003 0.000 HIS L 9 Details of bonding type rmsd covalent geometry : bond 0.00239 (13669) covalent geometry : angle 0.57083 (18315) hydrogen bonds : bond 0.02645 ( 744) hydrogen bonds : angle 3.46831 ( 2217) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3254 Ramachandran restraints generated. 1627 Oldfield, 0 Emsley, 1627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3254 Ramachandran restraints generated. 1627 Oldfield, 0 Emsley, 1627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 218 time to evaluate : 0.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 LYS cc_start: 0.9445 (mttt) cc_final: 0.9150 (mmtm) REVERT: A 64 GLU cc_start: 0.8683 (tm-30) cc_final: 0.8244 (tm-30) REVERT: B 106 TYR cc_start: 0.8878 (t80) cc_final: 0.8249 (t80) REVERT: B 141 ASP cc_start: 0.8607 (t70) cc_final: 0.8085 (t0) REVERT: B 146 MET cc_start: 0.8672 (mtm) cc_final: 0.8412 (mtm) REVERT: C 101 TYR cc_start: 0.8218 (t80) cc_final: 0.7920 (t80) REVERT: H 19 GLU cc_start: 0.8875 (mt-10) cc_final: 0.8414 (mt-10) REVERT: H 25 CYS cc_start: 0.8369 (m) cc_final: 0.8133 (t) REVERT: I 17 GLU cc_start: 0.9002 (mm-30) cc_final: 0.8734 (mp0) REVERT: J 99 GLU cc_start: 0.9128 (tp30) cc_final: 0.8862 (tm-30) REVERT: K 10 GLU cc_start: 0.8779 (tm-30) cc_final: 0.8514 (tm-30) REVERT: K 39 ASP cc_start: 0.8463 (m-30) cc_final: 0.8090 (m-30) REVERT: K 102 GLU cc_start: 0.8315 (mm-30) cc_final: 0.7906 (tp30) REVERT: K 103 ASP cc_start: 0.8562 (m-30) cc_final: 0.8149 (t0) REVERT: K 151 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8690 (tt) REVERT: L 48 MET cc_start: 0.9435 (tpp) cc_final: 0.9197 (tpp) REVERT: L 51 GLU cc_start: 0.8155 (mm-30) cc_final: 0.7529 (mm-30) REVERT: L 64 ARG cc_start: 0.9157 (mtm110) cc_final: 0.8744 (ptp-110) REVERT: L 69 SER cc_start: 0.8929 (m) cc_final: 0.8612 (p) REVERT: L 71 ARG cc_start: 0.9047 (mtm-85) cc_final: 0.8684 (ptp90) REVERT: R 1 MET cc_start: 0.8914 (ppp) cc_final: 0.8699 (tmm) REVERT: R 19 GLU cc_start: 0.8769 (mt-10) cc_final: 0.8539 (mt-10) REVERT: R 64 ARG cc_start: 0.9330 (mtp180) cc_final: 0.9017 (mtm180) REVERT: Q 1 MET cc_start: 0.8288 (mtt) cc_final: 0.7960 (mmt) REVERT: Q 37 GLU cc_start: 0.7168 (mm-30) cc_final: 0.6888 (mm-30) REVERT: Q 46 PHE cc_start: 0.9668 (m-10) cc_final: 0.9455 (m-80) REVERT: Q 64 ARG cc_start: 0.9205 (ttm170) cc_final: 0.8839 (ttm-80) REVERT: G 4 GLU cc_start: 0.8214 (tm-30) cc_final: 0.7737 (mp0) REVERT: G 44 LEU cc_start: 0.9316 (OUTLIER) cc_final: 0.9024 (mm) REVERT: G 156 LEU cc_start: 0.9230 (mt) cc_final: 0.8985 (pp) outliers start: 28 outliers final: 23 residues processed: 239 average time/residue: 0.1359 time to fit residues: 46.1817 Evaluate side-chains 235 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 210 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 164 CYS Chi-restraints excluded: chain C residue 10 ILE Chi-restraints excluded: chain C residue 16 SER Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 110 SER Chi-restraints excluded: chain H residue 141 LEU Chi-restraints excluded: chain H residue 158 ASN Chi-restraints excluded: chain I residue 13 LEU Chi-restraints excluded: chain I residue 74 MET Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 120 MET Chi-restraints excluded: chain K residue 25 CYS Chi-restraints excluded: chain K residue 112 LEU Chi-restraints excluded: chain K residue 120 MET Chi-restraints excluded: chain K residue 151 LEU Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain Q residue 22 GLU Chi-restraints excluded: chain G residue 6 ILE Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 27 ASP Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 91 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 104 optimal weight: 0.0970 chunk 102 optimal weight: 1.9990 chunk 115 optimal weight: 0.6980 chunk 44 optimal weight: 0.2980 chunk 37 optimal weight: 8.9990 chunk 151 optimal weight: 0.2980 chunk 142 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 99 optimal weight: 4.9990 chunk 1 optimal weight: 7.9990 chunk 59 optimal weight: 5.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 GLN B 107 GLN G 158 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.088761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.065851 restraints weight = 46553.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.068120 restraints weight = 24889.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.069631 restraints weight = 16890.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.070528 restraints weight = 13139.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.071269 restraints weight = 11225.677| |-----------------------------------------------------------------------------| r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.3870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 13669 Z= 0.105 Angle : 0.592 14.368 18315 Z= 0.294 Chirality : 0.036 0.174 2137 Planarity : 0.003 0.041 2331 Dihedral : 3.551 37.405 1809 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.75 % Allowed : 18.24 % Favored : 80.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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 aren not related in a simple way. whole: 1.40 (0.22), residues: 1627 helix: 1.63 (0.16), residues: 1243 sheet: None (None), residues: 0 loop : -1.42 (0.29), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG Q 78 TYR 0.018 0.001 TYR A 106 PHE 0.012 0.001 PHE A 181 HIS 0.002 0.000 HIS L 9 Details of bonding type rmsd covalent geometry : bond 0.00236 (13669) covalent geometry : angle 0.59236 (18315) hydrogen bonds : bond 0.02583 ( 744) hydrogen bonds : angle 3.46678 ( 2217) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3254 Ramachandran restraints generated. 1627 Oldfield, 0 Emsley, 1627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3254 Ramachandran restraints generated. 1627 Oldfield, 0 Emsley, 1627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 220 time to evaluate : 0.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 LYS cc_start: 0.9433 (mttt) cc_final: 0.9159 (mmtm) REVERT: A 64 GLU cc_start: 0.8652 (tm-30) cc_final: 0.8204 (tm-30) REVERT: B 106 TYR cc_start: 0.8915 (t80) cc_final: 0.8311 (t80) REVERT: B 141 ASP cc_start: 0.8605 (t70) cc_final: 0.8081 (t0) REVERT: B 146 MET cc_start: 0.8668 (mtm) cc_final: 0.8424 (mtm) REVERT: C 35 GLN cc_start: 0.8454 (tt0) cc_final: 0.8226 (tt0) REVERT: H 19 GLU cc_start: 0.8876 (mt-10) cc_final: 0.8406 (mt-10) REVERT: H 25 CYS cc_start: 0.8364 (m) cc_final: 0.8136 (t) REVERT: I 17 GLU cc_start: 0.8982 (mm-30) cc_final: 0.8714 (mp0) REVERT: J 99 GLU cc_start: 0.9140 (tp30) cc_final: 0.8861 (tm-30) REVERT: K 10 GLU cc_start: 0.8775 (tm-30) cc_final: 0.8506 (tm-30) REVERT: K 39 ASP cc_start: 0.8445 (m-30) cc_final: 0.8080 (m-30) REVERT: K 102 GLU cc_start: 0.8384 (mm-30) cc_final: 0.8032 (tp30) REVERT: K 103 ASP cc_start: 0.8623 (m-30) cc_final: 0.8175 (t0) REVERT: K 151 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8678 (tt) REVERT: L 22 GLU cc_start: 0.8896 (mt-10) cc_final: 0.8589 (mt-10) REVERT: L 35 LYS cc_start: 0.9234 (mttt) cc_final: 0.8885 (mmtm) REVERT: L 51 GLU cc_start: 0.8165 (mm-30) cc_final: 0.7538 (mm-30) REVERT: L 64 ARG cc_start: 0.9166 (mtm110) cc_final: 0.8698 (ptp-110) REVERT: L 69 SER cc_start: 0.8869 (m) cc_final: 0.8571 (p) REVERT: L 71 ARG cc_start: 0.9036 (mtm-85) cc_final: 0.8683 (ptp90) REVERT: R 1 MET cc_start: 0.8921 (ppp) cc_final: 0.8678 (tmm) REVERT: R 19 GLU cc_start: 0.8769 (mt-10) cc_final: 0.8470 (mt-10) REVERT: R 64 ARG cc_start: 0.9313 (mtp180) cc_final: 0.8758 (mpp80) REVERT: Q 1 MET cc_start: 0.8308 (mtt) cc_final: 0.7986 (mmt) REVERT: Q 37 GLU cc_start: 0.7161 (mm-30) cc_final: 0.6898 (mm-30) REVERT: Q 38 ARG cc_start: 0.7484 (ttp80) cc_final: 0.7263 (tpt90) REVERT: Q 46 PHE cc_start: 0.9669 (m-10) cc_final: 0.9445 (m-80) REVERT: Q 64 ARG cc_start: 0.9223 (ttm170) cc_final: 0.8378 (ttm170) REVERT: G 4 GLU cc_start: 0.8227 (tm-30) cc_final: 0.7743 (mp0) REVERT: G 44 LEU cc_start: 0.9314 (OUTLIER) cc_final: 0.9030 (mm) outliers start: 27 outliers final: 21 residues processed: 237 average time/residue: 0.1371 time to fit residues: 46.2459 Evaluate side-chains 234 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 211 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 107 GLN Chi-restraints excluded: chain B residue 164 CYS Chi-restraints excluded: chain B residue 181 PHE Chi-restraints excluded: chain C residue 10 ILE Chi-restraints excluded: chain C residue 16 SER Chi-restraints excluded: chain H residue 110 SER Chi-restraints excluded: chain H residue 158 ASN Chi-restraints excluded: chain I residue 13 LEU Chi-restraints excluded: chain I residue 74 MET Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 120 MET Chi-restraints excluded: chain K residue 25 CYS Chi-restraints excluded: chain K residue 112 LEU Chi-restraints excluded: chain K residue 120 MET Chi-restraints excluded: chain K residue 151 LEU Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain Q residue 22 GLU Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 27 ASP Chi-restraints excluded: chain G residue 44 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 122 optimal weight: 8.9990 chunk 109 optimal weight: 0.7980 chunk 66 optimal weight: 0.9990 chunk 98 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 chunk 110 optimal weight: 0.9990 chunk 148 optimal weight: 0.0470 chunk 51 optimal weight: 1.9990 chunk 120 optimal weight: 5.9990 chunk 113 optimal weight: 0.0770 chunk 31 optimal weight: 6.9990 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 107 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.089005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.066202 restraints weight = 46805.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.068518 restraints weight = 24891.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.070021 restraints weight = 16783.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.071045 restraints weight = 13020.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.071709 restraints weight = 10996.945| |-----------------------------------------------------------------------------| r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.3990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 13669 Z= 0.106 Angle : 0.612 14.318 18315 Z= 0.303 Chirality : 0.036 0.177 2137 Planarity : 0.003 0.036 2331 Dihedral : 3.541 30.761 1809 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.62 % Allowed : 19.08 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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 aren not related in a simple way. whole: 1.30 (0.22), residues: 1627 helix: 1.54 (0.16), residues: 1249 sheet: None (None), residues: 0 loop : -1.40 (0.29), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG Q 78 TYR 0.018 0.001 TYR H 119 PHE 0.015 0.001 PHE Q 82 HIS 0.002 0.000 HIS H 88 Details of bonding type rmsd covalent geometry : bond 0.00237 (13669) covalent geometry : angle 0.61223 (18315) hydrogen bonds : bond 0.02605 ( 744) hydrogen bonds : angle 3.52565 ( 2217) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3254 Ramachandran restraints generated. 1627 Oldfield, 0 Emsley, 1627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3254 Ramachandran restraints generated. 1627 Oldfield, 0 Emsley, 1627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 217 time to evaluate : 0.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 LYS cc_start: 0.9429 (mttt) cc_final: 0.9155 (mmtm) REVERT: A 64 GLU cc_start: 0.8636 (tm-30) cc_final: 0.8195 (tm-30) REVERT: B 106 TYR cc_start: 0.8847 (t80) cc_final: 0.8354 (t80) REVERT: B 141 ASP cc_start: 0.8596 (t70) cc_final: 0.8071 (t0) REVERT: B 146 MET cc_start: 0.8605 (mtm) cc_final: 0.8365 (mtm) REVERT: C 35 GLN cc_start: 0.8476 (tt0) cc_final: 0.8238 (tt0) REVERT: H 17 GLU cc_start: 0.8680 (OUTLIER) cc_final: 0.8357 (mt-10) REVERT: H 19 GLU cc_start: 0.8895 (mt-10) cc_final: 0.8615 (mt-10) REVERT: H 25 CYS cc_start: 0.8361 (m) cc_final: 0.8107 (t) REVERT: I 17 GLU cc_start: 0.8958 (mm-30) cc_final: 0.8701 (mp0) REVERT: J 99 GLU cc_start: 0.9128 (tp30) cc_final: 0.8861 (tm-30) REVERT: K 10 GLU cc_start: 0.8787 (tm-30) cc_final: 0.8493 (tm-30) REVERT: K 39 ASP cc_start: 0.8438 (m-30) cc_final: 0.8074 (m-30) REVERT: K 103 ASP cc_start: 0.8605 (m-30) cc_final: 0.8150 (t0) REVERT: K 151 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8640 (tt) REVERT: L 22 GLU cc_start: 0.8890 (mt-10) cc_final: 0.8585 (mt-10) REVERT: L 33 LYS cc_start: 0.8650 (tttp) cc_final: 0.8375 (tptt) REVERT: L 64 ARG cc_start: 0.9174 (mtm110) cc_final: 0.8670 (ptp-110) REVERT: L 69 SER cc_start: 0.8879 (m) cc_final: 0.8640 (p) REVERT: L 71 ARG cc_start: 0.9040 (mtm-85) cc_final: 0.8555 (mtm110) REVERT: R 19 GLU cc_start: 0.8709 (mt-10) cc_final: 0.8464 (mt-10) REVERT: R 64 ARG cc_start: 0.9327 (mtp180) cc_final: 0.8988 (mtm180) REVERT: Q 1 MET cc_start: 0.8306 (mtt) cc_final: 0.7983 (mmt) REVERT: Q 37 GLU cc_start: 0.7159 (mm-30) cc_final: 0.6902 (mm-30) REVERT: Q 38 ARG cc_start: 0.7494 (ttp80) cc_final: 0.7278 (tpt90) REVERT: G 4 GLU cc_start: 0.8225 (tm-30) cc_final: 0.7721 (mp0) REVERT: G 44 LEU cc_start: 0.9316 (OUTLIER) cc_final: 0.9035 (mm) outliers start: 25 outliers final: 21 residues processed: 233 average time/residue: 0.1385 time to fit residues: 45.6907 Evaluate side-chains 232 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 208 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 107 GLN Chi-restraints excluded: chain B residue 164 CYS Chi-restraints excluded: chain B residue 181 PHE Chi-restraints excluded: chain C residue 10 ILE Chi-restraints excluded: chain C residue 16 SER Chi-restraints excluded: chain H residue 17 GLU Chi-restraints excluded: chain H residue 110 SER Chi-restraints excluded: chain H residue 158 ASN Chi-restraints excluded: chain I residue 74 MET Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 120 MET Chi-restraints excluded: chain J residue 147 ASP Chi-restraints excluded: chain K residue 25 CYS Chi-restraints excluded: chain K residue 112 LEU Chi-restraints excluded: chain K residue 120 MET Chi-restraints excluded: chain K residue 151 LEU Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain Q residue 22 GLU Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 27 ASP Chi-restraints excluded: chain G residue 44 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 116 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 chunk 117 optimal weight: 2.9990 chunk 112 optimal weight: 5.9990 chunk 76 optimal weight: 3.9990 chunk 83 optimal weight: 7.9990 chunk 35 optimal weight: 0.9980 chunk 132 optimal weight: 6.9990 chunk 39 optimal weight: 0.9980 chunk 123 optimal weight: 9.9990 chunk 26 optimal weight: 5.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 107 GLN H 169 GLN I 8 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.087380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.064490 restraints weight = 46882.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.066671 restraints weight = 25802.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.068135 restraints weight = 17728.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.069061 restraints weight = 13882.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.069725 restraints weight = 11837.829| |-----------------------------------------------------------------------------| r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.4066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13669 Z= 0.140 Angle : 0.655 13.805 18315 Z= 0.328 Chirality : 0.038 0.214 2137 Planarity : 0.003 0.046 2331 Dihedral : 3.669 32.267 1809 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.94 % Allowed : 18.43 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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 aren not related in a simple way. whole: 1.31 (0.22), residues: 1627 helix: 1.56 (0.16), residues: 1245 sheet: None (None), residues: 0 loop : -1.42 (0.29), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG Q 77 TYR 0.017 0.001 TYR H 119 PHE 0.017 0.001 PHE Q 82 HIS 0.006 0.001 HIS H 88 Details of bonding type rmsd covalent geometry : bond 0.00327 (13669) covalent geometry : angle 0.65484 (18315) hydrogen bonds : bond 0.03116 ( 744) hydrogen bonds : angle 3.79991 ( 2217) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3254 Ramachandran restraints generated. 1627 Oldfield, 0 Emsley, 1627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3254 Ramachandran restraints generated. 1627 Oldfield, 0 Emsley, 1627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 212 time to evaluate : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 LYS cc_start: 0.9465 (mttt) cc_final: 0.9173 (mmtm) REVERT: A 64 GLU cc_start: 0.8700 (tm-30) cc_final: 0.8337 (tm-30) REVERT: A 143 PHE cc_start: 0.9139 (m-10) cc_final: 0.8870 (m-80) REVERT: B 106 TYR cc_start: 0.8849 (t80) cc_final: 0.8343 (t80) REVERT: B 124 LEU cc_start: 0.8732 (tp) cc_final: 0.8526 (tp) REVERT: B 141 ASP cc_start: 0.8649 (t70) cc_final: 0.8152 (t0) REVERT: B 146 MET cc_start: 0.8689 (mtm) cc_final: 0.8424 (mtm) REVERT: H 17 GLU cc_start: 0.8734 (OUTLIER) cc_final: 0.8406 (mt-10) REVERT: H 19 GLU cc_start: 0.8888 (mt-10) cc_final: 0.8415 (mt-10) REVERT: H 25 CYS cc_start: 0.8473 (m) cc_final: 0.8132 (t) REVERT: I 17 GLU cc_start: 0.9040 (mm-30) cc_final: 0.8691 (mp0) REVERT: J 99 GLU cc_start: 0.9152 (tp30) cc_final: 0.8824 (tm-30) REVERT: K 10 GLU cc_start: 0.8857 (tm-30) cc_final: 0.8549 (tm-30) REVERT: K 39 ASP cc_start: 0.8453 (m-30) cc_final: 0.8086 (m-30) REVERT: K 103 ASP cc_start: 0.8616 (m-30) cc_final: 0.8130 (t0) REVERT: K 151 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8704 (tt) REVERT: L 18 SER cc_start: 0.9215 (p) cc_final: 0.8829 (p) REVERT: L 22 GLU cc_start: 0.8948 (mt-10) cc_final: 0.8584 (mt-10) REVERT: L 33 LYS cc_start: 0.8708 (tttp) cc_final: 0.8415 (tptt) REVERT: L 64 ARG cc_start: 0.9167 (mtm110) cc_final: 0.8648 (ptp-110) REVERT: L 69 SER cc_start: 0.8903 (m) cc_final: 0.8593 (p) REVERT: L 71 ARG cc_start: 0.9078 (mtm-85) cc_final: 0.8727 (ptp90) REVERT: R 1 MET cc_start: 0.8952 (ppp) cc_final: 0.8741 (tmm) REVERT: R 22 GLU cc_start: 0.9222 (tt0) cc_final: 0.8846 (mt-10) REVERT: R 64 ARG cc_start: 0.9337 (mtp180) cc_final: 0.9018 (mtm180) REVERT: R 77 ARG cc_start: 0.9271 (tmm160) cc_final: 0.9067 (tmm160) REVERT: Q 1 MET cc_start: 0.8352 (mtt) cc_final: 0.7995 (mmt) REVERT: Q 9 HIS cc_start: 0.9615 (t-170) cc_final: 0.9253 (t70) REVERT: Q 37 GLU cc_start: 0.7285 (mm-30) cc_final: 0.7043 (mm-30) REVERT: Q 38 ARG cc_start: 0.7509 (ttp80) cc_final: 0.7186 (tpt90) REVERT: Q 46 PHE cc_start: 0.9648 (m-80) cc_final: 0.9272 (m-80) REVERT: G 4 GLU cc_start: 0.8246 (tm-30) cc_final: 0.7721 (mp0) REVERT: G 44 LEU cc_start: 0.9303 (OUTLIER) cc_final: 0.9015 (mm) outliers start: 30 outliers final: 24 residues processed: 233 average time/residue: 0.1358 time to fit residues: 45.1506 Evaluate side-chains 232 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 205 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 107 GLN Chi-restraints excluded: chain B residue 164 CYS Chi-restraints excluded: chain B residue 181 PHE Chi-restraints excluded: chain C residue 10 ILE Chi-restraints excluded: chain C residue 16 SER Chi-restraints excluded: chain H residue 17 GLU Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 110 SER Chi-restraints excluded: chain H residue 158 ASN Chi-restraints excluded: chain I residue 74 MET Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 120 MET Chi-restraints excluded: chain J residue 147 ASP Chi-restraints excluded: chain K residue 25 CYS Chi-restraints excluded: chain K residue 30 ILE Chi-restraints excluded: chain K residue 112 LEU Chi-restraints excluded: chain K residue 120 MET Chi-restraints excluded: chain K residue 151 LEU Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain Q residue 22 GLU Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 27 ASP Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 91 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 1 optimal weight: 6.9990 chunk 29 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 3 optimal weight: 0.1980 chunk 154 optimal weight: 6.9990 chunk 119 optimal weight: 0.9990 chunk 144 optimal weight: 8.9990 chunk 38 optimal weight: 0.9990 chunk 67 optimal weight: 0.9980 chunk 70 optimal weight: 0.2980 chunk 11 optimal weight: 2.9990 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 169 GLN I 8 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.088630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.065635 restraints weight = 46866.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.067928 restraints weight = 25227.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.069452 restraints weight = 17111.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.070464 restraints weight = 13272.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.071131 restraints weight = 11239.685| |-----------------------------------------------------------------------------| r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.4154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13669 Z= 0.115 Angle : 0.638 13.941 18315 Z= 0.319 Chirality : 0.037 0.220 2137 Planarity : 0.003 0.032 2331 Dihedral : 3.690 32.482 1809 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.89 % Favored : 97.05 % Rotamer: Outliers : 1.62 % Allowed : 19.21 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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 aren not related in a simple way. whole: 1.25 (0.22), residues: 1627 helix: 1.48 (0.16), residues: 1253 sheet: None (None), residues: 0 loop : -1.36 (0.29), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG Q 78 TYR 0.017 0.001 TYR H 119 PHE 0.013 0.001 PHE L 46 HIS 0.007 0.001 HIS H 88 Details of bonding type rmsd covalent geometry : bond 0.00260 (13669) covalent geometry : angle 0.63832 (18315) hydrogen bonds : bond 0.02798 ( 744) hydrogen bonds : angle 3.70243 ( 2217) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2568.71 seconds wall clock time: 45 minutes 8.32 seconds (2708.32 seconds total)